Fluorine in PDB 3sr0: Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
Enzymatic activity of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
All present enzymatic activity of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site:
2.7.4.3;
Protein crystallography data
The structure of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site, PDB code: 3sr0
was solved by
Y.-J.Cho,
D.Kern,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
41.79 /
1.56
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.950,
69.580,
85.670,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.8 /
18.9
|
Other elements in 3sr0:
The structure of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
(pdb code 3sr0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site, PDB code: 3sr0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 1 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F210
b:20.0
occ:0.80
|
F1
|
A:ALF210
|
0.0
|
20.0
|
0.8
|
|
AL
|
A:ALF210
|
1.8
|
19.5
|
0.8
|
|
MG
|
A:MG209
|
2.1
|
18.0
|
0.6
|
|
HH12
|
A:ARG150
|
2.3
|
19.9
|
1.0
|
|
HH12
|
A:ARG124
|
2.3
|
14.7
|
1.0
|
|
F4
|
A:ALF210
|
2.5
|
20.7
|
0.8
|
|
F3
|
A:ALF210
|
2.6
|
20.9
|
0.8
|
|
O3P
|
A:AMP208
|
2.6
|
17.7
|
1.0
|
|
O1B
|
A:ADP207
|
2.9
|
9.9
|
1.0
|
|
O
|
A:HOH332
|
2.9
|
23.8
|
1.0
|
|
NH1
|
A:ARG124
|
3.0
|
12.3
|
1.0
|
|
O
|
A:HOH314
|
3.0
|
16.9
|
1.0
|
|
NH1
|
A:ARG150
|
3.0
|
16.6
|
1.0
|
|
HH22
|
A:ARG150
|
3.3
|
19.3
|
1.0
|
|
HH22
|
A:ARG124
|
3.3
|
14.2
|
1.0
|
|
O2P
|
A:AMP208
|
3.4
|
15.4
|
1.0
|
|
HH11
|
A:ARG124
|
3.4
|
14.7
|
1.0
|
|
O3B
|
A:ADP207
|
3.5
|
9.7
|
1.0
|
|
HH11
|
A:ARG150
|
3.5
|
19.9
|
1.0
|
|
P
|
A:AMP208
|
3.5
|
14.3
|
1.0
|
|
F2
|
A:ALF210
|
3.5
|
19.0
|
0.8
|
|
PB
|
A:ADP207
|
3.7
|
9.1
|
1.0
|
|
CZ
|
A:ARG124
|
3.8
|
10.9
|
1.0
|
|
NH2
|
A:ARG124
|
3.8
|
11.9
|
1.0
|
|
NH2
|
A:ARG150
|
3.9
|
16.1
|
1.0
|
|
CZ
|
A:ARG150
|
3.9
|
16.2
|
1.0
|
|
HH22
|
A:ARG36
|
4.1
|
22.9
|
1.0
|
|
O1A
|
A:ADP207
|
4.1
|
10.2
|
1.0
|
|
O
|
A:HOH232
|
4.1
|
15.5
|
0.7
|
|
O
|
A:HOH294
|
4.1
|
20.5
|
1.0
|
|
O1P
|
A:AMP208
|
4.2
|
14.8
|
1.0
|
|
HH22
|
A:ARG161
|
4.2
|
27.7
|
1.0
|
|
O
|
A:HOH232
|
4.3
|
8.3
|
0.3
|
|
HH12
|
A:ARG36
|
4.4
|
22.1
|
1.0
|
|
O
|
A:HOH377
|
4.5
|
25.6
|
0.9
|
|
HH21
|
A:ARG124
|
4.6
|
14.2
|
1.0
|
|
HH12
|
A:ARG161
|
4.6
|
26.9
|
1.0
|
|
O3A
|
A:ADP207
|
4.6
|
9.1
|
1.0
|
|
H
|
A:GLY10
|
4.7
|
14.0
|
1.0
|
|
HH21
|
A:ARG150
|
4.7
|
19.3
|
1.0
|
|
HH22
|
A:ARG85
|
4.7
|
16.5
|
0.6
|
|
O
|
A:HOH238
|
4.7
|
22.4
|
1.0
|
|
NH2
|
A:ARG36
|
4.8
|
19.1
|
1.0
|
|
O5'
|
A:AMP208
|
4.9
|
13.0
|
1.0
|
|
NE
|
A:ARG124
|
4.9
|
9.3
|
1.0
|
|
PA
|
A:ADP207
|
5.0
|
8.3
|
1.0
|
|
O2B
|
A:ADP207
|
5.0
|
9.0
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 2 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F210
b:19.0
occ:0.80
|
F2
|
A:ALF210
|
0.0
|
19.0
|
0.8
|
|
AL
|
A:ALF210
|
1.8
|
19.5
|
0.8
|
|
O
|
A:HOH712
|
1.8
|
16.0
|
0.9
|
|
HA
|
A:PRO9
|
2.3
|
15.1
|
1.0
|
|
HH22
|
A:ARG85
|
2.4
|
16.5
|
0.6
|
|
HZ1
|
A:LYS13
|
2.4
|
16.0
|
1.0
|
|
F3
|
A:ALF210
|
2.4
|
20.9
|
0.8
|
|
F4
|
A:ALF210
|
2.6
|
20.7
|
0.8
|
|
O1B
|
A:ADP207
|
2.7
|
9.9
|
1.0
|
|
HH21
|
A:ARG85
|
2.8
|
16.5
|
0.6
|
|
O3P
|
A:AMP208
|
2.8
|
17.7
|
1.0
|
|
NH2
|
A:ARG85
|
2.9
|
13.8
|
0.6
|
|
HH12
|
A:ARG161
|
2.9
|
26.9
|
1.0
|
|
H
|
A:GLY10
|
3.0
|
14.0
|
1.0
|
|
NZ
|
A:LYS13
|
3.2
|
13.4
|
1.0
|
|
CA
|
A:PRO9
|
3.3
|
12.6
|
1.0
|
|
O
|
A:HOH238
|
3.3
|
22.4
|
1.0
|
|
HZ3
|
A:LYS13
|
3.3
|
16.0
|
1.0
|
|
HB3
|
A:PRO9
|
3.5
|
16.6
|
1.0
|
|
HH22
|
A:ARG161
|
3.5
|
27.7
|
1.0
|
|
F1
|
A:ALF210
|
3.5
|
20.0
|
0.8
|
|
HZ2
|
A:LYS13
|
3.7
|
16.0
|
1.0
|
|
NH1
|
A:ARG161
|
3.7
|
22.4
|
1.0
|
|
PB
|
A:ADP207
|
3.7
|
9.1
|
1.0
|
|
N
|
A:GLY10
|
3.7
|
11.7
|
1.0
|
|
CB
|
A:PRO9
|
3.9
|
13.9
|
1.0
|
|
O2B
|
A:ADP207
|
3.9
|
9.0
|
1.0
|
|
C
|
A:PRO9
|
4.0
|
11.2
|
1.0
|
|
P
|
A:AMP208
|
4.1
|
14.3
|
1.0
|
|
O1P
|
A:AMP208
|
4.1
|
14.8
|
1.0
|
|
HE2
|
A:LYS13
|
4.1
|
16.7
|
1.0
|
|
HH22
|
A:ARG85
|
4.1
|
11.9
|
0.5
|
|
CZ
|
A:ARG85
|
4.2
|
13.4
|
0.6
|
|
NH2
|
A:ARG161
|
4.2
|
23.1
|
1.0
|
|
N
|
A:PRO9
|
4.2
|
11.9
|
1.0
|
|
CE
|
A:LYS13
|
4.2
|
13.9
|
1.0
|
|
HB2
|
A:PRO9
|
4.2
|
16.6
|
1.0
|
|
HH11
|
A:ARG161
|
4.2
|
26.9
|
1.0
|
|
HH12
|
A:ARG124
|
4.2
|
14.7
|
1.0
|
|
O3B
|
A:ADP207
|
4.3
|
9.7
|
1.0
|
|
O
|
A:HOH591
|
4.3
|
29.7
|
1.0
|
|
MG
|
A:MG209
|
4.4
|
18.0
|
0.6
|
|
CZ
|
A:ARG161
|
4.4
|
23.0
|
1.0
|
|
HE3
|
A:LYS13
|
4.4
|
16.7
|
1.0
|
|
O
|
A:HOH232
|
4.4
|
15.5
|
0.7
|
|
O
|
A:HOH290
|
4.4
|
13.8
|
1.0
|
|
NH2
|
A:ARG85
|
4.4
|
9.9
|
0.5
|
|
O
|
A:PRO8
|
4.5
|
11.3
|
1.0
|
|
HH12
|
A:ARG85
|
4.5
|
16.7
|
0.6
|
|
HH22
|
A:ARG124
|
4.6
|
14.2
|
1.0
|
|
HH21
|
A:ARG85
|
4.7
|
11.9
|
0.5
|
|
C
|
A:PRO8
|
4.7
|
11.0
|
1.0
|
|
NH1
|
A:ARG85
|
4.8
|
13.9
|
0.6
|
|
HH12
|
A:ARG85
|
4.8
|
13.3
|
0.5
|
|
H
|
A:ALA11
|
4.9
|
13.1
|
1.0
|
|
O5'
|
A:AMP208
|
4.9
|
13.0
|
1.0
|
|
HH21
|
A:ARG161
|
4.9
|
27.7
|
1.0
|
|
HH22
|
A:ARG150
|
4.9
|
19.3
|
1.0
|
|
HD21
|
A:LEU121
|
5.0
|
18.4
|
1.0
|
|
HE
|
A:ARG85
|
5.0
|
15.2
|
0.6
|
|
CA
|
A:GLY10
|
5.0
|
11.3
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 3 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F210
b:20.9
occ:0.80
|
F3
|
A:ALF210
|
0.0
|
20.9
|
0.8
|
|
AL
|
A:ALF210
|
1.8
|
19.5
|
0.8
|
|
O
|
A:HOH232
|
2.2
|
15.5
|
0.7
|
|
MG
|
A:MG209
|
2.3
|
18.0
|
0.6
|
|
O
|
A:HOH238
|
2.3
|
22.4
|
1.0
|
|
F2
|
A:ALF210
|
2.4
|
19.0
|
0.8
|
|
F1
|
A:ALF210
|
2.6
|
20.0
|
0.8
|
|
O3P
|
A:AMP208
|
2.8
|
17.7
|
1.0
|
|
HH22
|
A:ARG85
|
2.8
|
16.5
|
0.6
|
|
O3B
|
A:ADP207
|
2.9
|
9.7
|
1.0
|
|
O1B
|
A:ADP207
|
2.9
|
9.9
|
1.0
|
|
O1P
|
A:AMP208
|
3.0
|
14.8
|
1.0
|
|
O
|
A:HOH712
|
3.2
|
16.0
|
0.9
|
|
PB
|
A:ADP207
|
3.3
|
9.1
|
1.0
|
|
HZ1
|
A:LYS13
|
3.4
|
16.0
|
1.0
|
|
O
|
A:HOH332
|
3.4
|
23.8
|
1.0
|
|
P
|
A:AMP208
|
3.4
|
14.3
|
1.0
|
|
O
|
A:HOH232
|
3.5
|
8.3
|
0.3
|
|
F4
|
A:ALF210
|
3.6
|
20.7
|
0.8
|
|
NH2
|
A:ARG85
|
3.6
|
13.8
|
0.6
|
|
HZ3
|
A:LYS13
|
3.7
|
16.0
|
1.0
|
|
HE2
|
A:LYS13
|
3.7
|
16.7
|
1.0
|
|
O
|
A:HOH377
|
3.9
|
25.6
|
0.9
|
|
O2B
|
A:ADP207
|
3.9
|
9.0
|
1.0
|
|
NZ
|
A:LYS13
|
3.9
|
13.4
|
1.0
|
|
HH21
|
A:ARG85
|
4.0
|
16.5
|
0.6
|
|
O2P
|
A:AMP208
|
4.0
|
15.4
|
1.0
|
|
HB2
|
A:LYS13
|
4.1
|
11.3
|
1.0
|
|
HH12
|
A:ARG85
|
4.1
|
16.7
|
0.6
|
|
HH12
|
A:ARG124
|
4.2
|
14.7
|
1.0
|
|
O
|
A:HOH259
|
4.3
|
16.6
|
1.0
|
|
CE
|
A:LYS13
|
4.3
|
13.9
|
1.0
|
|
H
|
A:GLY14
|
4.4
|
10.0
|
1.0
|
|
HH12
|
A:ARG161
|
4.5
|
26.9
|
1.0
|
|
O
|
A:HOH314
|
4.5
|
16.9
|
1.0
|
|
H
|
A:GLY10
|
4.5
|
14.0
|
1.0
|
|
OD1
|
A:ASP81
|
4.6
|
12.4
|
1.0
|
|
HH12
|
A:ARG150
|
4.6
|
19.9
|
1.0
|
|
HH12
|
A:ARG85
|
4.6
|
13.3
|
0.5
|
|
HA
|
A:PRO9
|
4.7
|
15.1
|
1.0
|
|
CZ
|
A:ARG85
|
4.7
|
13.4
|
0.6
|
|
HZ2
|
A:LYS13
|
4.7
|
16.0
|
1.0
|
|
HA3
|
A:GLY82
|
4.7
|
11.4
|
1.0
|
|
NH1
|
A:ARG85
|
4.7
|
13.9
|
0.6
|
|
HE3
|
A:LYS13
|
4.8
|
16.7
|
1.0
|
|
O5'
|
A:AMP208
|
4.8
|
13.0
|
1.0
|
|
O3A
|
A:ADP207
|
4.8
|
9.1
|
1.0
|
|
HH22
|
A:ARG85
|
4.9
|
11.9
|
0.5
|
|
Fluorine binding site 4 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 4 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F210
b:20.7
occ:0.80
|
F4
|
A:ALF210
|
0.0
|
20.7
|
0.8
|
|
AL
|
A:ALF210
|
1.8
|
19.5
|
0.8
|
|
HH22
|
A:ARG161
|
1.8
|
27.7
|
1.0
|
|
HH22
|
A:ARG124
|
2.0
|
14.2
|
1.0
|
|
O3P
|
A:AMP208
|
2.5
|
17.7
|
1.0
|
|
F1
|
A:ALF210
|
2.5
|
20.0
|
0.8
|
|
HH12
|
A:ARG124
|
2.5
|
14.7
|
1.0
|
|
F2
|
A:ALF210
|
2.6
|
19.0
|
0.8
|
|
NH2
|
A:ARG161
|
2.7
|
23.1
|
1.0
|
|
O1B
|
A:ADP207
|
2.9
|
9.9
|
1.0
|
|
NH2
|
A:ARG124
|
2.9
|
11.9
|
1.0
|
|
HH12
|
A:ARG161
|
2.9
|
26.9
|
1.0
|
|
HH22
|
A:ARG150
|
3.0
|
19.3
|
1.0
|
|
HH21
|
A:ARG161
|
3.2
|
27.7
|
1.0
|
|
NH1
|
A:ARG124
|
3.2
|
12.3
|
1.0
|
|
H
|
A:GLY10
|
3.4
|
14.0
|
1.0
|
|
HH12
|
A:ARG150
|
3.5
|
19.9
|
1.0
|
|
CZ
|
A:ARG124
|
3.5
|
10.9
|
1.0
|
|
HH21
|
A:ARG124
|
3.5
|
14.2
|
1.0
|
|
NH2
|
A:ARG150
|
3.5
|
16.1
|
1.0
|
|
NH1
|
A:ARG161
|
3.5
|
22.4
|
1.0
|
|
CZ
|
A:ARG161
|
3.5
|
23.0
|
1.0
|
|
F3
|
A:ALF210
|
3.6
|
20.9
|
0.8
|
|
HD21
|
A:LEU121
|
3.7
|
18.4
|
1.0
|
|
HA
|
A:PRO9
|
3.7
|
15.1
|
1.0
|
|
HB3
|
A:PRO9
|
3.8
|
16.6
|
1.0
|
|
HB2
|
A:PRO9
|
3.9
|
16.6
|
1.0
|
|
NH1
|
A:ARG150
|
4.0
|
16.6
|
1.0
|
|
P
|
A:AMP208
|
4.0
|
14.3
|
1.0
|
|
HH21
|
A:ARG150
|
4.0
|
19.3
|
1.0
|
|
HD22
|
A:LEU121
|
4.0
|
18.4
|
1.0
|
|
HH11
|
A:ARG124
|
4.0
|
14.7
|
1.0
|
|
N
|
A:GLY10
|
4.0
|
11.7
|
1.0
|
|
CZ
|
A:ARG150
|
4.1
|
16.2
|
1.0
|
|
CB
|
A:PRO9
|
4.2
|
13.9
|
1.0
|
|
CD2
|
A:LEU121
|
4.2
|
15.3
|
1.0
|
|
CA
|
A:PRO9
|
4.3
|
12.6
|
1.0
|
|
O
|
A:HOH712
|
4.3
|
16.0
|
0.9
|
|
PB
|
A:ADP207
|
4.4
|
9.1
|
1.0
|
|
HH11
|
A:ARG161
|
4.4
|
26.9
|
1.0
|
|
MG
|
A:MG209
|
4.4
|
18.0
|
0.6
|
|
HH22
|
A:ARG85
|
4.4
|
16.5
|
0.6
|
|
O2P
|
A:AMP208
|
4.4
|
15.4
|
1.0
|
|
H5'2
|
A:AMP208
|
4.5
|
13.4
|
1.0
|
|
HD23
|
A:LEU121
|
4.5
|
18.4
|
1.0
|
|
C
|
A:PRO9
|
4.6
|
11.2
|
1.0
|
|
HA2
|
A:GLY10
|
4.6
|
13.5
|
1.0
|
|
HH11
|
A:ARG150
|
4.6
|
19.9
|
1.0
|
|
O5'
|
A:AMP208
|
4.7
|
13.0
|
1.0
|
|
NE
|
A:ARG124
|
4.8
|
9.3
|
1.0
|
|
NE
|
A:ARG161
|
4.8
|
22.5
|
1.0
|
|
O1P
|
A:AMP208
|
4.8
|
14.8
|
1.0
|
|
O
|
A:HOH350
|
4.9
|
19.7
|
1.0
|
|
HZ1
|
A:LYS13
|
4.9
|
16.0
|
1.0
|
|
O3B
|
A:ADP207
|
4.9
|
9.7
|
1.0
|
|
CA
|
A:GLY10
|
4.9
|
11.3
|
1.0
|
|
NH2
|
A:ARG85
|
5.0
|
13.8
|
0.6
|
|
Fluorine binding site 5 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 5 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F210
b:22.0
occ:0.77
|
F1
|
B:ALF210
|
0.0
|
22.0
|
0.8
|
|
O
|
B:HOH389
|
1.7
|
17.6
|
0.8
|
|
AL
|
B:ALF210
|
1.8
|
19.5
|
0.8
|
|
F3
|
B:ALF210
|
2.5
|
19.8
|
0.8
|
|
HA
|
B:PRO9
|
2.5
|
12.0
|
1.0
|
|
F4
|
B:ALF210
|
2.5
|
19.0
|
0.8
|
|
HZ1
|
B:LYS13
|
2.7
|
15.9
|
1.0
|
|
O2P
|
B:AMP208
|
2.7
|
17.3
|
1.0
|
|
HH22
|
B:ARG161
|
2.8
|
14.1
|
0.5
|
|
O2B
|
B:ADP207
|
2.9
|
9.2
|
1.0
|
|
O
|
B:HOH310
|
2.9
|
17.5
|
1.0
|
|
HB3
|
B:PRO9
|
3.3
|
14.5
|
1.0
|
|
H
|
B:GLY10
|
3.4
|
11.4
|
1.0
|
|
CA
|
B:PRO9
|
3.4
|
10.1
|
1.0
|
|
NZ
|
B:LYS13
|
3.5
|
13.2
|
1.0
|
|
F2
|
B:ALF210
|
3.6
|
17.6
|
0.8
|
|
NH2
|
B:ARG161
|
3.6
|
11.8
|
0.5
|
|
HZ3
|
B:LYS13
|
3.6
|
15.9
|
1.0
|
|
HH12
|
B:ARG161
|
3.6
|
14.5
|
0.5
|
|
HH12
|
B:ARG85
|
3.7
|
22.5
|
1.0
|
|
P
|
B:AMP208
|
3.8
|
12.1
|
1.0
|
|
CB
|
B:PRO9
|
3.8
|
12.1
|
1.0
|
|
O3P
|
B:AMP208
|
3.9
|
13.1
|
1.0
|
|
PB
|
B:ADP207
|
3.9
|
9.2
|
1.0
|
|
HH11
|
B:ARG161
|
3.9
|
17.8
|
0.5
|
|
HE2
|
B:LYS13
|
4.0
|
14.0
|
1.0
|
|
O
|
B:HOH635
|
4.0
|
14.2
|
0.8
|
|
HZ2
|
B:LYS13
|
4.0
|
15.9
|
1.0
|
|
HH21
|
B:ARG161
|
4.1
|
14.1
|
0.5
|
|
NH1
|
B:ARG85
|
4.1
|
18.8
|
1.0
|
|
N
|
B:GLY10
|
4.1
|
9.6
|
1.0
|
|
O1B
|
B:ADP207
|
4.2
|
8.8
|
1.0
|
|
HB2
|
B:PRO9
|
4.2
|
14.5
|
1.0
|
|
HH12
|
B:ARG124
|
4.2
|
13.7
|
1.0
|
|
NH1
|
B:ARG161
|
4.3
|
12.1
|
0.5
|
|
CE
|
B:LYS13
|
4.3
|
11.7
|
1.0
|
|
HH11
|
B:ARG85
|
4.3
|
22.5
|
1.0
|
|
C
|
B:PRO9
|
4.3
|
10.4
|
1.0
|
|
CZ
|
B:ARG161
|
4.4
|
12.5
|
0.5
|
|
N
|
B:PRO9
|
4.4
|
9.8
|
1.0
|
|
O3B
|
B:ADP207
|
4.4
|
9.3
|
1.0
|
|
HE3
|
B:LYS13
|
4.4
|
14.0
|
1.0
|
|
HH22
|
B:ARG150
|
4.5
|
13.1
|
1.0
|
|
O
|
B:HOH272
|
4.5
|
13.5
|
1.0
|
|
HH22
|
B:ARG124
|
4.5
|
11.5
|
1.0
|
|
MG
|
B:MG209
|
4.6
|
29.6
|
0.9
|
|
HH22
|
B:ARG85
|
4.6
|
18.7
|
1.0
|
|
NH1
|
B:ARG161
|
4.7
|
14.9
|
0.5
|
|
O
|
B:PRO8
|
4.7
|
8.8
|
1.0
|
|
CZ
|
B:ARG85
|
4.8
|
16.5
|
1.0
|
|
HH12
|
B:ARG161
|
4.8
|
17.8
|
0.5
|
|
O1P
|
B:AMP208
|
4.8
|
11.4
|
1.0
|
|
O5'
|
B:AMP208
|
4.9
|
12.5
|
1.0
|
|
C
|
B:PRO8
|
4.9
|
8.3
|
1.0
|
|
NH2
|
B:ARG85
|
4.9
|
15.6
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 6 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F210
b:17.6
occ:0.77
|
F2
|
B:ALF210
|
0.0
|
17.6
|
0.8
|
|
AL
|
B:ALF210
|
1.8
|
19.5
|
0.8
|
|
HH12
|
B:ARG150
|
1.9
|
14.4
|
1.0
|
|
MG
|
B:MG209
|
2.1
|
29.6
|
0.9
|
|
HH12
|
B:ARG124
|
2.3
|
13.7
|
1.0
|
|
F3
|
B:ALF210
|
2.5
|
19.8
|
0.8
|
|
F4
|
B:ALF210
|
2.6
|
19.0
|
0.8
|
|
NH1
|
B:ARG150
|
2.7
|
12.1
|
1.0
|
|
NH1
|
B:ARG124
|
2.8
|
11.5
|
1.0
|
|
O2B
|
B:ADP207
|
3.0
|
9.2
|
1.0
|
|
O
|
B:HOH348
|
3.0
|
22.1
|
1.0
|
|
O
|
B:HOH216
|
3.1
|
21.6
|
1.0
|
|
HH11
|
B:ARG150
|
3.1
|
14.4
|
1.0
|
|
HH22
|
B:ARG150
|
3.1
|
13.1
|
1.0
|
|
O2P
|
B:AMP208
|
3.2
|
17.3
|
1.0
|
|
HH11
|
B:ARG124
|
3.2
|
13.7
|
1.0
|
|
HH22
|
B:ARG124
|
3.4
|
11.5
|
1.0
|
|
O1P
|
B:AMP208
|
3.4
|
11.4
|
1.0
|
|
O3B
|
B:ADP207
|
3.4
|
9.3
|
1.0
|
|
CZ
|
B:ARG150
|
3.6
|
11.3
|
1.0
|
|
F1
|
B:ALF210
|
3.6
|
22.0
|
0.8
|
|
CZ
|
B:ARG124
|
3.6
|
10.7
|
1.0
|
|
NH2
|
B:ARG150
|
3.7
|
10.9
|
1.0
|
|
P
|
B:AMP208
|
3.7
|
12.1
|
1.0
|
|
NH2
|
B:ARG124
|
3.8
|
9.6
|
1.0
|
|
PB
|
B:ADP207
|
3.8
|
9.2
|
1.0
|
|
O
|
B:HOH635
|
3.9
|
14.2
|
0.8
|
|
O
|
B:HOH264
|
3.9
|
15.5
|
1.0
|
|
HH22
|
B:ARG36
|
4.0
|
13.7
|
1.0
|
|
O1A
|
B:ADP207
|
4.1
|
8.4
|
1.0
|
|
HH12
|
B:ARG161
|
4.3
|
14.5
|
0.5
|
|
O
|
B:HOH369
|
4.3
|
16.1
|
0.3
|
|
HH12
|
B:ARG36
|
4.4
|
12.8
|
1.0
|
|
O3P
|
B:AMP208
|
4.4
|
13.1
|
1.0
|
|
HH21
|
B:ARG150
|
4.5
|
13.1
|
1.0
|
|
HH21
|
B:ARG124
|
4.5
|
11.5
|
1.0
|
|
O3A
|
B:ADP207
|
4.6
|
8.4
|
1.0
|
|
HH11
|
B:ARG161
|
4.6
|
17.8
|
0.5
|
|
HH22
|
B:ARG161
|
4.6
|
14.1
|
0.5
|
|
NH2
|
B:ARG36
|
4.7
|
11.4
|
1.0
|
|
NE
|
B:ARG124
|
4.7
|
9.9
|
1.0
|
|
HH12
|
B:ARG161
|
4.7
|
17.8
|
0.5
|
|
H
|
B:GLY10
|
4.8
|
11.4
|
1.0
|
|
O
|
B:HOH310
|
4.8
|
17.5
|
1.0
|
|
NE
|
B:ARG150
|
4.8
|
12.6
|
1.0
|
|
HD2
|
B:ARG124
|
4.9
|
12.0
|
1.0
|
|
O
|
B:HOH369
|
4.9
|
14.4
|
0.7
|
|
PA
|
B:ADP207
|
5.0
|
8.2
|
1.0
|
|
NH1
|
B:ARG36
|
5.0
|
10.7
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 7 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F210
b:19.8
occ:0.77
|
F3
|
B:ALF210
|
0.0
|
19.8
|
0.8
|
|
AL
|
B:ALF210
|
1.8
|
19.5
|
0.8
|
|
O
|
B:HOH635
|
1.8
|
14.2
|
0.8
|
|
MG
|
B:MG209
|
2.4
|
29.6
|
0.9
|
|
O
|
B:HOH310
|
2.4
|
17.5
|
1.0
|
|
F1
|
B:ALF210
|
2.5
|
22.0
|
0.8
|
|
F2
|
B:ALF210
|
2.5
|
17.6
|
0.8
|
|
O3B
|
B:ADP207
|
2.9
|
9.3
|
1.0
|
|
O2B
|
B:ADP207
|
3.0
|
9.2
|
1.0
|
|
O2P
|
B:AMP208
|
3.1
|
17.3
|
1.0
|
|
O3P
|
B:AMP208
|
3.2
|
13.1
|
1.0
|
|
O
|
B:HOH348
|
3.3
|
22.1
|
1.0
|
|
O
|
B:HOH369
|
3.4
|
16.1
|
0.3
|
|
PB
|
B:ADP207
|
3.4
|
9.2
|
1.0
|
|
P
|
B:AMP208
|
3.4
|
12.1
|
1.0
|
|
O
|
B:HOH389
|
3.5
|
17.6
|
0.8
|
|
F4
|
B:ALF210
|
3.5
|
19.0
|
0.8
|
|
HZ1
|
B:LYS13
|
3.8
|
15.9
|
1.0
|
|
HE2
|
B:LYS13
|
3.8
|
14.0
|
1.0
|
|
O1P
|
B:AMP208
|
3.8
|
11.4
|
1.0
|
|
O
|
B:HOH219
|
4.1
|
11.1
|
1.0
|
|
HZ3
|
B:LYS13
|
4.1
|
15.9
|
1.0
|
|
O1B
|
B:ADP207
|
4.1
|
8.8
|
1.0
|
|
HH12
|
B:ARG124
|
4.1
|
13.7
|
1.0
|
|
HB2
|
B:LYS13
|
4.1
|
10.6
|
1.0
|
|
HH12
|
B:ARG150
|
4.2
|
14.4
|
1.0
|
|
NZ
|
B:LYS13
|
4.2
|
13.2
|
1.0
|
|
O
|
B:HOH369
|
4.3
|
14.4
|
0.7
|
|
H
|
B:GLY14
|
4.4
|
9.4
|
1.0
|
|
HH22
|
B:ARG161
|
4.5
|
14.1
|
0.5
|
|
OD1
|
B:ASP81
|
4.5
|
11.4
|
1.0
|
|
O
|
B:HOH216
|
4.5
|
21.6
|
1.0
|
|
CE
|
B:LYS13
|
4.5
|
11.7
|
1.0
|
|
HH22
|
B:ARG150
|
4.6
|
13.1
|
1.0
|
|
HA
|
B:PRO9
|
4.7
|
12.0
|
1.0
|
|
H
|
B:GLY10
|
4.7
|
11.4
|
1.0
|
|
HH22
|
B:ARG85
|
4.8
|
18.7
|
1.0
|
|
O3A
|
B:ADP207
|
4.8
|
8.4
|
1.0
|
|
NH1
|
B:ARG124
|
4.9
|
11.5
|
1.0
|
|
O5'
|
B:AMP208
|
4.9
|
12.5
|
1.0
|
|
HE3
|
B:LYS13
|
4.9
|
14.0
|
1.0
|
|
HH12
|
B:ARG85
|
4.9
|
22.5
|
1.0
|
|
HA3
|
B:GLY14
|
5.0
|
9.7
|
1.0
|
|
N
|
B:GLY14
|
5.0
|
7.9
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 3sr0
Go back to
Fluorine Binding Sites List in 3sr0
Fluorine binding site 8 out
of 8 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F210
b:19.0
occ:0.77
|
F4
|
B:ALF210
|
0.0
|
19.0
|
0.8
|
|
AL
|
B:ALF210
|
1.8
|
19.5
|
0.8
|
|
HH12
|
B:ARG161
|
2.0
|
14.5
|
0.5
|
|
HH22
|
B:ARG124
|
2.0
|
11.5
|
1.0
|
|
HH11
|
B:ARG161
|
2.3
|
17.8
|
0.5
|
|
HH12
|
B:ARG124
|
2.5
|
13.7
|
1.0
|
|
F1
|
B:ALF210
|
2.5
|
22.0
|
0.8
|
|
F2
|
B:ALF210
|
2.6
|
17.6
|
0.8
|
|
HH12
|
B:ARG161
|
2.6
|
17.8
|
0.5
|
|
O2P
|
B:AMP208
|
2.7
|
17.3
|
1.0
|
|
NH1
|
B:ARG161
|
2.7
|
14.9
|
0.5
|
|
O2B
|
B:ADP207
|
2.8
|
9.2
|
1.0
|
|
NH1
|
B:ARG161
|
2.8
|
12.1
|
0.5
|
|
NH2
|
B:ARG124
|
2.8
|
9.6
|
1.0
|
|
HH22
|
B:ARG150
|
2.9
|
13.1
|
1.0
|
|
HH22
|
B:ARG161
|
2.9
|
14.1
|
0.5
|
|
NH1
|
B:ARG124
|
3.2
|
11.5
|
1.0
|
|
HH11
|
B:ARG161
|
3.3
|
14.5
|
0.5
|
|
H
|
B:GLY10
|
3.4
|
11.4
|
1.0
|
|
HH12
|
B:ARG150
|
3.4
|
14.4
|
1.0
|
|
NH2
|
B:ARG150
|
3.4
|
10.9
|
1.0
|
|
CZ
|
B:ARG124
|
3.4
|
10.7
|
1.0
|
|
HH21
|
B:ARG124
|
3.5
|
11.5
|
1.0
|
|
F3
|
B:ALF210
|
3.5
|
19.8
|
0.8
|
|
NH2
|
B:ARG161
|
3.6
|
11.8
|
0.5
|
|
HD21
|
B:LEU121
|
3.6
|
13.4
|
1.0
|
|
HB3
|
B:PRO9
|
3.6
|
14.5
|
1.0
|
|
CZ
|
B:ARG161
|
3.6
|
12.5
|
0.5
|
|
HA
|
B:PRO9
|
3.6
|
12.0
|
1.0
|
|
HB2
|
B:PRO9
|
3.8
|
14.5
|
1.0
|
|
NH1
|
B:ARG150
|
3.9
|
12.1
|
1.0
|
|
HH21
|
B:ARG150
|
3.9
|
13.1
|
1.0
|
|
CZ
|
B:ARG150
|
4.0
|
11.3
|
1.0
|
|
HH11
|
B:ARG124
|
4.0
|
13.7
|
1.0
|
|
HD22
|
B:LEU121
|
4.0
|
13.4
|
1.0
|
|
CB
|
B:PRO9
|
4.0
|
12.1
|
1.0
|
|
N
|
B:GLY10
|
4.0
|
9.6
|
1.0
|
|
CZ
|
B:ARG161
|
4.1
|
13.8
|
0.5
|
|
P
|
B:AMP208
|
4.1
|
12.1
|
1.0
|
|
CD2
|
B:LEU121
|
4.1
|
11.2
|
1.0
|
|
O
|
B:HOH389
|
4.1
|
17.6
|
0.8
|
|
CA
|
B:PRO9
|
4.2
|
10.1
|
1.0
|
|
HD23
|
B:LEU121
|
4.2
|
13.4
|
1.0
|
|
PB
|
B:ADP207
|
4.3
|
9.2
|
1.0
|
|
HH21
|
B:ARG161
|
4.4
|
14.1
|
0.5
|
|
HE
|
B:ARG161
|
4.4
|
16.2
|
0.5
|
|
MG
|
B:MG209
|
4.4
|
29.6
|
0.9
|
|
O1P
|
B:AMP208
|
4.5
|
11.4
|
1.0
|
|
C
|
B:PRO9
|
4.5
|
10.4
|
1.0
|
|
HH11
|
B:ARG150
|
4.5
|
14.4
|
1.0
|
|
HA2
|
B:GLY10
|
4.7
|
12.0
|
1.0
|
|
H5'2
|
B:AMP208
|
4.7
|
12.9
|
1.0
|
|
NE
|
B:ARG161
|
4.7
|
13.6
|
0.5
|
|
NE
|
B:ARG124
|
4.8
|
9.9
|
1.0
|
|
O3B
|
B:ADP207
|
4.8
|
9.3
|
1.0
|
|
HZ1
|
B:LYS13
|
4.8
|
15.9
|
1.0
|
|
HH22
|
B:ARG161
|
4.9
|
14.7
|
0.5
|
|
NE
|
B:ARG161
|
4.9
|
12.5
|
0.5
|
|
O3P
|
B:AMP208
|
4.9
|
13.1
|
1.0
|
|
CA
|
B:GLY10
|
5.0
|
10.1
|
1.0
|
|
HH12
|
B:ARG85
|
5.0
|
22.5
|
1.0
|
|
NH2
|
B:ARG161
|
5.0
|
12.2
|
0.5
|
|
Reference:
S.J.Kerns,
R.V.Agafonov,
Y.J.Cho,
F.Pontiggia,
R.Otten,
D.V.Pachov,
S.Kutter,
L.A.Phung,
P.N.Murphy,
V.Thai,
T.Alber,
M.F.Hagan,
D.Kern.
The Energy Landscape of Adenylate Kinase During Catalysis. Nat.Struct.Mol.Biol. V. 22 124 2015.
ISSN: ISSN 1545-9993
PubMed: 25580578
DOI: 10.1038/NSMB.2941
Page generated: Mon Jul 14 19:21:55 2025
|
