Fluorine in PDB 1kdn: Structure of Nucleoside Diphosphate Kinase
Enzymatic activity of Structure of Nucleoside Diphosphate Kinase
All present enzymatic activity of Structure of Nucleoside Diphosphate Kinase:
2.7.4.6;
Protein crystallography data
The structure of Structure of Nucleoside Diphosphate Kinase, PDB code: 1kdn
was solved by
J.Cherfils,
Y.W.Xu,
S.Morera,
J.Janin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
N/A /
2.00
|
|
Space group
|
P 31 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.354,
71.354,
153.494,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
17.7 /
17.9
|
Other elements in 1kdn:
The structure of Structure of Nucleoside Diphosphate Kinase also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Nucleoside Diphosphate Kinase
(pdb code 1kdn). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the
Structure of Nucleoside Diphosphate Kinase, PDB code: 1kdn:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Fluorine binding site 1 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 1 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F157
b:23.3
occ:1.00
|
F1
|
A:AF3157
|
0.0
|
23.3
|
1.0
|
|
AL
|
A:AF3157
|
1.8
|
22.4
|
1.0
|
|
NZ
|
A:LYS16
|
2.6
|
7.5
|
1.0
|
|
OH
|
A:TYR56
|
2.7
|
13.4
|
1.0
|
|
CE
|
A:LYS16
|
2.9
|
10.2
|
1.0
|
|
O3'
|
A:ADP158
|
3.0
|
11.5
|
1.0
|
|
O3B
|
A:ADP158
|
3.0
|
9.4
|
1.0
|
|
F2
|
A:AF3157
|
3.2
|
24.0
|
1.0
|
|
F3
|
A:AF3157
|
3.4
|
19.1
|
1.0
|
|
CB
|
A:HIS122
|
3.4
|
5.3
|
1.0
|
|
ND1
|
A:HIS122
|
3.4
|
7.3
|
1.0
|
|
CZ
|
A:TYR56
|
3.6
|
12.4
|
1.0
|
|
CE1
|
A:TYR56
|
3.7
|
9.7
|
1.0
|
|
C4'
|
A:ADP158
|
3.7
|
12.4
|
1.0
|
|
CA
|
A:HIS122
|
3.8
|
5.5
|
1.0
|
|
CG
|
A:HIS122
|
3.8
|
8.2
|
1.0
|
|
C5'
|
A:ADP158
|
4.0
|
11.3
|
1.0
|
|
C3'
|
A:ADP158
|
4.0
|
13.1
|
1.0
|
|
NH2
|
A:ARG109
|
4.0
|
5.4
|
1.0
|
|
O
|
A:ILE121
|
4.1
|
10.5
|
1.0
|
|
CD
|
A:LYS16
|
4.4
|
11.4
|
1.0
|
|
PB
|
A:ADP158
|
4.4
|
11.2
|
1.0
|
|
N
|
A:HIS122
|
4.5
|
7.5
|
1.0
|
|
CE1
|
A:HIS122
|
4.7
|
5.8
|
1.0
|
|
O2'
|
A:ADP158
|
4.7
|
16.2
|
1.0
|
|
C
|
A:ILE121
|
4.7
|
8.2
|
1.0
|
|
OD1
|
A:ASN119
|
4.7
|
11.4
|
1.0
|
|
CE2
|
A:TYR56
|
4.9
|
12.9
|
1.0
|
|
O1B
|
A:ADP158
|
4.9
|
14.0
|
1.0
|
|
C2'
|
A:ADP158
|
5.0
|
14.7
|
1.0
|
|
Fluorine binding site 2 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 2 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F157
b:24.0
occ:1.00
|
F2
|
A:AF3157
|
0.0
|
24.0
|
1.0
|
|
AL
|
A:AF3157
|
1.9
|
22.4
|
1.0
|
|
NH2
|
A:ARG92
|
2.6
|
18.4
|
1.0
|
|
ND1
|
A:HIS122
|
2.8
|
7.3
|
1.0
|
|
O3B
|
A:ADP158
|
2.9
|
9.4
|
1.0
|
|
N
|
A:GLY123
|
2.9
|
5.2
|
1.0
|
|
F3
|
A:AF3157
|
3.1
|
19.1
|
1.0
|
|
CA
|
A:HIS122
|
3.1
|
5.5
|
1.0
|
|
O1B
|
A:ADP158
|
3.2
|
14.0
|
1.0
|
|
F1
|
A:AF3157
|
3.2
|
23.3
|
1.0
|
|
O
|
A:GLY123
|
3.3
|
9.7
|
1.0
|
|
NH2
|
A:ARG109
|
3.3
|
5.4
|
1.0
|
|
PB
|
A:ADP158
|
3.4
|
11.2
|
1.0
|
|
C
|
A:HIS122
|
3.5
|
7.5
|
1.0
|
|
CG
|
A:HIS122
|
3.5
|
8.2
|
1.0
|
|
CE1
|
A:HIS122
|
3.5
|
5.8
|
1.0
|
|
CB
|
A:HIS122
|
3.6
|
5.3
|
1.0
|
|
O
|
A:HOH690
|
3.7
|
9.1
|
1.0
|
|
CZ
|
A:ARG92
|
3.9
|
18.7
|
1.0
|
|
MG
|
A:MG156
|
4.0
|
14.1
|
1.0
|
|
CA
|
A:GLY123
|
4.0
|
4.2
|
1.0
|
|
C
|
A:GLY123
|
4.0
|
8.6
|
1.0
|
|
O2B
|
A:ADP158
|
4.1
|
9.6
|
1.0
|
|
O
|
A:ILE121
|
4.1
|
10.5
|
1.0
|
|
N
|
A:HIS122
|
4.3
|
7.5
|
1.0
|
|
NE2
|
A:HIS122
|
4.4
|
5.1
|
1.0
|
|
CZ
|
A:ARG109
|
4.4
|
9.0
|
1.0
|
|
CD2
|
A:HIS122
|
4.4
|
6.5
|
1.0
|
|
NE
|
A:ARG92
|
4.6
|
21.5
|
1.0
|
|
C
|
A:ILE121
|
4.6
|
8.2
|
1.0
|
|
NH1
|
A:ARG92
|
4.7
|
20.5
|
1.0
|
|
O
|
A:HIS122
|
4.7
|
8.6
|
1.0
|
|
O3'
|
A:ADP158
|
4.7
|
11.5
|
1.0
|
|
NH1
|
A:ARG109
|
4.8
|
9.4
|
1.0
|
|
O3A
|
A:ADP158
|
4.8
|
13.4
|
1.0
|
|
Fluorine binding site 3 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 3 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F157
b:19.1
occ:1.00
|
F3
|
A:AF3157
|
0.0
|
19.1
|
1.0
|
|
MG
|
A:MG156
|
1.9
|
14.1
|
1.0
|
|
AL
|
A:AF3157
|
1.9
|
22.4
|
1.0
|
|
O
|
A:HOH671
|
2.6
|
20.4
|
1.0
|
|
O
|
A:HOH690
|
2.8
|
9.1
|
1.0
|
|
O1B
|
A:ADP158
|
2.9
|
14.0
|
1.0
|
|
O1A
|
A:ADP158
|
2.9
|
14.1
|
1.0
|
|
ND1
|
A:HIS122
|
3.0
|
7.3
|
1.0
|
|
F2
|
A:AF3157
|
3.1
|
24.0
|
1.0
|
|
O3B
|
A:ADP158
|
3.1
|
9.4
|
1.0
|
|
CE1
|
A:HIS122
|
3.3
|
5.8
|
1.0
|
|
F1
|
A:AF3157
|
3.4
|
23.3
|
1.0
|
|
PB
|
A:ADP158
|
3.4
|
11.2
|
1.0
|
|
CE1
|
A:TYR56
|
3.7
|
9.7
|
1.0
|
|
C5'
|
A:ADP158
|
3.7
|
11.3
|
1.0
|
|
PA
|
A:ADP158
|
3.9
|
13.4
|
1.0
|
|
O3A
|
A:ADP158
|
3.9
|
13.4
|
1.0
|
|
O
|
A:HOH612
|
4.0
|
17.4
|
1.0
|
|
O
|
A:HOH698
|
4.0
|
12.4
|
1.0
|
|
O5'
|
A:ADP158
|
4.2
|
10.4
|
1.0
|
|
CG
|
A:HIS122
|
4.3
|
8.2
|
1.0
|
|
CD1
|
A:TYR56
|
4.4
|
12.5
|
1.0
|
|
NH2
|
A:ARG92
|
4.6
|
18.4
|
1.0
|
|
NE2
|
A:HIS122
|
4.6
|
5.1
|
1.0
|
|
OH
|
A:TYR56
|
4.6
|
13.4
|
1.0
|
|
CZ
|
A:TYR56
|
4.6
|
12.4
|
1.0
|
|
NE2
|
A:HIS59
|
4.7
|
12.4
|
1.0
|
|
O
|
A:GLY123
|
4.7
|
9.7
|
1.0
|
|
O3'
|
A:ADP158
|
4.7
|
11.5
|
1.0
|
|
C4'
|
A:ADP158
|
4.7
|
12.4
|
1.0
|
|
O2B
|
A:ADP158
|
4.9
|
9.6
|
1.0
|
|
O
|
A:HOH683
|
4.9
|
11.0
|
1.0
|
|
Fluorine binding site 4 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 4 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F157
b:29.1
occ:1.00
|
F1
|
B:AF3157
|
0.0
|
29.1
|
1.0
|
|
AL
|
B:AF3157
|
1.8
|
27.6
|
1.0
|
|
OH
|
B:TYR56
|
2.4
|
17.8
|
1.0
|
|
NZ
|
B:LYS16
|
3.0
|
16.1
|
1.0
|
|
O3B
|
B:ADP158
|
3.1
|
19.2
|
1.0
|
|
O3'
|
B:ADP158
|
3.1
|
13.1
|
1.0
|
|
F3
|
B:AF3157
|
3.1
|
32.3
|
1.0
|
|
ND1
|
B:HIS122
|
3.3
|
7.5
|
1.0
|
|
F2
|
B:AF3157
|
3.3
|
26.1
|
1.0
|
|
CZ
|
B:TYR56
|
3.4
|
19.4
|
1.0
|
|
CE
|
B:LYS16
|
3.4
|
14.4
|
1.0
|
|
CE1
|
B:TYR56
|
3.4
|
15.4
|
1.0
|
|
CB
|
B:HIS122
|
3.5
|
5.7
|
1.0
|
|
C4'
|
B:ADP158
|
3.6
|
17.6
|
1.0
|
|
C5'
|
B:ADP158
|
3.8
|
14.8
|
1.0
|
|
CG
|
B:HIS122
|
3.8
|
9.2
|
1.0
|
|
CA
|
B:HIS122
|
3.8
|
6.6
|
1.0
|
|
C3'
|
B:ADP158
|
3.9
|
15.6
|
1.0
|
|
PB
|
B:ADP158
|
4.4
|
18.3
|
1.0
|
|
NH2
|
B:ARG109
|
4.4
|
7.7
|
1.0
|
|
CE1
|
B:HIS122
|
4.4
|
7.0
|
1.0
|
|
O
|
B:ILE121
|
4.6
|
9.2
|
1.0
|
|
CE2
|
B:TYR56
|
4.7
|
19.4
|
1.0
|
|
N
|
B:HIS122
|
4.7
|
8.8
|
1.0
|
|
O1B
|
B:ADP158
|
4.7
|
22.8
|
1.0
|
|
CD1
|
B:TYR56
|
4.8
|
17.5
|
1.0
|
|
O5'
|
B:ADP158
|
4.8
|
19.4
|
1.0
|
|
CD
|
B:LYS16
|
4.8
|
11.7
|
1.0
|
|
MG
|
B:MG156
|
4.9
|
21.7
|
1.0
|
|
C
|
B:HIS122
|
5.0
|
6.7
|
1.0
|
|
C
|
B:ILE121
|
5.0
|
7.6
|
1.0
|
|
Fluorine binding site 5 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 5 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F157
b:26.1
occ:1.00
|
F2
|
B:AF3157
|
0.0
|
26.1
|
1.0
|
|
AL
|
B:AF3157
|
1.9
|
27.6
|
1.0
|
|
N
|
B:GLY123
|
2.8
|
7.4
|
1.0
|
|
O3B
|
B:ADP158
|
3.0
|
19.2
|
1.0
|
|
ND1
|
B:HIS122
|
3.2
|
7.5
|
1.0
|
|
F3
|
B:AF3157
|
3.2
|
32.3
|
1.0
|
|
O
|
B:GLY123
|
3.2
|
11.9
|
1.0
|
|
CA
|
B:HIS122
|
3.2
|
6.6
|
1.0
|
|
F1
|
B:AF3157
|
3.3
|
29.1
|
1.0
|
|
O1B
|
B:ADP158
|
3.3
|
22.8
|
1.0
|
|
NH2
|
B:ARG92
|
3.3
|
35.9
|
1.0
|
|
NH2
|
B:ARG109
|
3.4
|
7.7
|
1.0
|
|
C
|
B:HIS122
|
3.5
|
6.7
|
1.0
|
|
PB
|
B:ADP158
|
3.5
|
18.3
|
1.0
|
|
CG
|
B:HIS122
|
3.8
|
9.2
|
1.0
|
|
CA
|
B:GLY123
|
3.8
|
8.9
|
1.0
|
|
CB
|
B:HIS122
|
3.9
|
5.7
|
1.0
|
|
O
|
B:HOH669
|
3.9
|
16.7
|
1.0
|
|
CZ
|
B:ARG92
|
3.9
|
31.6
|
1.0
|
|
CE1
|
B:HIS122
|
3.9
|
7.0
|
1.0
|
|
C
|
B:GLY123
|
4.0
|
9.3
|
1.0
|
|
O2B
|
B:ADP158
|
4.1
|
17.0
|
1.0
|
|
NH1
|
B:ARG92
|
4.1
|
34.8
|
1.0
|
|
O
|
B:ILE121
|
4.2
|
9.2
|
1.0
|
|
MG
|
B:MG156
|
4.3
|
21.7
|
1.0
|
|
N
|
B:HIS122
|
4.4
|
8.8
|
1.0
|
|
CZ
|
B:ARG109
|
4.5
|
7.6
|
1.0
|
|
O
|
B:HIS122
|
4.7
|
7.4
|
1.0
|
|
CD2
|
B:HIS122
|
4.7
|
8.4
|
1.0
|
|
C
|
B:ILE121
|
4.7
|
7.6
|
1.0
|
|
O3'
|
B:ADP158
|
4.8
|
13.1
|
1.0
|
|
NH1
|
B:ARG109
|
4.8
|
7.4
|
1.0
|
|
NE2
|
B:HIS122
|
4.8
|
8.0
|
1.0
|
|
NE
|
B:ARG92
|
4.9
|
26.7
|
1.0
|
|
O3A
|
B:ADP158
|
5.0
|
18.5
|
1.0
|
|
Fluorine binding site 6 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 6 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F157
b:32.3
occ:1.00
|
F3
|
B:AF3157
|
0.0
|
32.3
|
1.0
|
|
AL
|
B:AF3157
|
1.9
|
27.6
|
1.0
|
|
MG
|
B:MG156
|
1.9
|
21.7
|
1.0
|
|
O
|
B:HOH604
|
2.7
|
29.9
|
1.0
|
|
O1B
|
B:ADP158
|
2.9
|
22.8
|
1.0
|
|
O
|
B:HOH669
|
2.9
|
16.7
|
1.0
|
|
ND1
|
B:HIS122
|
3.1
|
7.5
|
1.0
|
|
F1
|
B:AF3157
|
3.1
|
29.1
|
1.0
|
|
O1A
|
B:ADP158
|
3.1
|
19.4
|
1.0
|
|
O3B
|
B:ADP158
|
3.2
|
19.2
|
1.0
|
|
F2
|
B:AF3157
|
3.2
|
26.1
|
1.0
|
|
CE1
|
B:HIS122
|
3.4
|
7.0
|
1.0
|
|
PB
|
B:ADP158
|
3.5
|
18.3
|
1.0
|
|
C5'
|
B:ADP158
|
3.6
|
14.8
|
1.0
|
|
O
|
B:HOH847
|
3.7
|
25.2
|
1.0
|
|
CE1
|
B:TYR56
|
3.7
|
15.4
|
1.0
|
|
PA
|
B:ADP158
|
4.1
|
19.6
|
1.0
|
|
O3A
|
B:ADP158
|
4.2
|
18.5
|
1.0
|
|
O
|
B:HOH603
|
4.2
|
16.0
|
1.0
|
|
O5'
|
B:ADP158
|
4.3
|
19.4
|
1.0
|
|
CG
|
B:HIS122
|
4.4
|
9.2
|
1.0
|
|
CD1
|
B:TYR56
|
4.5
|
17.5
|
1.0
|
|
O
|
B:GLY123
|
4.5
|
11.9
|
1.0
|
|
OH
|
B:TYR56
|
4.5
|
17.8
|
1.0
|
|
NE2
|
B:HIS59
|
4.6
|
19.9
|
1.0
|
|
CZ
|
B:TYR56
|
4.6
|
19.4
|
1.0
|
|
C4'
|
B:ADP158
|
4.7
|
17.6
|
1.0
|
|
NE2
|
B:HIS122
|
4.7
|
8.0
|
1.0
|
|
O
|
B:HOH639
|
4.8
|
15.0
|
1.0
|
|
O3'
|
B:ADP158
|
4.9
|
13.1
|
1.0
|
|
O2B
|
B:ADP158
|
4.9
|
17.0
|
1.0
|
|
Fluorine binding site 7 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 7 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F157
b:22.3
occ:1.00
|
F1
|
C:AF3157
|
0.0
|
22.3
|
1.0
|
|
AL
|
C:AF3157
|
1.9
|
23.5
|
1.0
|
|
NH2
|
C:ARG92
|
2.6
|
26.3
|
1.0
|
|
O3B
|
C:ADP158
|
2.7
|
13.8
|
1.0
|
|
N
|
C:GLY123
|
3.0
|
9.0
|
1.0
|
|
NH2
|
C:ARG109
|
3.1
|
8.0
|
1.0
|
|
CA
|
C:HIS122
|
3.1
|
7.5
|
1.0
|
|
ND1
|
C:HIS122
|
3.2
|
6.2
|
1.0
|
|
F3
|
C:AF3157
|
3.2
|
23.3
|
1.0
|
|
F2
|
C:AF3157
|
3.3
|
24.4
|
1.0
|
|
O1B
|
C:ADP158
|
3.4
|
12.6
|
1.0
|
|
PB
|
C:ADP158
|
3.4
|
11.0
|
1.0
|
|
C
|
C:HIS122
|
3.5
|
9.3
|
1.0
|
|
O
|
C:GLY123
|
3.5
|
11.8
|
1.0
|
|
CG
|
C:HIS122
|
3.7
|
6.0
|
1.0
|
|
CB
|
C:HIS122
|
3.7
|
7.3
|
1.0
|
|
CZ
|
C:ARG92
|
3.9
|
23.8
|
1.0
|
|
CE1
|
C:HIS122
|
3.9
|
4.6
|
1.0
|
|
O2B
|
C:ADP158
|
4.0
|
12.5
|
1.0
|
|
O
|
C:HOH667
|
4.0
|
13.4
|
1.0
|
|
O
|
C:ILE121
|
4.0
|
11.8
|
1.0
|
|
CA
|
C:GLY123
|
4.1
|
7.4
|
1.0
|
|
C
|
C:GLY123
|
4.2
|
8.7
|
1.0
|
|
CZ
|
C:ARG109
|
4.3
|
7.2
|
1.0
|
|
N
|
C:HIS122
|
4.3
|
9.2
|
1.0
|
|
MG
|
C:MG156
|
4.3
|
22.6
|
1.0
|
|
C
|
C:ILE121
|
4.6
|
9.3
|
1.0
|
|
CD2
|
C:HIS122
|
4.6
|
7.6
|
1.0
|
|
NE
|
C:ARG92
|
4.6
|
22.7
|
1.0
|
|
O3'
|
C:ADP158
|
4.7
|
11.8
|
1.0
|
|
NH1
|
C:ARG92
|
4.7
|
28.1
|
1.0
|
|
NH1
|
C:ARG109
|
4.7
|
9.5
|
1.0
|
|
NE2
|
C:HIS122
|
4.7
|
8.9
|
1.0
|
|
O
|
C:HIS122
|
4.8
|
10.8
|
1.0
|
|
O3A
|
C:ADP158
|
4.8
|
15.2
|
1.0
|
|
Fluorine binding site 8 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 8 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F157
b:24.4
occ:1.00
|
F2
|
C:AF3157
|
0.0
|
24.4
|
1.0
|
|
AL
|
C:AF3157
|
1.8
|
23.5
|
1.0
|
|
OH
|
C:TYR56
|
2.5
|
16.6
|
1.0
|
|
NZ
|
C:LYS16
|
2.9
|
15.9
|
1.0
|
|
CE
|
C:LYS16
|
3.1
|
14.6
|
1.0
|
|
F3
|
C:AF3157
|
3.1
|
23.3
|
1.0
|
|
O3B
|
C:ADP158
|
3.2
|
13.8
|
1.0
|
|
O3'
|
C:ADP158
|
3.2
|
11.8
|
1.0
|
|
ND1
|
C:HIS122
|
3.2
|
6.2
|
1.0
|
|
F1
|
C:AF3157
|
3.3
|
22.3
|
1.0
|
|
CB
|
C:HIS122
|
3.4
|
7.3
|
1.0
|
|
CZ
|
C:TYR56
|
3.4
|
16.2
|
1.0
|
|
CE1
|
C:TYR56
|
3.4
|
17.2
|
1.0
|
|
CG
|
C:HIS122
|
3.7
|
6.0
|
1.0
|
|
C5'
|
C:ADP158
|
3.7
|
15.8
|
1.0
|
|
C4'
|
C:ADP158
|
3.8
|
15.1
|
1.0
|
|
CA
|
C:HIS122
|
3.8
|
7.5
|
1.0
|
|
C3'
|
C:ADP158
|
4.1
|
14.5
|
1.0
|
|
NH2
|
C:ARG109
|
4.4
|
8.0
|
1.0
|
|
O
|
C:ILE121
|
4.4
|
11.8
|
1.0
|
|
CE1
|
C:HIS122
|
4.4
|
4.6
|
1.0
|
|
CD
|
C:LYS16
|
4.5
|
12.2
|
1.0
|
|
PB
|
C:ADP158
|
4.5
|
11.0
|
1.0
|
|
N
|
C:HIS122
|
4.7
|
9.2
|
1.0
|
|
CE2
|
C:TYR56
|
4.7
|
15.6
|
1.0
|
|
CD1
|
C:TYR56
|
4.7
|
17.6
|
1.0
|
|
O2'
|
C:ADP158
|
4.7
|
21.7
|
1.0
|
|
C
|
C:ILE121
|
4.9
|
9.3
|
1.0
|
|
O5'
|
C:ADP158
|
4.9
|
16.4
|
1.0
|
|
OD1
|
C:ASN119
|
4.9
|
10.4
|
1.0
|
|
O1B
|
C:ADP158
|
5.0
|
12.6
|
1.0
|
|
Fluorine binding site 9 out
of 9 in 1kdn
Go back to
Fluorine Binding Sites List in 1kdn
Fluorine binding site 9 out
of 9 in the Structure of Nucleoside Diphosphate Kinase
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Structure of Nucleoside Diphosphate Kinase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F157
b:23.3
occ:1.00
|
F3
|
C:AF3157
|
0.0
|
23.3
|
1.0
|
|
AL
|
C:AF3157
|
1.9
|
23.5
|
1.0
|
|
MG
|
C:MG156
|
2.0
|
22.6
|
1.0
|
|
O
|
C:HOH722
|
2.8
|
25.3
|
1.0
|
|
ND1
|
C:HIS122
|
3.0
|
6.2
|
1.0
|
|
O
|
C:HOH667
|
3.0
|
13.4
|
1.0
|
|
O1B
|
C:ADP158
|
3.0
|
12.6
|
1.0
|
|
O3B
|
C:ADP158
|
3.0
|
13.8
|
1.0
|
|
O1A
|
C:ADP158
|
3.0
|
14.3
|
1.0
|
|
F2
|
C:AF3157
|
3.1
|
24.4
|
1.0
|
|
F1
|
C:AF3157
|
3.2
|
22.3
|
1.0
|
|
CE1
|
C:HIS122
|
3.3
|
4.6
|
1.0
|
|
PB
|
C:ADP158
|
3.5
|
11.0
|
1.0
|
|
C5'
|
C:ADP158
|
3.5
|
15.8
|
1.0
|
|
CE1
|
C:TYR56
|
3.6
|
17.2
|
1.0
|
|
PA
|
C:ADP158
|
3.9
|
16.7
|
1.0
|
|
O3A
|
C:ADP158
|
3.9
|
15.2
|
1.0
|
|
O
|
C:HOH766
|
4.0
|
26.4
|
1.0
|
|
O5'
|
C:ADP158
|
4.1
|
16.4
|
1.0
|
|
O
|
C:HOH622
|
4.1
|
13.1
|
1.0
|
|
CG
|
C:HIS122
|
4.3
|
6.0
|
1.0
|
|
CD1
|
C:TYR56
|
4.3
|
17.6
|
1.0
|
|
OH
|
C:TYR56
|
4.6
|
16.6
|
1.0
|
|
NE2
|
C:HIS122
|
4.6
|
8.9
|
1.0
|
|
O3'
|
C:ADP158
|
4.6
|
11.8
|
1.0
|
|
CZ
|
C:TYR56
|
4.6
|
16.2
|
1.0
|
|
C4'
|
C:ADP158
|
4.7
|
15.1
|
1.0
|
|
O
|
C:GLY123
|
4.7
|
11.8
|
1.0
|
|
O2B
|
C:ADP158
|
4.9
|
12.5
|
1.0
|
|
NH2
|
C:ARG92
|
4.9
|
26.3
|
1.0
|
|
NE2
|
C:HIS59
|
5.0
|
20.3
|
1.0
|
|
CB
|
C:HIS122
|
5.0
|
7.3
|
1.0
|
|
O
|
C:HOH630
|
5.0
|
12.4
|
1.0
|
|
Reference:
Y.W.Xu,
S.Morera,
J.Janin,
J.Cherfils.
ALF3 Mimics the Transition State of Protein Phosphorylation in the Crystal Structure of Nucleoside Diphosphate Kinase and Mgadp. Proc.Natl.Acad.Sci.Usa V. 94 3579 1997.
ISSN: ISSN 0027-8424
PubMed: 9108019
DOI: 10.1073/PNAS.94.8.3579
Page generated: Mon Jul 14 11:03:01 2025
|
