Fluorine in PDB 1qf9: pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase
Enzymatic activity of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase
All present enzymatic activity of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase:
2.7.4.14;
Protein crystallography data
The structure of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase, PDB code: 1qf9
was solved by
I.Schlichting,
J.Reinstein,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.70
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.000,
78.000,
100.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.6 /
24.4
|
Other elements in 1qf9:
The structure of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase
(pdb code 1qf9). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase, PDB code: 1qf9:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 1qf9
Go back to
Fluorine Binding Sites List in 1qf9
Fluorine binding site 1 out
of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F499
b:27.8
occ:1.00
|
F1
|
A:ALF499
|
0.0
|
27.8
|
1.0
|
AL
|
A:ALF499
|
1.7
|
23.9
|
1.0
|
F3
|
A:ALF499
|
2.3
|
29.5
|
1.0
|
F4
|
A:ALF499
|
2.4
|
24.7
|
1.0
|
O3B
|
A:ADP195
|
2.7
|
12.7
|
1.0
|
O3P
|
A:C5P196
|
2.7
|
16.1
|
1.0
|
NH2
|
A:ARG148
|
2.9
|
19.3
|
1.0
|
CA
|
A:PRO15
|
3.0
|
15.4
|
1.0
|
NH1
|
A:ARG148
|
3.1
|
22.1
|
1.0
|
N
|
A:GLY16
|
3.2
|
13.7
|
1.0
|
NH2
|
A:ARG93
|
3.3
|
15.7
|
1.0
|
F2
|
A:ALF499
|
3.3
|
24.9
|
1.0
|
CZ
|
A:ARG148
|
3.4
|
26.1
|
1.0
|
NZ
|
A:LYS19
|
3.5
|
9.5
|
1.0
|
C
|
A:PRO15
|
3.6
|
14.2
|
1.0
|
CB
|
A:PRO15
|
3.7
|
15.8
|
1.0
|
N
|
A:PRO15
|
4.0
|
15.7
|
1.0
|
PB
|
A:ADP195
|
4.1
|
14.1
|
1.0
|
P
|
A:C5P196
|
4.1
|
15.9
|
1.0
|
O
|
A:GLY14
|
4.1
|
16.4
|
1.0
|
O1B
|
A:ADP195
|
4.3
|
13.8
|
1.0
|
O2P
|
A:C5P196
|
4.3
|
14.4
|
1.0
|
O
|
A:HOH712
|
4.4
|
22.4
|
0.9
|
C
|
A:GLY14
|
4.4
|
16.7
|
1.0
|
CA
|
A:GLY16
|
4.5
|
13.1
|
1.0
|
CE
|
A:LYS19
|
4.5
|
14.0
|
1.0
|
CZ
|
A:ARG93
|
4.6
|
17.2
|
1.0
|
CG
|
A:PRO15
|
4.6
|
15.7
|
1.0
|
NE
|
A:ARG148
|
4.7
|
25.0
|
1.0
|
O2B
|
A:ADP195
|
4.7
|
13.4
|
1.0
|
NH2
|
A:ARG137
|
4.8
|
14.3
|
1.0
|
O
|
A:PRO15
|
4.8
|
13.5
|
1.0
|
O
|
A:HOH198
|
4.8
|
29.7
|
1.0
|
MG
|
A:MG500
|
4.9
|
19.2
|
1.0
|
O5'
|
A:C5P196
|
4.9
|
13.8
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 1qf9
Go back to
Fluorine Binding Sites List in 1qf9
Fluorine binding site 2 out
of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F499
b:24.9
occ:1.00
|
F2
|
A:ALF499
|
0.0
|
24.9
|
1.0
|
AL
|
A:ALF499
|
1.6
|
23.9
|
1.0
|
MG
|
A:MG500
|
2.3
|
19.2
|
1.0
|
F4
|
A:ALF499
|
2.3
|
24.7
|
1.0
|
F3
|
A:ALF499
|
2.4
|
29.5
|
1.0
|
O3P
|
A:C5P196
|
2.5
|
16.1
|
1.0
|
O3B
|
A:ADP195
|
2.5
|
12.7
|
1.0
|
NH1
|
A:ARG137
|
2.8
|
16.0
|
1.0
|
O
|
A:HOH215
|
3.2
|
14.5
|
1.0
|
P
|
A:C5P196
|
3.2
|
15.9
|
1.0
|
O1P
|
A:C5P196
|
3.3
|
16.3
|
1.0
|
O2B
|
A:ADP195
|
3.3
|
13.4
|
1.0
|
O
|
A:HOH220
|
3.3
|
12.5
|
1.0
|
F1
|
A:ALF499
|
3.3
|
27.8
|
1.0
|
NH1
|
A:ARG131
|
3.3
|
12.7
|
1.0
|
PB
|
A:ADP195
|
3.5
|
14.1
|
1.0
|
NH2
|
A:ARG137
|
3.6
|
14.3
|
1.0
|
CZ
|
A:ARG137
|
3.6
|
16.9
|
1.0
|
O
|
A:HOH198
|
3.7
|
29.7
|
1.0
|
O2P
|
A:C5P196
|
3.8
|
14.4
|
1.0
|
NH2
|
A:ARG131
|
4.0
|
15.1
|
1.0
|
CZ
|
A:ARG131
|
4.0
|
16.4
|
1.0
|
O3A
|
A:ADP195
|
4.3
|
13.8
|
1.0
|
O
|
A:HOH553
|
4.4
|
15.5
|
0.8
|
O
|
A:HOH227
|
4.6
|
23.4
|
1.0
|
O2A
|
A:ADP195
|
4.6
|
11.3
|
1.0
|
O1B
|
A:ADP195
|
4.6
|
13.8
|
1.0
|
O5'
|
A:C5P196
|
4.7
|
13.8
|
1.0
|
NH1
|
A:ARG148
|
4.7
|
22.1
|
1.0
|
NE
|
A:ARG137
|
4.9
|
18.6
|
1.0
|
NH2
|
A:ARG148
|
4.9
|
19.3
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 1qf9
Go back to
Fluorine Binding Sites List in 1qf9
Fluorine binding site 3 out
of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F499
b:29.5
occ:1.00
|
F3
|
A:ALF499
|
0.0
|
29.5
|
1.0
|
AL
|
A:ALF499
|
1.6
|
23.9
|
1.0
|
F1
|
A:ALF499
|
2.3
|
27.8
|
1.0
|
F2
|
A:ALF499
|
2.4
|
24.9
|
1.0
|
O3P
|
A:C5P196
|
2.5
|
16.1
|
1.0
|
O3B
|
A:ADP195
|
2.5
|
12.7
|
1.0
|
O
|
A:HOH198
|
2.6
|
29.7
|
1.0
|
O2P
|
A:C5P196
|
2.9
|
14.4
|
1.0
|
NZ
|
A:LYS19
|
3.0
|
9.5
|
1.0
|
MG
|
A:MG500
|
3.0
|
19.2
|
1.0
|
P
|
A:C5P196
|
3.2
|
15.9
|
1.0
|
CE
|
A:LYS19
|
3.3
|
14.0
|
1.0
|
O2B
|
A:ADP195
|
3.3
|
13.4
|
1.0
|
PB
|
A:ADP195
|
3.3
|
14.1
|
1.0
|
NH2
|
A:ARG93
|
3.3
|
15.7
|
1.0
|
F4
|
A:ALF499
|
3.3
|
24.7
|
1.0
|
O1B
|
A:ADP195
|
3.7
|
13.8
|
1.0
|
O1P
|
A:C5P196
|
4.0
|
16.3
|
1.0
|
CZ
|
A:ARG93
|
4.3
|
17.2
|
1.0
|
O
|
A:HOH215
|
4.3
|
14.5
|
1.0
|
NH2
|
A:ARG148
|
4.4
|
19.3
|
1.0
|
NH1
|
A:ARG93
|
4.4
|
14.5
|
1.0
|
O5'
|
A:C5P196
|
4.5
|
13.8
|
1.0
|
N
|
A:GLY16
|
4.7
|
13.7
|
1.0
|
O3A
|
A:ADP195
|
4.7
|
13.8
|
1.0
|
CD
|
A:LYS19
|
4.7
|
15.6
|
1.0
|
O
|
A:HOH208
|
4.7
|
21.8
|
1.0
|
O
|
A:HOH227
|
4.8
|
23.4
|
1.0
|
OD1
|
A:ASP89
|
4.8
|
14.4
|
1.0
|
O
|
A:HOH220
|
5.0
|
12.5
|
1.0
|
NH1
|
A:ARG148
|
5.0
|
22.1
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 1qf9
Go back to
Fluorine Binding Sites List in 1qf9
Fluorine binding site 4 out
of 4 in the pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog in Ump/Cmp Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F499
b:24.7
occ:1.00
|
F4
|
A:ALF499
|
0.0
|
24.7
|
1.0
|
AL
|
A:ALF499
|
1.7
|
23.9
|
1.0
|
F2
|
A:ALF499
|
2.3
|
24.9
|
1.0
|
F1
|
A:ALF499
|
2.4
|
27.8
|
1.0
|
O3B
|
A:ADP195
|
2.7
|
12.7
|
1.0
|
NH1
|
A:ARG148
|
2.7
|
22.1
|
1.0
|
NH2
|
A:ARG131
|
2.7
|
15.1
|
1.0
|
O3P
|
A:C5P196
|
2.8
|
16.1
|
1.0
|
NH1
|
A:ARG131
|
3.1
|
12.7
|
1.0
|
NH2
|
A:ARG137
|
3.2
|
14.3
|
1.0
|
F3
|
A:ALF499
|
3.3
|
29.5
|
1.0
|
CZ
|
A:ARG131
|
3.3
|
16.4
|
1.0
|
NH1
|
A:ARG137
|
3.5
|
16.0
|
1.0
|
CZ
|
A:ARG148
|
3.6
|
26.1
|
1.0
|
CZ
|
A:ARG137
|
3.6
|
16.9
|
1.0
|
NH2
|
A:ARG148
|
3.7
|
19.3
|
1.0
|
N
|
A:GLY16
|
3.9
|
13.7
|
1.0
|
CD2
|
A:LEU128
|
4.0
|
14.1
|
1.0
|
P
|
A:C5P196
|
4.1
|
15.9
|
1.0
|
PB
|
A:ADP195
|
4.2
|
14.1
|
1.0
|
O
|
A:HOH810
|
4.4
|
27.4
|
1.0
|
MG
|
A:MG500
|
4.5
|
19.2
|
1.0
|
CA
|
A:PRO15
|
4.5
|
15.4
|
1.0
|
CA
|
A:GLY16
|
4.5
|
13.1
|
1.0
|
C
|
A:PRO15
|
4.6
|
14.2
|
1.0
|
O1P
|
A:C5P196
|
4.6
|
16.3
|
1.0
|
NE
|
A:ARG131
|
4.7
|
16.3
|
1.0
|
NE
|
A:ARG137
|
4.7
|
18.6
|
1.0
|
O3A
|
A:ADP195
|
4.7
|
13.8
|
1.0
|
O2B
|
A:ADP195
|
4.7
|
13.4
|
1.0
|
NE
|
A:ARG148
|
4.7
|
25.0
|
1.0
|
CB
|
A:PRO15
|
4.8
|
15.8
|
1.0
|
OD1
|
A:ASP140
|
5.0
|
16.2
|
1.0
|
|
Reference:
I.Schlichting,
J.Reinstein.
pH Influences Fluoride Coordination Number of the Alfx Phosphoryl Transfer Transition State Analog. Nat.Struct.Biol. V. 6 721 1999.
ISSN: ISSN 1072-8368
PubMed: 10426946
DOI: 10.1038/11485
Page generated: Wed Jul 31 12:32:11 2024
|