Fluorine in PDB 1bwf: Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion
Enzymatic activity of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion
All present enzymatic activity of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion:
2.7.1.30;
Protein crystallography data
The structure of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion, PDB code: 1bwf
was solved by
C.E.Bystrom,
D.W.Pettigrew,
B.P.Branchaud,
S.J.Remington,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
3.00
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.767,
200.293,
114.738,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1bwf:
The structure of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion
(pdb code 1bwf). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion, PDB code: 1bwf:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 1bwf
Go back to
Fluorine Binding Sites List in 1bwf
Fluorine binding site 1 out
of 4 in the Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:F601
b:42.7
occ:1.00
|
F1B
|
Y:ATF601
|
0.0
|
42.7
|
1.0
|
C3B
|
Y:ATF601
|
1.3
|
42.7
|
1.0
|
F2B
|
Y:ATF601
|
2.2
|
42.7
|
1.0
|
PB
|
Y:ATF601
|
2.4
|
42.7
|
1.0
|
PG
|
Y:ATF601
|
2.4
|
42.7
|
1.0
|
O3A
|
Y:ATF601
|
2.5
|
42.7
|
1.0
|
O1G
|
Y:ATF601
|
2.6
|
42.7
|
1.0
|
OG1
|
Y:THR267
|
2.7
|
38.2
|
1.0
|
O1B
|
Y:ATF601
|
3.2
|
42.7
|
1.0
|
O3G
|
Y:ATF601
|
3.4
|
42.7
|
1.0
|
OG1
|
Y:THR14
|
3.6
|
55.0
|
1.0
|
O2G
|
Y:ATF601
|
3.7
|
42.7
|
1.0
|
O2B
|
Y:ATF601
|
3.7
|
42.7
|
1.0
|
N
|
Y:THR267
|
3.8
|
30.5
|
1.0
|
CB
|
Y:THR267
|
3.8
|
24.1
|
1.0
|
PA
|
Y:ATF601
|
4.0
|
42.7
|
1.0
|
CA
|
Y:THR267
|
4.3
|
26.8
|
1.0
|
CG2
|
Y:THR14
|
4.3
|
39.5
|
1.0
|
C4'
|
Y:ATF601
|
4.4
|
42.7
|
1.0
|
C5'
|
Y:ATF601
|
4.4
|
42.7
|
1.0
|
C3'
|
Y:ATF601
|
4.6
|
42.7
|
1.0
|
CB
|
Y:THR14
|
4.6
|
47.1
|
1.0
|
O2A
|
Y:ATF601
|
4.6
|
42.7
|
1.0
|
C
|
Y:GLY266
|
4.7
|
33.3
|
1.0
|
O3'
|
Y:ATF601
|
4.8
|
42.7
|
1.0
|
O5'
|
Y:ATF601
|
4.8
|
42.7
|
1.0
|
N
|
Y:THR14
|
4.9
|
26.9
|
1.0
|
NE2
|
Y:GLN314
|
4.9
|
95.9
|
1.0
|
O1A
|
Y:ATF601
|
5.0
|
42.7
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 1bwf
Go back to
Fluorine Binding Sites List in 1bwf
Fluorine binding site 2 out
of 4 in the Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:F601
b:42.7
occ:1.00
|
F2B
|
Y:ATF601
|
0.0
|
42.7
|
1.0
|
C3B
|
Y:ATF601
|
1.4
|
42.7
|
1.0
|
F1B
|
Y:ATF601
|
2.2
|
42.7
|
1.0
|
PG
|
Y:ATF601
|
2.5
|
42.7
|
1.0
|
O1B
|
Y:ATF601
|
2.5
|
42.7
|
1.0
|
PB
|
Y:ATF601
|
2.5
|
42.7
|
1.0
|
O2G
|
Y:ATF601
|
2.7
|
42.7
|
1.0
|
OG1
|
Y:THR267
|
2.7
|
38.2
|
1.0
|
N
|
Y:THR267
|
2.9
|
30.5
|
1.0
|
CB
|
Y:THR267
|
3.0
|
24.1
|
1.0
|
O1G
|
Y:ATF601
|
3.4
|
42.7
|
1.0
|
CA
|
Y:THR267
|
3.6
|
26.8
|
1.0
|
O3A
|
Y:ATF601
|
3.7
|
42.7
|
1.0
|
O3G
|
Y:ATF601
|
3.7
|
42.7
|
1.0
|
O2B
|
Y:ATF601
|
3.8
|
42.7
|
1.0
|
C
|
Y:GLY266
|
4.0
|
33.3
|
1.0
|
CA
|
Y:GLY266
|
4.2
|
30.1
|
1.0
|
MG
|
Y:MG602
|
4.3
|
43.3
|
1.0
|
CG2
|
Y:THR267
|
4.4
|
9.8
|
1.0
|
OG1
|
Y:THR13
|
4.5
|
27.5
|
1.0
|
O2A
|
Y:ATF601
|
4.7
|
42.7
|
1.0
|
CB
|
Y:THR13
|
4.8
|
16.7
|
1.0
|
PA
|
Y:ATF601
|
4.8
|
42.7
|
1.0
|
N
|
Y:THR13
|
4.8
|
20.2
|
1.0
|
C
|
Y:THR267
|
4.8
|
24.7
|
1.0
|
N
|
Y:GLY268
|
4.9
|
20.9
|
1.0
|
O3
|
Y:GOL600
|
5.0
|
14.1
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 1bwf
Go back to
Fluorine Binding Sites List in 1bwf
Fluorine binding site 3 out
of 4 in the Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:F601
b:56.2
occ:1.00
|
F1B
|
O:ATF601
|
0.0
|
56.2
|
1.0
|
C3B
|
O:ATF601
|
1.4
|
56.2
|
1.0
|
F2B
|
O:ATF601
|
2.3
|
56.2
|
1.0
|
O3A
|
O:ATF601
|
2.4
|
56.2
|
1.0
|
PB
|
O:ATF601
|
2.4
|
56.2
|
1.0
|
PG
|
O:ATF601
|
2.5
|
56.2
|
1.0
|
O2G
|
O:ATF601
|
2.7
|
56.2
|
1.0
|
N
|
O:THR267
|
3.0
|
30.4
|
1.0
|
O1B
|
O:ATF601
|
3.3
|
56.2
|
1.0
|
O1G
|
O:ATF601
|
3.4
|
56.2
|
1.0
|
OG1
|
O:THR267
|
3.5
|
41.2
|
1.0
|
PA
|
O:ATF601
|
3.5
|
56.2
|
1.0
|
O5'
|
O:ATF601
|
3.5
|
56.2
|
1.0
|
C5'
|
O:ATF601
|
3.6
|
56.2
|
1.0
|
O2B
|
O:ATF601
|
3.6
|
56.2
|
1.0
|
C
|
O:GLY266
|
3.7
|
37.2
|
1.0
|
CA
|
O:GLY266
|
3.7
|
34.1
|
1.0
|
O3G
|
O:ATF601
|
3.7
|
56.2
|
1.0
|
CB
|
O:THR267
|
3.8
|
26.4
|
1.0
|
CA
|
O:THR267
|
3.9
|
27.7
|
1.0
|
O1A
|
O:ATF601
|
4.2
|
56.2
|
1.0
|
C4'
|
O:ATF601
|
4.2
|
56.2
|
1.0
|
O
|
O:GLY266
|
4.7
|
38.0
|
1.0
|
O2A
|
O:ATF601
|
4.8
|
56.2
|
1.0
|
O3'
|
O:ATF601
|
4.8
|
56.2
|
1.0
|
MG
|
O:MG602
|
4.8
|
56.1
|
1.0
|
C3'
|
O:ATF601
|
4.9
|
56.2
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 1bwf
Go back to
Fluorine Binding Sites List in 1bwf
Fluorine binding site 4 out
of 4 in the Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Escherichia Coli Glycerol Kinase Mutant with Bound Atp Analog Showing Substantial Domain Motion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:F601
b:56.2
occ:1.00
|
F2B
|
O:ATF601
|
0.0
|
56.2
|
1.0
|
C3B
|
O:ATF601
|
1.4
|
56.2
|
1.0
|
F1B
|
O:ATF601
|
2.3
|
56.2
|
1.0
|
PB
|
O:ATF601
|
2.5
|
56.2
|
1.0
|
PG
|
O:ATF601
|
2.5
|
56.2
|
1.0
|
O1B
|
O:ATF601
|
2.6
|
56.2
|
1.0
|
O3G
|
O:ATF601
|
2.6
|
56.2
|
1.0
|
OG1
|
O:THR14
|
2.8
|
71.1
|
1.0
|
O2G
|
O:ATF601
|
3.5
|
56.2
|
1.0
|
O2B
|
O:ATF601
|
3.5
|
56.2
|
1.0
|
O3A
|
O:ATF601
|
3.6
|
56.2
|
1.0
|
O1G
|
O:ATF601
|
3.6
|
56.2
|
1.0
|
OG1
|
O:THR267
|
3.7
|
41.2
|
1.0
|
CB
|
O:THR14
|
4.0
|
63.5
|
1.0
|
CG2
|
O:THR14
|
4.2
|
55.0
|
1.0
|
PA
|
O:ATF601
|
4.5
|
56.2
|
1.0
|
O1A
|
O:ATF601
|
4.5
|
56.2
|
1.0
|
C5'
|
O:ATF601
|
4.5
|
56.2
|
1.0
|
CB
|
O:THR267
|
4.6
|
26.4
|
1.0
|
N
|
O:THR14
|
4.7
|
42.0
|
1.0
|
O5'
|
O:ATF601
|
4.8
|
56.2
|
1.0
|
N
|
O:THR267
|
4.8
|
30.4
|
1.0
|
CA
|
O:THR14
|
5.0
|
44.2
|
1.0
|
|
Reference:
C.E.Bystrom,
D.W.Pettigrew,
B.P.Branchaud,
P.O'brien,
S.J.Remington.
Crystal Structures of Escherichia Coli Glycerol Kinase Variant S58-->W in Complex with Nonhydrolyzable Atp Analogues Reveal A Putative Active Conformation of the Enzyme As A Result of Domain Motion. Biochemistry V. 38 3508 1999.
ISSN: ISSN 0006-2960
PubMed: 10090737
DOI: 10.1021/BI982460Z
Page generated: Wed Jul 31 10:59:42 2024
|