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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:

Magnesium (Mg) 2 atoms

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

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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: Sun Dec 13 11:28:34 2020

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