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Vanadium in PDB 1e59: E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate

Enzymatic activity of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate

All present enzymatic activity of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate:
5.4.2.1;

Protein crystallography data

The structure of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate, PDB code: 1e59 was solved by C.S.Bond, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.249, 112.142, 40.948, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 21.3

Other elements in 1e59:

The structure of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Vanadium Binding Sites:

The binding sites of Vanadium atom in the E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate (pdb code 1e59). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 4 binding sites of Vanadium where determined in the E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate, PDB code: 1e59:
Jump to Vanadium binding site number: 1; 2; 3; 4;

Vanadium binding site 1 out of 4 in 1e59

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Vanadium binding site 1 out of 4 in the E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:19.2
occ:0.50
 V1 A:VO31001 0.0 19.2 0.5
O1 A:VO31001 1.7 37.9 0.5
O30 A:VO31001 1.8 51.8 0.5
O0 A:VO31001 1.8 40.0 0.0
O3 A:VO31001 1.8 20.8 1.0
V2 A:VO31001 3.3 12.4 1.0
O00 A:VO31001 3.3 30.4 0.5
O A:HOH2114 3.7 13.4 1.0
O A:HOH2009 3.8 19.3 1.0
O A:HOH2263 3.9 24.0 1.0
ND2 A:ASN16 3.9 27.5 1.0
O A:HOH2262 4.0 28.0 1.0
O2 A:VO31001 4.0 17.1 1.0
O6 A:VO31001 4.2 17.1 1.0
O A:HOH2209 4.2 12.1 1.0
O A:HOH2115 4.2 16.9 1.0
NH2 A:ARG9 4.4 14.4 1.0
O4 A:VO31001 4.6 12.8 1.0
O A:HOH2006 4.7 18.8 1.0
CB A:ASN16 4.7 22.8 1.0
V4 A:VO31001 4.7 38.9 0.5
OG1 A:THR22 4.8 12.5 1.0
CG A:ASN16 4.8 26.7 1.0

Vanadium binding site 2 out of 4 in 1e59

Go back to Vanadium Binding Sites List in 1e59
Vanadium binding site 2 out of 4 in the E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:12.4
occ:1.00
 V2 A:VO31001 0.0 12.4 1.0
O2 A:VO31001 1.7 17.1 1.0
O4 A:VO31001 1.7 12.8 1.0
O3 A:VO31001 1.8 20.8 1.0
O6 A:VO31001 1.8 17.1 1.0
V1 A:VO31001 3.3 19.2 0.5
V3 A:VO31001 3.5 14.7 1.0
O30 A:VO31001 3.8 51.8 0.5
O A:HOH2115 3.9 16.9 1.0
O A:HOH2116 3.9 11.1 1.0
N A:THR22 3.9 8.1 1.0
CE2 A:TYR91 4.0 10.4 1.0
O A:HOH2114 4.1 13.4 1.0
O5 A:VO31001 4.1 13.8 1.0
CB A:THR22 4.1 9.9 1.0
NZ A:LYS99 4.2 19.2 1.0
O0 A:VO31001 4.2 40.0 0.0
N A:GLY23 4.3 9.4 1.0
CD2 A:TYR91 4.3 10.1 1.0
OE2 A:GLU88 4.4 10.1 1.0
O1 A:VO31001 4.4 37.9 0.5
OG1 A:THR22 4.4 12.5 1.0
O7 A:VO31001 4.5 13.4 1.0
CA A:THR22 4.5 8.6 1.0
O8 A:VO31001 4.6 9.4 0.5
O00 A:VO31001 4.7 30.4 0.5
O A:HOH2262 4.7 28.0 1.0
CD A:GLU88 4.8 7.4 1.0
CG A:GLU88 4.8 7.7 1.0
CE A:LYS99 4.9 14.5 1.0
C A:THR22 4.9 9.2 1.0
C A:PHE21 4.9 10.1 1.0

Vanadium binding site 3 out of 4 in 1e59

Go back to Vanadium Binding Sites List in 1e59
Vanadium binding site 3 out of 4 in the E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:14.7
occ:1.00
 V3 A:VO31001 0.0 14.7 1.0
O7 A:VO31001 1.7 13.4 1.0
O5 A:VO31001 1.7 13.8 1.0
O8 A:VO31001 1.7 9.4 0.5
O6 A:VO31001 1.8 17.1 1.0
V4 A:VO31001 3.4 38.9 0.5
V2 A:VO31001 3.5 12.4 1.0
OH A:TYR91 3.6 12.7 1.0
O A:HOH2115 3.7 16.9 1.0
CE2 A:TYR91 3.9 10.4 1.0
NZ A:LYS99 3.9 19.2 1.0
NH2 A:ARG115 4.0 36.8 1.0
NH1 A:ARG116 4.0 14.8 1.0
ND2 A:ASN185 4.0 9.0 1.0
O2 A:VO31001 4.0 17.1 1.0
O00 A:VO31001 4.1 30.4 0.5
CZ A:TYR91 4.2 11.6 1.0
NH2 A:ARG116 4.2 20.1 1.0
O11 A:VO31001 4.2 40.0 0.0
NE A:ARG115 4.3 20.9 1.0
O A:HOH2116 4.3 11.1 1.0
O10 A:VO31001 4.4 40.0 0.0
O A:HOH2210 4.5 16.8 1.0
O4 A:VO31001 4.5 12.8 1.0
O3 A:VO31001 4.5 20.8 1.0
CZ A:ARG115 4.5 28.3 1.0
CZ A:ARG116 4.6 13.4 1.0
NH2 A:ARG89 4.6 11.9 1.0
CE A:LYS99 4.9 14.5 1.0

Vanadium binding site 4 out of 4 in 1e59

Go back to Vanadium Binding Sites List in 1e59
Vanadium binding site 4 out of 4 in the E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of E.Coli Cofactor-Dependent Phosphoglycerate Mutase Complexed with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1001

b:38.9
occ:0.50
 V4 A:VO31001 0.0 38.9 0.5
O10 A:VO31001 1.6 40.0 0.0
O11 A:VO31001 1.7 40.0 0.0
O00 A:VO31001 1.8 30.4 0.5
O8 A:VO31001 1.8 9.4 0.5
V3 A:VO31001 3.4 14.7 1.0
O0 A:VO31001 3.5 40.0 0.0
NH2 A:ARG9 3.7 14.4 1.0
NH2 A:ARG115 3.7 36.8 1.0
O A:HOH2115 3.8 16.9 1.0
NH2 A:ARG116 3.9 20.1 1.0
O A:HOH2210 4.1 16.8 1.0
O6 A:VO31001 4.1 17.1 1.0
O A:HOH2264 4.1 21.1 1.0
O5 A:VO31001 4.2 13.8 1.0
O7 A:VO31001 4.6 13.4 1.0
OD1 A:ASN206 4.7 29.6 1.0
NZ A:LYS99 4.7 19.2 1.0
V1 A:VO31001 4.7 19.2 0.5
CZ A:ARG9 4.8 11.9 1.0
O30 A:VO31001 4.9 51.8 0.5
NH1 A:ARG9 4.9 16.4 1.0
CZ A:ARG115 5.0 28.3 1.0

Reference:

C.S.Bond, M.White, W.N.Hunter. Mechanistic Implications For Escherichia Coli Cofactor-Dependent Phosphoglycerate Mutase Based on the High-Resolution Crystal Structure of A Vanadate Complex. J.Mol.Biol. V. 316 1071 2002.
ISSN: ISSN 0022-2836
PubMed: 11884145
DOI: 10.1006/JMBI.2002.5418
Page generated: Fri Oct 11 11:22:41 2024

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