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Vanadium in PDB 2gso: Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate

Enzymatic activity of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate

All present enzymatic activity of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate:
3.6.1.9;

Protein crystallography data

The structure of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate, PDB code: 2gso was solved by J.G.Zalatan, T.D.Fenn, A.T.Brunger, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.040, 78.776, 129.686, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.3

Other elements in 2gso:

The structure of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate (pdb code 2gso). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate, PDB code: 2gso:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 2gso

Go back to Vanadium Binding Sites List in 2gso
Vanadium binding site 1 out of 2 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1004

b:17.7
occ:1.00
V A:VO41004 0.0 17.7 1.0
O2 A:VO41004 1.8 18.9 1.0
OG1 A:THR90 1.9 11.2 1.0
O4 A:VO41004 1.9 17.1 1.0
O1 A:VO41004 2.0 16.0 1.0
O3 A:VO41004 2.0 16.0 1.0
CB A:THR90 2.9 11.8 1.0
O A:HOH1431 3.0 40.3 1.0
ZN A:ZN1001 3.1 12.2 1.0
ZN A:ZN1000 3.3 12.0 1.0
CE1 A:HIS363 3.7 10.9 1.0
N A:THR90 3.8 11.0 1.0
NE2 A:HIS363 3.8 11.3 1.0
CG2 A:THR90 3.8 11.9 1.0
CA A:THR90 3.9 11.1 1.0
O A:HOH1033 4.0 21.4 1.0
OD2 A:ASP210 4.1 13.6 1.0
ND2 A:ASN111 4.1 14.2 1.0
O A:HOH1283 4.2 37.6 1.0
O A:HOH1367 4.3 42.3 1.0
NE2 A:HIS258 4.3 10.7 1.0
OD2 A:ASP54 4.6 15.3 1.0
OD1 A:ASP54 4.6 12.2 1.0
OD1 A:ASP210 4.7 14.9 1.0
CG A:ASP210 4.7 13.2 1.0
NE2 A:HIS214 4.8 12.7 1.0
ND1 A:HIS363 5.0 10.8 1.0
C A:LEU89 5.0 11.4 1.0

Vanadium binding site 2 out of 2 in 2gso

Go back to Vanadium Binding Sites List in 2gso
Vanadium binding site 2 out of 2 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V1005

b:17.4
occ:1.00
V B:VO41005 0.0 17.4 1.0
O2 B:VO41005 1.8 19.1 1.0
O1 B:VO41005 1.9 16.1 1.0
OG1 B:THR90 1.9 12.0 1.0
O3 B:VO41005 1.9 16.8 1.0
O4 B:VO41005 1.9 16.5 1.0
O B:HOH1234 2.8 32.4 1.0
CB B:THR90 2.9 12.7 1.0
ZN B:ZN1003 3.2 12.8 1.0
ZN B:ZN1002 3.3 13.1 1.0
CE1 B:HIS363 3.7 11.6 1.0
N B:THR90 3.8 12.0 1.0
NE2 B:HIS363 3.9 12.3 1.0
CG2 B:THR90 3.9 12.6 1.0
O B:HOH1292 3.9 24.0 1.0
CA B:THR90 4.0 11.9 1.0
ND2 B:ASN111 4.1 14.4 1.0
OD2 B:ASP210 4.1 14.5 1.0
O B:HOH1329 4.2 46.5 1.0
NE2 B:HIS258 4.3 12.6 1.0
O B:HOH1343 4.3 38.0 1.0
OD1 B:ASP54 4.5 11.5 1.0
OD2 B:ASP54 4.6 15.5 1.0
OD1 B:ASP210 4.6 14.6 1.0
CG B:ASP210 4.6 13.0 1.0
NE2 B:HIS214 4.8 12.8 1.0
CE1 B:HIS258 5.0 11.4 1.0
ND1 B:HIS363 5.0 11.3 1.0
CG B:ASN111 5.0 14.2 1.0
CG B:ASP54 5.0 12.3 1.0
C B:LEU89 5.0 11.9 1.0

Reference:

J.G.Zalatan, T.D.Fenn, A.T.Brunger, D.Herschlag. Structural and Functional Comparisons of Nucleotide Pyrophosphatase/Phosphodiesterase and Alkaline Phosphatase: Implications For Mechanism and Evolution Biochemistry V. 45 9788 2006.
ISSN: ISSN 0006-2960
PubMed: 16893180
DOI: 10.1021/BI060847T
Page generated: Thu Oct 29 07:04:48 2020

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