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Zinc 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:

Vanadium (V) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate, PDB code: 2gso:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 1 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1000

b:12.0
occ:1.00
 NE2 A:HIS258 2.0 10.7 1.0
OD1 A:ASP54 2.0 12.2 1.0
OG1 A:THR90 2.1 11.2 1.0
OD2 A:ASP257 2.1 11.7 1.0
O3 A:VO41004 2.3 16.0 1.0
CG A:ASP54 2.8 12.2 1.0
OD2 A:ASP54 2.9 15.3 1.0
CE1 A:HIS258 2.9 9.8 1.0
CG A:ASP257 3.0 11.1 1.0
CD2 A:HIS258 3.0 11.6 1.0
CB A:THR90 3.1 11.8 1.0
OD1 A:ASP257 3.2 11.3 1.0
V A:VO41004 3.3 17.7 1.0
CA A:THR90 3.5 11.1 1.0
CG2 A:THR90 3.5 11.9 1.0
O A:HOH1431 4.0 40.3 1.0
N A:THR90 4.0 11.0 1.0
ND1 A:HIS258 4.1 10.0 1.0
OD1 A:ASP210 4.1 14.9 1.0
CE1 A:HIS363 4.1 10.9 1.0
CG A:HIS258 4.1 10.4 1.0
ZN A:ZN1001 4.1 12.2 1.0
CB A:ASP54 4.2 11.6 1.0
NE2 A:HIS363 4.3 11.3 1.0
CB A:ASP257 4.3 11.2 1.0
CG A:ASP210 4.3 13.2 1.0
N A:GLY55 4.3 11.3 1.0
O1 A:VO41004 4.3 16.0 1.0
CE1 A:HIS94 4.5 12.5 1.0
O2 A:VO41004 4.6 18.9 1.0
CA A:ASP54 4.6 11.4 1.0
OD2 A:ASP210 4.6 13.6 1.0
O4 A:VO41004 4.7 17.1 1.0
C A:ASP54 4.8 11.4 1.0
C A:LEU89 4.8 11.4 1.0
C A:THR90 4.8 11.7 1.0
CB A:ASP210 4.9 12.1 1.0
ND1 A:HIS363 4.9 10.8 1.0
ND1 A:HIS94 4.9 11.6 1.0

Zinc binding site 2 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 2 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn1001

b:12.2
occ:1.00
 NE2 A:HIS214 2.0 12.7 1.0
NE2 A:HIS363 2.1 11.3 1.0
O3 A:VO41004 2.1 16.0 1.0
OD1 A:ASP210 2.2 14.9 1.0
O4 A:VO41004 2.2 17.1 1.0
OD2 A:ASP210 2.5 13.6 1.0
CG A:ASP210 2.6 13.2 1.0
CE1 A:HIS214 3.0 12.6 1.0
CD2 A:HIS363 3.1 11.7 1.0
CD2 A:HIS214 3.1 13.8 1.0
CE1 A:HIS363 3.1 10.9 1.0
V A:VO41004 3.1 17.7 1.0
O A:HOH1033 4.0 21.4 1.0
CE1 A:HIS258 4.0 9.8 1.0
O1 A:VO41004 4.1 16.0 1.0
ND1 A:HIS214 4.1 14.1 1.0
CB A:ASP210 4.1 12.1 1.0
ZN A:ZN1000 4.1 12.0 1.0
CG A:HIS214 4.2 13.1 1.0
ND1 A:HIS363 4.2 10.8 1.0
CG A:HIS363 4.2 10.0 1.0
NE2 A:HIS258 4.2 10.7 1.0
O A:HOH1431 4.2 40.3 1.0
OG1 A:THR90 4.3 11.2 1.0
O A:HOH1283 4.4 37.6 1.0
O2 A:VO41004 4.4 18.9 1.0
OD1 A:ASP54 4.5 12.2 1.0
CE A:MET260 4.7 13.0 1.0
O A:HOH1022 4.8 14.2 1.0
O A:ASP210 4.9 12.4 1.0
CA A:ASP210 5.0 12.4 1.0

Zinc binding site 3 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 3 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:13.1
occ:1.00
 NE2 B:HIS258 2.0 12.6 1.0
OD1 B:ASP54 2.0 11.5 1.0
OG1 B:THR90 2.1 12.0 1.0
OD2 B:ASP257 2.1 12.0 1.0
O3 B:VO41005 2.3 16.8 1.0
CG B:ASP54 2.8 12.3 1.0
CE1 B:HIS258 3.0 11.4 1.0
OD2 B:ASP54 3.0 15.5 1.0
CG B:ASP257 3.0 12.3 1.0
CD2 B:HIS258 3.0 11.5 1.0
CB B:THR90 3.1 12.7 1.0
OD1 B:ASP257 3.2 11.8 1.0
V B:VO41005 3.3 17.4 1.0
CA B:THR90 3.5 11.9 1.0
CG2 B:THR90 3.5 12.6 1.0
O B:HOH1234 3.8 32.4 1.0
N B:THR90 3.9 12.0 1.0
ND1 B:HIS258 4.1 11.4 1.0
OD1 B:ASP210 4.1 14.6 1.0
CE1 B:HIS363 4.1 11.6 1.0
CG B:HIS258 4.1 12.1 1.0
O1 B:VO41005 4.1 16.1 1.0
ZN B:ZN1003 4.2 12.8 1.0
CB B:ASP54 4.2 11.4 1.0
N B:GLY55 4.3 11.6 1.0
CB B:ASP257 4.3 11.7 1.0
CG B:ASP210 4.3 13.0 1.0
NE2 B:HIS363 4.3 12.3 1.0
O2 B:VO41005 4.6 19.1 1.0
CA B:ASP54 4.6 11.2 1.0
O4 B:VO41005 4.6 16.5 1.0
OD2 B:ASP210 4.6 14.5 1.0
CE1 B:HIS94 4.6 11.6 1.0
C B:LEU89 4.7 11.9 1.0
C B:ASP54 4.7 11.4 1.0
C B:THR90 4.8 12.0 1.0
CB B:ASP210 4.9 12.1 1.0
ND1 B:HIS363 4.9 11.3 1.0
CA B:GLY55 4.9 11.7 1.0

Zinc binding site 4 out of 4 in 2gso

Go back to Zinc Binding Sites List in 2gso
Zinc binding site 4 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:12.8
occ:1.00
 NE2 B:HIS214 2.0 12.8 1.0
NE2 B:HIS363 2.0 12.3 1.0
O4 B:VO41005 2.1 16.5 1.0
O3 B:VO41005 2.1 16.8 1.0
OD1 B:ASP210 2.2 14.6 1.0
OD2 B:ASP210 2.6 14.5 1.0
CG B:ASP210 2.7 13.0 1.0
CE1 B:HIS214 2.9 12.6 1.0
CE1 B:HIS363 3.0 11.6 1.0
CD2 B:HIS363 3.0 12.3 1.0
CD2 B:HIS214 3.1 13.4 1.0
V B:VO41005 3.2 17.4 1.0
O B:HOH1292 3.7 24.0 1.0
CE1 B:HIS258 4.0 11.4 1.0
O1 B:VO41005 4.0 16.1 1.0
ND1 B:HIS214 4.1 14.3 1.0
ND1 B:HIS363 4.1 11.3 1.0
CB B:ASP210 4.2 12.1 1.0
ZN B:ZN1002 4.2 13.1 1.0
CG B:HIS363 4.2 10.6 1.0
CG B:HIS214 4.2 13.8 1.0
NE2 B:HIS258 4.2 12.6 1.0
O B:HOH1234 4.2 32.4 1.0
OG1 B:THR90 4.4 12.0 1.0
O2 B:VO41005 4.4 19.1 1.0
OD1 B:ASP54 4.6 11.5 1.0
CE B:MET260 4.6 14.4 1.0
O B:HOH1329 4.8 46.5 1.0
O B:HOH1025 4.8 16.0 1.0
O B:ASP210 4.9 12.1 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 17 00:23:03 2024

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