Zinc in PDB 2gsn: Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

All present enzymatic activity of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase:
3.6.1.9;

The structure of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase, PDB code: 2gsn 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 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.683, 78.692, 129.527, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.3

The binding sites of Zinc atom in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase (pdb code 2gsn). 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, PDB code: 2gsn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:30.8 occ:1.00 OD1 A:ASP54 1.9 22.9 1.0 OG1 A:THR90 2.0 23.4 1.0 OD2 A:ASP257 2.0 23.3 1.0 NE2 A:HIS258 2.1 22.7 1.0 CG A:ASP54 2.8 23.2 1.0 CG A:ASP257 2.8 22.9 1.0 CD2 A:HIS258 2.9 21.6 1.0 OD1 A:ASP257 2.9 24.1 1.0 CB A:THR90 3.0 23.0 1.0 OD2 A:ASP54 3.0 26.8 1.0 CE1 A:HIS258 3.1 24.4 1.0 CG2 A:THR90 3.3 23.5 1.0 CA A:THR90 3.4 22.8 1.0 OD1 A:ASP210 3.8 22.3 1.0 O A:HOH1277 3.9 17.4 1.0 CE1 A:HIS363 4.0 23.5 1.0 N A:THR90 4.0 23.2 1.0 CG A:HIS258 4.1 23.4 1.0 ND1 A:HIS258 4.1 22.5 1.0 CB A:ASP54 4.2 21.8 1.0 NE2 A:HIS363 4.2 24.4 1.0 CB A:ASP257 4.2 22.9 1.0 ZN A:ZN1001 4.3 32.1 1.0 N A:GLY55 4.3 22.3 1.0 CG A:ASP210 4.3 22.2 1.0 CE1 A:HIS94 4.3 25.5 1.0 O A:HOH1228 4.4 41.1 1.0 CA A:ASP54 4.5 22.2 1.0 C A:THR90 4.6 22.6 1.0 ND1 A:HIS94 4.6 23.4 1.0 C A:ASP54 4.7 22.1 1.0 OD2 A:ASP210 4.7 23.8 1.0 C A:LEU89 4.7 23.5 1.0 ND1 A:HIS363 4.8 23.1 1.0 O A:THR90 4.9 22.0 1.0 CA A:GLY55 4.9 22.5 1.0 CB A:ASP210 4.9 22.2 1.0 O A:HOH1005 4.9 14.9 1.0

Zinc binding site 2 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:32.1 occ:1.00 O A:HOH1277 2.0 17.4 1.0 NE2 A:HIS214 2.0 22.2 1.0 NE2 A:HIS363 2.1 24.4 1.0 OD1 A:ASP210 2.2 22.3 1.0 OD2 A:ASP210 2.4 23.8 1.0 CG A:ASP210 2.6 22.2 1.0 CD2 A:HIS363 3.0 23.1 1.0 CD2 A:HIS214 3.0 21.9 1.0 CE1 A:HIS214 3.0 22.8 1.0 CE1 A:HIS363 3.1 23.5 1.0 OG1 A:THR90 3.8 23.4 1.0 CE1 A:HIS258 4.1 24.4 1.0 ND1 A:HIS214 4.1 22.7 1.0 CB A:ASP210 4.2 22.2 1.0 CG A:HIS363 4.2 22.0 1.0 CG A:HIS214 4.2 21.8 1.0 O A:HOH1228 4.2 41.1 1.0 O A:HOH1225 4.2 48.9 1.0 NE2 A:HIS258 4.2 22.7 1.0 ND1 A:HIS363 4.2 23.1 1.0 O A:HOH1005 4.2 14.9 1.0 O A:HOH1030 4.3 23.5 1.0 ZN A:ZN1000 4.3 30.8 1.0 OD1 A:ASP54 4.5 22.9 1.0 CE A:MET260 4.7 26.3 1.0 O A:ASP210 4.7 22.2 1.0 O A:HOH1019 4.8 18.3 1.0 CA A:ASP210 4.9 22.2 1.0 C A:ASP210 5.0 22.6 1.0

Zinc binding site 3 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:31.5 occ:1.00 OD1 B:ASP54 2.0 24.1 1.0 NE2 B:HIS258 2.1 22.9 1.0 OD2 B:ASP257 2.1 23.1 1.0 OG1 B:THR90 2.1 22.8 1.0 CG B:ASP54 2.8 24.1 1.0 CG B:ASP257 2.9 23.9 1.0 CD2 B:HIS258 2.9 22.4 1.0 OD2 B:ASP54 3.0 27.1 1.0 CB B:THR90 3.0 23.4 1.0 OD1 B:ASP257 3.0 24.1 1.0 CE1 B:HIS258 3.1 25.2 1.0 CG2 B:THR90 3.3 24.3 1.0 CA B:THR90 3.4 23.2 1.0 O B:HOH1340 3.8 24.7 1.0 OD1 B:ASP210 3.9 24.6 1.0 CG B:HIS258 4.0 23.9 1.0 N B:THR90 4.1 23.7 1.0 ND1 B:HIS258 4.1 23.7 1.0 CE1 B:HIS363 4.1 24.8 1.0 CB B:ASP54 4.2 22.6 1.0 N B:GLY55 4.2 22.4 1.0 O B:HOH1263 4.3 35.1 1.0 CB B:ASP257 4.3 23.1 1.0 CG B:ASP210 4.3 22.2 1.0 ZN B:ZN1003 4.4 32.2 1.0 NE2 B:HIS363 4.4 24.2 1.0 CE1 B:HIS94 4.5 25.8 1.0 CA B:ASP54 4.5 22.3 1.0 C B:THR90 4.7 23.4 1.0 C B:ASP54 4.7 22.3 1.0 OD2 B:ASP210 4.7 25.3 1.0 C B:LEU89 4.8 23.4 1.0 O B:HOH1043 4.8 20.3 1.0 ND1 B:HIS94 4.8 23.0 1.0 ND1 B:HIS363 4.8 24.0 1.0 CB B:ASP210 4.8 21.4 1.0 CA B:GLY55 4.9 22.5 1.0 O B:THR90 4.9 23.4 1.0

Zinc binding site 4 out of 4 in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:32.2 occ:1.00 NE2 B:HIS214 2.0 22.8 1.0 NE2 B:HIS363 2.0 24.2 1.0 O B:HOH1340 2.0 24.7 1.0 OD1 B:ASP210 2.2 24.6 1.0 OD2 B:ASP210 2.5 25.3 1.0 CG B:ASP210 2.7 22.2 1.0 CE1 B:HIS214 2.9 22.8 1.0 CD2 B:HIS363 3.0 22.9 1.0 CE1 B:HIS363 3.0 24.8 1.0 CD2 B:HIS214 3.1 21.9 1.0 OG1 B:THR90 4.1 22.8 1.0 ND1 B:HIS214 4.1 24.4 1.0 O B:HOH1106 4.1 28.6 1.0 CE1 B:HIS258 4.1 25.2 1.0 ND1 B:HIS363 4.1 24.0 1.0 CG B:HIS363 4.1 23.3 1.0 CG B:HIS214 4.2 22.5 1.0 O B:HOH1043 4.2 20.3 1.0 CB B:ASP210 4.2 21.4 1.0 NE2 B:HIS258 4.2 22.9 1.0 O B:HOH1263 4.2 35.1 1.0 ZN B:ZN1002 4.4 31.5 1.0 OD1 B:ASP54 4.6 24.1 1.0 CE B:MET260 4.6 26.4 1.0 O B:HOH1024 4.7 18.7 1.0 O B:ASP210 4.7 21.9 1.0 CA B:ASP210 4.9 21.8 1.0

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