Zinc in PDB 2gsu: Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Amp

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

The structure of Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Amp, PDB code: 2gsu 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)	46.88 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.578, 78.450, 129.490, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 30.3

The binding sites of Zinc atom in the Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with Amp (pdb code 2gsu). 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 Amp, PDB code: 2gsu:
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 in Complex with Amp


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:32.9 occ:1.00 OG1 A:THR90 1.8 30.2 1.0 OD1 A:ASP54 1.9 37.5 1.0 OD2 A:ASP257 2.0 36.0 1.0 NE2 A:HIS258 2.2 27.0 1.0 CG A:ASP257 2.8 32.4 1.0 CG A:ASP54 2.9 32.7 1.0 OD1 A:ASP257 2.9 31.7 1.0 CB A:THR90 2.9 29.9 1.0 CD2 A:HIS258 3.0 25.8 1.0 CE1 A:HIS258 3.2 27.0 1.0 OD2 A:ASP54 3.3 35.0 1.0 CG2 A:THR90 3.4 30.7 1.0 CA A:THR90 3.4 30.1 1.0 O1P A:AMP1004 3.6 32.9 0.6 CE1 A:HIS363 3.8 26.5 1.0 OD1 A:ASP210 3.8 34.2 1.0 OD2 A:ASP210 3.9 29.9 1.0 CG A:ASP210 3.9 30.1 1.0 NE2 A:HIS363 4.1 27.9 1.0 N A:THR90 4.1 30.2 1.0 CG A:HIS258 4.1 29.5 1.0 ND1 A:HIS258 4.2 25.7 1.0 CB A:ASP257 4.2 31.2 1.0 CB A:ASP54 4.3 30.5 1.0 N A:GLY55 4.3 30.7 1.0 CE1 A:HIS94 4.3 28.7 1.0 ZN A:ZN1001 4.3 31.1 1.0 O2P A:AMP1004 4.5 30.4 0.6 ND1 A:HIS363 4.5 25.7 1.0 CA A:ASP54 4.6 29.9 1.0 P A:AMP1004 4.6 32.9 0.6 C A:ASP54 4.7 30.4 1.0 C A:THR90 4.7 30.0 1.0 C A:LEU89 4.7 30.6 1.0 ND1 A:HIS94 4.8 25.7 1.0 CB A:ASP210 4.8 29.3 1.0 CA A:GLY55 4.9 30.5 1.0 O A:THR90 4.9 28.6 1.0

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:31.1 occ:1.00 NE2 A:HIS363 2.0 27.9 1.0 O1P A:AMP1004 2.0 32.9 0.6 NE2 A:HIS214 2.0 28.2 1.0 OD2 A:ASP210 2.1 29.9 1.0 CE1 A:HIS214 2.9 30.9 1.0 P A:AMP1004 2.9 32.9 0.6 CG A:ASP210 2.9 30.1 1.0 CD2 A:HIS363 2.9 26.9 1.0 CE1 A:HIS363 3.0 26.5 1.0 O3P A:AMP1004 3.0 35.0 0.6 OD1 A:ASP210 3.0 34.2 1.0 CD2 A:HIS214 3.1 28.7 1.0 O2P A:AMP1004 3.9 30.4 0.6 OG1 A:THR90 4.0 30.2 1.0 ND1 A:HIS214 4.0 27.6 1.0 ND1 A:HIS363 4.1 25.7 1.0 CG A:HIS363 4.1 28.2 1.0 O5' A:AMP1004 4.1 36.9 0.6 CG A:HIS214 4.2 27.4 1.0 O A:HOH1257 4.3 36.3 1.0 ZN A:ZN1000 4.3 32.9 1.0 CE1 A:HIS258 4.3 27.0 1.0 CB A:ASP210 4.3 29.3 1.0 NE2 A:HIS258 4.4 27.0 1.0 O3' A:AMP1004 4.4 44.3 0.6 O A:HOH1040 4.6 23.1 1.0 C5' A:AMP1004 4.7 39.8 0.6 O A:HOH1146 4.7 40.6 1.0 O A:ASP210 4.8 30.5 1.0 CE A:MET260 4.8 30.6 1.0 C3' A:AMP1004 5.0 43.0 0.6

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:35.4 occ:1.00 OD1 B:ASP54 1.9 33.4 1.0 OD2 B:ASP257 2.0 36.2 1.0 NE2 B:HIS258 2.0 27.9 1.0 OG1 B:THR90 2.3 32.9 1.0 CG B:ASP54 2.7 32.7 1.0 CD2 B:HIS258 2.7 24.6 1.0 OD2 B:ASP54 2.9 32.3 1.0 CG B:ASP257 3.0 33.3 1.0 CE1 B:HIS258 3.1 28.1 1.0 O1P B:AMP1005 3.1 39.2 0.8 CB B:THR90 3.3 29.8 1.0 OD1 B:ASP257 3.3 30.4 1.0 CA B:THR90 3.6 30.0 1.0 CG2 B:THR90 3.7 30.2 1.0 OD1 B:ASP210 3.9 31.0 1.0 CG B:HIS258 3.9 28.2 1.0 CB B:ASP54 4.0 30.4 1.0 ND1 B:HIS258 4.1 28.1 1.0 N B:GLY55 4.2 30.3 1.0 N B:THR90 4.2 30.4 1.0 CB B:ASP257 4.3 31.4 1.0 CE1 B:HIS363 4.3 26.8 1.0 CG B:ASP210 4.4 29.0 1.0 CA B:ASP54 4.4 30.0 1.0 ZN B:ZN1003 4.4 33.8 1.0 NE2 B:HIS363 4.5 26.6 1.0 CE1 B:HIS94 4.5 29.7 1.0 P B:AMP1005 4.6 40.4 0.8 C5' B:AMP1005 4.6 41.9 0.8 C B:ASP54 4.7 30.8 1.0 CB B:ASP210 4.8 29.0 1.0 C B:LEU89 4.8 30.7 1.0 C B:THR90 4.8 29.7 1.0 CA B:GLY55 4.8 29.7 1.0 ND1 B:HIS94 5.0 27.1 1.0 O5' B:AMP1005 5.0 42.3 0.8

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


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 Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:33.8 occ:1.00 O3P B:AMP1005 2.0 41.4 0.8 OD1 B:ASP210 2.0 31.0 1.0 NE2 B:HIS214 2.1 29.7 1.0 NE2 B:HIS363 2.2 26.6 1.0 O1P B:AMP1005 2.6 39.2 0.8 O B:HOH1204 2.7 36.3 1.0 P B:AMP1005 2.7 40.4 0.8 CG B:ASP210 2.9 29.0 1.0 CE1 B:HIS214 3.1 30.3 1.0 OD2 B:ASP210 3.1 35.6 1.0 CD2 B:HIS363 3.1 25.7 1.0 CD2 B:HIS214 3.2 27.5 1.0 CE1 B:HIS363 3.2 26.8 1.0 O2P B:AMP1005 3.8 40.8 0.8 O5' B:AMP1005 3.9 42.3 0.8 CE1 B:HIS258 4.1 28.1 1.0 NE2 B:HIS258 4.1 27.9 1.0 C5' B:AMP1005 4.2 41.9 0.8 ND1 B:HIS214 4.2 27.6 1.0 OG1 B:THR90 4.2 32.9 1.0 CB B:ASP210 4.3 29.0 1.0 CG B:HIS214 4.3 27.3 1.0 CG B:HIS363 4.3 28.6 1.0 ND1 B:HIS363 4.3 26.0 1.0 ZN B:ZN1002 4.4 35.4 1.0 OD1 B:ASP54 4.5 33.4 1.0 O B:ASP210 4.6 27.9 1.0 CE B:MET260 4.8 32.7 1.0 C B:ASP210 5.0 28.6 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