Zinc in PDB 7n1s: Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

The structure of Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase, PDB code: 7n1s was solved by D.Fernandez, L.Li, J.A.Brown, J.A.Carozza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.61 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.204, 77.712, 129.292, 90, 90, 90
R / Rfree (%)	21.4 / 25.7

The binding sites of Zinc atom in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase (pdb code 7n1s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase, PDB code: 7n1s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure Analysis 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 Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:49.2 occ:1.00 OD1 A:ASP54 2.0 50.8 1.0 OD2 A:ASP257 2.1 33.1 1.0 OG1 A:THR90 2.2 41.8 1.0 NE2 A:HIS258 2.3 41.4 1.0 CG A:ASP54 2.7 45.5 1.0 OD2 A:ASP54 2.9 45.4 1.0 CG A:ASP257 3.1 31.3 1.0 CE1 A:HIS258 3.1 42.5 1.0 CB A:THR90 3.1 37.6 1.0 CD2 A:HIS258 3.2 36.7 1.0 CG2 A:THR90 3.3 39.0 1.0 OD1 A:ASP257 3.4 30.5 1.0 CA A:THR90 3.6 37.6 1.0 CG A:ASP210 4.1 46.9 1.0 OD1 A:ASP210 4.1 55.2 1.0 OD2 A:ASP210 4.1 57.2 1.0 CB A:ASP54 4.2 39.4 1.0 ND1 A:HIS258 4.2 38.0 1.0 N A:THR90 4.2 35.4 1.0 N A:GLY55 4.3 34.4 1.0 CG A:HIS258 4.3 35.0 1.0 CE1 A:HIS363 4.3 38.0 1.0 CB A:ASP257 4.4 28.6 1.0 NE2 A:HIS363 4.4 48.4 1.0 CA A:ASP54 4.6 34.1 1.0 CE1 A:HIS94 4.6 33.8 1.0 CB A:ASP210 4.7 41.2 1.0 C A:ASP54 4.7 35.5 1.0 ND1 A:HIS363 4.8 40.3 1.0 CA A:GLY55 4.9 33.2 1.0 C A:THR90 4.9 33.0 1.0 CD2 A:HIS363 4.9 42.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure Analysis 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 Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:45.9 occ:1.00 OG1 B:THR90 2.1 40.7 1.0 OD1 B:ASP54 2.1 42.3 1.0 OD2 B:ASP257 2.2 40.7 1.0 NE2 B:HIS258 2.3 41.1 1.0 CG B:ASP54 2.8 43.2 1.0 OD2 B:ASP54 2.9 45.2 1.0 CB B:THR90 3.0 35.3 1.0 CG B:ASP257 3.1 34.0 1.0 CE1 B:HIS258 3.2 39.1 1.0 CD2 B:HIS258 3.3 37.9 1.0 CG2 B:THR90 3.3 38.2 1.0 OD1 B:ASP257 3.4 32.0 1.0 CA B:THR90 3.5 31.8 1.0 N B:THR90 4.1 33.0 1.0 CG B:ASP210 4.2 43.6 1.0 OD2 B:ASP210 4.2 56.0 1.0 CB B:ASP54 4.2 36.5 1.0 OD1 B:ASP210 4.2 53.9 1.0 CE1 B:HIS363 4.2 38.9 1.0 ND1 B:HIS258 4.2 42.3 1.0 CG B:HIS258 4.3 40.3 1.0 N B:GLY55 4.3 37.7 1.0 NE2 B:HIS363 4.4 41.4 1.0 CB B:ASP257 4.4 34.6 1.0 CA B:ASP54 4.7 34.0 1.0 CE1 B:HIS94 4.7 37.8 1.0 ND1 B:HIS363 4.7 42.2 1.0 C B:ASP54 4.8 35.4 1.0 CB B:ASP210 4.8 39.5 1.0 C B:THR90 4.9 31.8 1.0 C B:LEU89 4.9 30.9 1.0 CD2 B:HIS363 5.0 36.2 1.0 CA B:GLY55 5.0 34.6 1.0

J.A.Carozza, A.F.Cordova, J.A.Brown, Y.Alsaif, V.Bohnert, X.Cao, R.E.Mardjuki, G.Skariah, D.Fernandez, L.Li. ENPP1'S Regulation of Extracellular Cgamp Is A Ubiquitous Mechanism of Attenuating Sting Signaling. Proc.Natl.Acad.Sci.Usa V. 119 89119 2022.
ISSN: ESSN 1091-6490
PubMed: 35588451
DOI: 10.1073/PNAS.2119189119