Zinc in PDB 1v8t: Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn

All present enzymatic activity of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn:
3.6.1.13;

The structure of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn, PDB code: 1v8t was solved by S.Yoshiba, T.Ooga, N.Nakagawa, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu, R.Masui, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.32 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	49.930, 49.930, 117.950, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 24.5

The binding sites of Zinc atom in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn (pdb code 1v8t). 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 the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn, PDB code: 1v8t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn


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 the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:95.0 occ:1.00 OE2 A:GLU82 2.7 20.6 1.0 OE1 A:GLU82 2.8 22.0 1.0 CD A:GLU82 3.1 19.9 1.0 OE2 A:GLU86 3.4 17.9 1.0 O1P A:R5P601 3.4 57.7 1.0 O A:ALA66 3.7 14.3 1.0 O2P A:R5P601 3.9 58.2 1.0 P A:R5P601 4.0 59.1 1.0 CA A:GLY67 4.0 13.4 1.0 O3P A:R5P601 4.2 55.5 1.0 CD A:GLU86 4.3 18.0 1.0 CG A:GLU82 4.6 16.0 1.0 CG A:GLU86 4.6 15.7 1.0 C A:ALA66 4.6 12.3 1.0 N A:GLY67 4.8 12.7 1.0 O A:HOH618 4.9 20.5 1.0 NH1 A:ARG81 5.0 7.2 1.0 OE1 A:GLU85 5.0 18.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn


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 the Adp-Ribose Pyrophosphatase Complexed with Ribose-5'-Phosphate and Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:75.3 occ:1.00 OE2 A:GLU70 2.4 29.7 1.0 OE1 A:GLU70 2.6 31.4 1.0 CD A:GLU70 2.8 28.6 1.0 CG A:GLU70 4.3 25.1 1.0

S.Yoshiba, T.Ooga, N.Nakagawa, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu, R.Masui. Structural Insights Into the Thermus Thermophilus Adp-Ribose Pyrophosphatase Mechanism Via Crystal Structures with the Bound Substrate and Metal J.Biol.Chem. V. 279 37163 2004.
ISSN: ISSN 0021-9258
PubMed: 15210687
DOI: 10.1074/JBC.M403817200