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Zinc in PDB 1v8r: Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Zn

Enzymatic activity of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Zn

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

Protein crystallography data

The structure of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Zn, PDB code: 1v8r 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) 19.02 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 49.710, 49.710, 118.140, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose and Zn (pdb code 1v8r). 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 Adp-Ribose and Zn, PDB code: 1v8r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1v8r

Go back to Zinc Binding Sites List in 1v8r
Zinc binding site 1 out of 2 in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose 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 Adp-Ribose and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:74.7
occ:1.00
O A:HOH669 2.0 27.1 1.0
O A:HOH655 2.3 22.9 1.0
OE2 A:GLU82 2.4 16.7 1.0
O A:HOH673 2.5 39.0 1.0
O1A A:APR619 2.8 67.8 1.0
OE1 A:GLU82 2.9 22.9 1.0
CD A:GLU82 3.0 16.4 1.0
OE2 A:GLU86 3.7 17.3 1.0
PA A:APR619 3.8 63.1 1.0
O3A A:APR619 3.9 64.7 1.0
OE1 A:GLU85 4.1 15.1 1.0
CG A:GLU86 4.3 9.6 1.0
O A:ALA66 4.3 14.4 1.0
CD A:GLU86 4.3 14.4 1.0
O A:HOH671 4.4 31.8 1.0
O5' A:APR619 4.5 67.8 1.0
CG A:GLU82 4.5 15.2 1.0
NH1 A:ARG81 4.6 12.5 1.0
C5' A:APR619 4.7 56.5 1.0
CA A:GLY67 4.8 12.7 1.0
O2A A:APR619 4.9 57.0 1.0

Zinc binding site 2 out of 2 in 1v8r

Go back to Zinc Binding Sites List in 1v8r
Zinc binding site 2 out of 2 in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase Complexed with Adp-Ribose 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 Adp-Ribose and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:90.8
occ:1.00
OE1 A:GLU70 2.2 43.2 1.0
CD A:GLU70 2.9 29.7 1.0
OE2 A:GLU70 2.9 53.7 1.0
O A:HOH671 4.1 31.8 1.0
CG A:GLU70 4.4 35.4 1.0
O5' A:APR619 4.8 67.8 1.0

Reference:

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
Page generated: Mon Jan 25 16:14:52 2021

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