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Magnesium in PDB 1v8v: Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg

Enzymatic activity of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg

All present enzymatic activity of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg:
3.6.1.13;

Protein crystallography data

The structure of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg, PDB code: 1v8v 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) 39.35 / 1.97
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 49.860, 49.860, 118.050, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg (pdb code 1v8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg, PDB code: 1v8v:

Magnesium binding site 1 out of 1 in 1v8v

Go back to Magnesium Binding Sites List in 1v8v
Magnesium binding site 1 out of 1 in the Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of the Adp-Ribose Pyrophosphatase of E86Q Mutant, Complexed with Adp-Ribose and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:49.4
occ:1.00
 OE1 A:GLU82 1.9 28.9 1.0
O1A A:APR619 2.1 66.9 1.0
NH1 A:ARG81 2.8 14.0 1.0
CD A:GLU82 3.1 23.3 1.0
PA A:APR619 3.2 65.7 1.0
O A:HOH662 3.3 62.3 1.0
O A:LEU68 3.3 17.4 1.0
NH2 A:ARG81 3.3 13.1 1.0
O2A A:APR619 3.3 66.0 1.0
CZ A:ARG81 3.5 15.0 1.0
N A:LEU68 3.6 15.9 1.0
OE2 A:GLU82 3.6 26.7 1.0
O5' A:APR619 4.0 65.4 1.0
OE2 A:GLU70 4.0 35.2 1.0
CA A:GLY67 4.2 15.8 1.0
O A:HOH630 4.2 20.4 1.0
C A:LEU68 4.2 18.2 1.0
C A:GLY67 4.2 15.1 1.0
CG A:GLU82 4.3 21.6 1.0
CA A:LEU68 4.3 17.2 1.0
O A:HOH660 4.4 60.4 1.0
O3A A:APR619 4.4 66.2 1.0
CB A:LEU68 4.7 19.5 1.0
NE A:ARG81 4.8 13.9 1.0
OE1 A:GLU85 4.8 15.4 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: Tue Aug 13 15:01:58 2024

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