Magnesium in PDB 2yzv: Adp-Ribosylglycohydrolase-Related Protein Complex

The structure of Adp-Ribosylglycohydrolase-Related Protein Complex, PDB code: 2yzv was solved by A.Ebihara, M.Manzoku, S.Yokoyama, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.53 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.971, 73.591, 78.211, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.8

The binding sites of Magnesium atom in the Adp-Ribosylglycohydrolase-Related Protein Complex (pdb code 2yzv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Adp-Ribosylglycohydrolase-Related Protein Complex, PDB code: 2yzv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Adp-Ribosylglycohydrolase-Related Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adp-Ribosylglycohydrolase-Related Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:18.4 occ:1.00 OD1 A:ASP251 2.3 25.4 1.0 OG1 A:THR254 2.4 15.5 1.0 OD2 A:ASP253 2.5 15.5 1.0 OD1 A:ASP253 2.6 16.9 1.0 CG A:ASP253 2.9 15.7 1.0 CG A:ASP251 3.0 21.8 1.0 OD2 A:ASP251 3.2 25.0 1.0 MG A:MG502 3.5 30.0 1.0 CB A:THR254 3.5 11.4 1.0 OE2 A:GLU29 3.7 29.3 1.0 N A:THR254 3.9 10.6 1.0 OD1 A:ASP58 4.0 22.7 1.0 OD2 A:ASP58 4.3 20.1 1.0 CA A:THR254 4.3 11.1 1.0 CB A:ASP253 4.4 12.0 1.0 CB A:ASP251 4.4 16.1 1.0 CD A:GLU29 4.6 25.5 1.0 CG A:ASP58 4.6 21.3 1.0 CG2 A:THR254 4.7 13.6 1.0 CA A:ASP251 4.7 13.8 1.0 C A:ASP253 4.8 10.5 1.0 O A:ASP251 4.8 11.8 1.0 C A:ASP251 4.9 12.2 1.0 CA A:ASP253 5.0 10.3 1.0 OD1 A:ASN128 5.0 14.6 1.0 N A:ASP253 5.0 9.7 1.0

Magnesium binding site 2 out of 2 in the Adp-Ribosylglycohydrolase-Related Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adp-Ribosylglycohydrolase-Related Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.0 occ:1.00 OD1 A:ASP58 1.9 22.7 1.0 OD1 A:ASP253 2.0 16.9 1.0 OG1 A:THR56 2.1 15.3 1.0 CB A:THR56 3.1 14.9 1.0 CG A:ASP58 3.1 21.3 1.0 CG A:ASP253 3.2 15.7 1.0 OD1 A:ASP57 3.4 33.4 1.0 OD2 A:ASP57 3.5 34.9 1.0 MG A:MG501 3.5 18.4 1.0 CG A:ASP57 3.6 29.2 1.0 CG2 A:THR56 3.8 18.8 1.0 N A:ASP58 3.8 17.5 1.0 N A:ASP57 3.9 17.6 1.0 OD2 A:ASP58 3.9 20.1 1.0 OD1 A:ASP22 4.0 15.9 1.0 CB A:ASP253 4.0 12.0 1.0 OD2 A:ASP253 4.1 15.5 1.0 CB A:ASP58 4.2 18.7 1.0 OG1 A:THR254 4.3 15.5 1.0 CA A:THR56 4.4 15.2 1.0 C A:THR56 4.4 15.8 1.0 CA A:ASP58 4.5 17.9 1.0 CA A:ASP57 4.6 19.4 1.0 C A:ASP57 4.6 18.2 1.0 CB A:ASP57 4.7 24.8 1.0 CG A:ASP22 4.8 11.8 1.0 OD2 A:ASP22 4.8 11.7 1.0 OE2 A:GLU29 4.9 29.3 1.0 OE1 A:GLU29 4.9 26.6 1.0

A.Ebihara, M.Manzoku, S.Yokoyama, S.Kuramitsu. Adp-Ribosylglycohydrolase-Related Protein Complex To Be Published.