Gadolinium in PDB 2yzw: Adp-Ribosylglycohydrolase-Related Protein Complex

The structure of Adp-Ribosylglycohydrolase-Related Protein Complex, PDB code: 2yzw 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)	50.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.147, 73.950, 78.606, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.4

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

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Adp-Ribosylglycohydrolase-Related Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd501 b:15.5 occ:1.00 OD1 A:ASP251 2.2 10.5 1.0 OE2 A:GLU29 2.3 16.9 1.0 OD2 A:ASP253 2.5 8.3 1.0 O A:HOH535 2.5 15.1 1.0 O A:HOH507 2.5 11.1 1.0 OG1 A:THR254 2.7 9.3 1.0 CG A:ASP251 3.2 11.4 1.0 CG A:ASP253 3.3 9.5 1.0 CD A:GLU29 3.4 15.7 1.0 OD1 A:ASP253 3.5 9.4 1.0 OD2 A:ASP251 3.5 12.3 1.0 GD A:GD3502 3.8 12.7 1.0 OE1 A:GLU29 3.9 14.8 1.0 CB A:THR254 3.9 8.2 1.0 O A:HOH505 3.9 12.0 1.0 N A:THR254 4.3 7.6 1.0 O A:HOH503 4.3 6.5 1.0 CB A:ASP251 4.5 8.7 1.0 O A:HOH556 4.6 15.9 1.0 CA A:ASP251 4.6 9.2 1.0 OD2 A:ASP58 4.6 11.8 1.0 CG A:GLU29 4.7 15.9 1.0 OD1 A:ASP58 4.7 11.0 1.0 CA A:THR254 4.7 8.1 1.0 CB A:ASP253 4.8 9.8 1.0 O A:HOH676 4.9 34.3 1.0 C A:ASP251 5.0 8.9 1.0

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


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Adp-Ribosylglycohydrolase-Related Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd502 b:12.7 occ:1.00 OD2 A:ASP57 2.2 12.8 1.0 OD1 A:ASP253 2.3 9.4 1.0 OD1 A:ASP58 2.3 11.0 1.0 O A:HOH507 2.4 11.1 1.0 O A:HOH505 2.4 12.0 1.0 OG1 A:THR56 2.6 10.3 1.0 CG A:ASP57 3.4 11.8 1.0 CG A:ASP253 3.4 9.5 1.0 CG A:ASP58 3.5 13.0 1.0 CB A:THR56 3.6 10.8 1.0 GD A:GD3501 3.8 15.5 1.0 OD2 A:ASP253 3.9 8.3 1.0 O A:HOH503 4.0 6.5 1.0 OD1 A:ASP57 4.0 13.3 1.0 OD2 A:ASP58 4.1 11.8 1.0 N A:ASP57 4.1 9.5 1.0 N A:ASP58 4.2 7.7 1.0 CG2 A:THR56 4.3 12.6 1.0 OE1 A:GLU29 4.5 14.8 1.0 OD1 A:ASP22 4.5 8.2 1.0 CB A:ASP57 4.6 11.4 1.0 OG1 A:THR254 4.6 9.3 1.0 CB A:ASP253 4.6 9.8 1.0 CB A:ASP58 4.7 8.7 1.0 CA A:ASP57 4.8 10.0 1.0 OE2 A:GLU29 4.8 16.9 1.0 CA A:THR56 4.8 10.1 1.0 C A:THR56 4.8 9.5 1.0 C A:ASP57 5.0 8.8 1.0

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