Nickel in PDB 4ic3: Crystal Structure of the F495L Mutant Xiap Ring Domain

The structure of Crystal Structure of the F495L Mutant Xiap Ring Domain, PDB code: 4ic3 was solved by Y.Nakatani, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.34 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.735, 48.471, 39.967, 90.00, 97.47, 90.00
R / Rfree (%)	17.6 / 22.2

The structure of Crystal Structure of the F495L Mutant Xiap Ring Domain also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of the F495L Mutant Xiap Ring Domain (pdb code 4ic3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the F495L Mutant Xiap Ring Domain, PDB code: 4ic3:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the F495L Mutant Xiap Ring Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the F495L Mutant Xiap Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1003 b:53.4 occ:1.00 O A:HOH1145 2.5 46.5 1.0 OD1 A:ASP455 2.6 38.5 1.0 O A:HOH1118 2.6 35.0 1.0 O A:HOH1120 2.6 34.4 1.0 OD2 A:ASP455 2.7 38.4 1.0 CG A:ASP455 3.0 37.8 1.0 O A:CYS453 3.9 28.4 1.0 O A:HOH1140 4.2 41.6 1.0 CB A:ASP455 4.5 30.6 1.0 O A:HOH1139 4.7 40.3 1.0 O A:HOH1143 4.8 40.3 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the F495L Mutant Xiap Ring Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the F495L Mutant Xiap Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1003 b:35.3 occ:1.00 OD1 B:ASP455 2.2 19.3 1.0 O B:HOH1148 2.3 30.7 1.0 O B:HOH1149 2.4 35.4 1.0 O B:HOH1130 2.6 38.7 1.0 O B:HOH1144 2.6 30.9 1.0 CG B:ASP455 3.1 20.4 1.0 OD2 B:ASP455 3.3 23.3 1.0 O B:HOH1119 3.7 33.0 1.0 O B:CYS453 4.1 22.8 1.0 O B:HOH1121 4.4 30.1 1.0 O B:MET454 4.4 18.6 1.0 CB B:ASP455 4.4 16.6 1.0 CA B:ASP455 4.7 16.3 1.0 C B:MET454 4.7 18.0 1.0 N B:ASP455 4.9 14.7 1.0

Y.Nakatani, T.Kleffmann, K.Linke, S.M.Condon, M.G.Hinds, C.L.Day. Regulation of Ubiquitin Transfer By Xiap, A Dimeric Ring E3 Ligase Biochem.J. V. 450 629 2013.
ISSN: ISSN 0264-6021
PubMed: 23259674
DOI: 10.1042/BJ20121702