Zinc in PDB 4ic2: Crystal Structure of the Xiap Ring Domain

The structure of Crystal Structure of the Xiap Ring Domain, PDB code: 4ic2 was solved by K.Linke, Y.Nakatani, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.32 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.653, 48.672, 39.860, 90.00, 97.24, 90.00
R / Rfree (%)	18.9 / 23.7

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

Nickel

(Ni)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Xiap Ring Domain (pdb code 4ic2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Xiap Ring Domain, PDB code: 4ic2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Xiap Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Xiap Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:30.3 occ:1.00 SG A:CYS474 2.3 25.4 1.0 SG A:CYS471 2.3 24.7 1.0 SG A:CYS453 2.4 34.3 1.0 SG A:CYS450 2.5 29.0 1.0 CB A:CYS474 3.0 24.4 1.0 CB A:CYS450 3.2 28.8 1.0 CB A:CYS453 3.2 35.0 1.0 CB A:CYS471 3.5 26.9 1.0 N A:CYS453 3.6 32.1 1.0 N A:CYS471 3.9 27.0 1.0 CA A:CYS453 4.0 32.0 1.0 NH2 A:ARG456 4.2 39.3 1.0 NE A:ARG456 4.2 41.2 1.0 N A:CYS474 4.2 26.1 1.0 CA A:CYS474 4.2 27.0 1.0 CA A:CYS471 4.3 28.0 1.0 CZ A:ARG456 4.6 43.2 1.0 CA A:CYS450 4.6 31.8 1.0 CB A:ILE452 4.7 26.8 1.0 C A:ILE452 4.7 31.6 1.0 N A:MET454 4.8 34.4 1.0 C A:CYS453 4.8 36.4 1.0 C A:CYS471 4.9 25.9 1.0 CB A:ARG456 4.9 34.0 1.0 C A:THR470 5.0 26.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Xiap Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Xiap Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:30.0 occ:1.00 ND1 A:HIS467 2.2 31.7 1.0 SG A:CYS465 2.3 28.0 1.0 SG A:CYS481 2.3 26.7 1.0 SG A:CYS484 2.5 33.2 1.0 CB A:CYS481 3.0 27.5 1.0 CG A:HIS467 3.1 32.0 1.0 CE1 A:HIS467 3.1 30.5 1.0 CB A:CYS465 3.2 32.8 1.0 CB A:CYS484 3.4 33.2 1.0 CB A:HIS467 3.4 29.9 1.0 N A:CYS484 3.9 34.7 1.0 CA A:CYS484 4.2 32.9 1.0 NE2 A:HIS467 4.2 31.2 1.0 CD2 A:HIS467 4.2 29.3 1.0 N A:HIS467 4.4 27.9 1.0 CA A:CYS481 4.5 26.5 1.0 CA A:HIS467 4.5 26.8 1.0 CA A:CYS465 4.5 29.6 1.0 CB A:MET483 4.6 33.9 1.0 C A:MET483 4.7 34.0 1.0 C A:CYS465 4.7 29.8 1.0 O A:HOH1101 4.7 28.4 1.0 OG1 A:THR486 4.7 28.3 1.0 C A:CYS484 4.8 33.1 1.0 O A:CYS465 4.9 27.3 1.0 CB A:THR486 4.9 29.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Xiap Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Xiap Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:30.2 occ:1.00 SG B:CYS453 2.4 29.0 1.0 SG B:CYS450 2.4 20.9 1.0 SG B:CYS471 2.4 21.6 1.0 SG B:CYS474 2.4 27.0 1.0 CB B:CYS450 3.1 24.0 1.0 CB B:CYS474 3.2 27.9 1.0 CB B:CYS453 3.2 27.2 1.0 CB B:CYS471 3.5 20.8 1.0 N B:CYS453 3.8 27.1 1.0 N B:CYS471 3.9 21.4 1.0 CA B:CYS453 4.1 27.7 1.0 N B:CYS474 4.3 24.7 1.0 CA B:CYS471 4.3 22.6 1.0 CA B:CYS474 4.3 27.2 1.0 NH1 B:ARG456 4.4 34.2 1.0 CA B:CYS450 4.6 22.8 1.0 CG B:ARG456 4.7 28.3 1.0 CB B:ILE452 4.8 24.1 1.0 N B:MET454 4.8 23.1 1.0 C B:CYS453 4.9 27.9 1.0 C B:ILE452 4.9 28.0 1.0 C B:CYS471 4.9 22.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Xiap Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Xiap Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:20.8 occ:1.00 ND1 B:HIS467 2.1 22.0 1.0 SG B:CYS481 2.3 17.9 1.0 SG B:CYS484 2.3 18.3 1.0 SG B:CYS465 2.4 20.2 1.0 CB B:CYS481 3.0 16.6 1.0 CG B:HIS467 3.1 23.8 1.0 CE1 B:HIS467 3.1 25.8 1.0 CB B:CYS465 3.2 19.1 1.0 CB B:HIS467 3.4 20.2 1.0 CB B:CYS484 3.6 20.2 1.0 N B:CYS484 3.8 23.4 1.0 NE2 B:HIS467 4.2 29.3 1.0 CD2 B:HIS467 4.2 28.9 1.0 CA B:CYS484 4.3 22.1 1.0 CB B:MET483 4.4 21.4 1.0 N B:HIS467 4.4 21.0 1.0 CA B:HIS467 4.5 23.4 1.0 CA B:CYS481 4.5 20.1 1.0 CA B:CYS465 4.6 21.6 1.0 C B:MET483 4.8 23.5 1.0 C B:CYS465 4.9 22.8 1.0 O B:HOH1110 4.9 16.7 1.0 C B:CYS484 4.9 20.4 1.0 CA B:MET483 4.9 22.9 1.0 N B:MET483 5.0 22.9 1.0 N B:TYR485 5.0 21.2 1.0 OG1 B:THR486 5.0 19.9 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