Zinc in PDB 8w5a: Crystal Structure of the Ring Domain of Human Xiap

All present enzymatic activity of Crystal Structure of the Ring Domain of Human Xiap:
2.3.2.27;

The structure of Crystal Structure of the Ring Domain of Human Xiap, PDB code: 8w5a was solved by Q.Zhang, H.Sun, X.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.32 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.696, 48.742, 39.639, 90, 97.28, 90
R / Rfree (%)	21.7 / 24.8

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

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Ring Domain of Human Xiap (pdb code 8w5a). 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 Ring Domain of Human Xiap, PDB code: 8w5a:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 Ring Domain of Human Xiap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:19.4 occ:1.00 ND1 A:HIS467 2.0 22.2 1.0 SG A:CYS481 2.3 18.2 1.0 SG A:CYS484 2.3 22.5 1.0 SG A:CYS465 2.3 18.2 1.0 CB A:CYS481 3.0 19.4 1.0 CE1 A:HIS467 3.0 25.1 1.0 CG A:HIS467 3.0 20.0 1.0 CB A:CYS465 3.2 20.9 1.0 CB A:HIS467 3.4 18.6 1.0 CB A:CYS484 3.5 26.0 1.0 N A:CYS484 3.9 27.0 1.0 NE2 A:HIS467 4.1 26.8 1.0 CD2 A:HIS467 4.1 22.4 1.0 CA A:CYS484 4.3 24.4 1.0 N A:HIS467 4.4 16.0 1.0 CA A:CYS481 4.4 17.7 1.0 CA A:HIS467 4.5 16.0 1.0 CA A:CYS465 4.6 23.3 1.0 CB A:MET483 4.7 28.9 1.0 C A:CYS465 4.8 19.5 1.0 C A:MET483 4.8 25.9 1.0 C A:CYS484 4.9 22.4 1.0 C A:CYS481 4.9 20.3 1.0 O A:CYS465 5.0 19.1 1.0 OG1 A:THR486 5.0 22.9 1.0 CB A:THR486 5.0 22.5 1.0

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


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 Ring Domain of Human Xiap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:18.0 occ:1.00 SG A:CYS453 2.3 19.5 1.0 SG A:CYS450 2.3 17.2 1.0 SG A:CYS474 2.3 21.2 1.0 SG A:CYS471 2.3 18.2 1.0 CB A:CYS474 3.1 17.9 1.0 CB A:CYS450 3.1 17.7 1.0 CB A:CYS453 3.2 23.9 1.0 CB A:CYS471 3.6 18.3 1.0 N A:CYS453 3.7 20.4 1.0 N A:CYS471 4.0 13.4 1.0 CA A:CYS453 4.0 22.6 1.0 N A:CYS474 4.2 17.7 1.0 CA A:CYS474 4.2 19.0 1.0 CA A:CYS471 4.3 16.8 1.0 NE A:ARG456 4.4 31.6 1.0 CA A:CYS450 4.6 17.5 1.0 NH2 A:ARG456 4.8 35.5 1.0 C A:ILE452 4.8 19.0 1.0 C A:CYS453 4.8 26.2 1.0 CB A:ILE452 4.9 24.1 1.0 N A:MET454 4.9 22.9 1.0 C A:CYS471 5.0 17.0 1.0

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


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 Ring Domain of Human Xiap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:8.6 occ:0.70 SG B:CYS471 2.3 15.1 1.0 SG B:CYS474 2.3 17.8 1.0 SG B:CYS453 2.3 15.1 1.0 SG B:CYS450 2.4 11.1 1.0 CB B:CYS450 3.1 12.8 1.0 CB B:CYS453 3.2 17.0 1.0 CB B:CYS474 3.2 16.9 1.0 CB B:CYS471 3.5 10.8 1.0 N B:CYS453 3.7 14.9 1.0 N B:CYS471 4.0 11.8 1.0 CA B:CYS453 4.0 13.6 1.0 N B:CYS474 4.2 15.6 1.0 CA B:CYS471 4.3 12.3 1.0 NH1 B:ARG456 4.3 23.7 1.0 CA B:CYS474 4.4 16.4 1.0 CA B:CYS450 4.6 12.9 1.0 CB B:ILE452 4.8 17.3 1.0 C B:ILE452 4.9 18.7 1.0 C B:CYS453 4.9 16.4 1.0 CG B:ARG456 4.9 14.4 1.0

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


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 Ring Domain of Human Xiap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:9.0 occ:1.00 ND1 B:HIS467 2.0 11.7 1.0 SG B:CYS484 2.3 7.6 1.0 SG B:CYS465 2.3 9.4 1.0 SG B:CYS481 2.3 10.1 1.0 CE1 B:HIS467 2.9 19.2 1.0 CB B:CYS481 3.0 12.1 1.0 CG B:HIS467 3.0 14.5 1.0 CB B:CYS465 3.2 9.8 1.0 CB B:HIS467 3.4 12.0 1.0 CB B:CYS484 3.4 12.3 1.0 N B:CYS484 3.9 16.1 1.0 NE2 B:HIS467 4.1 22.8 1.0 CD2 B:HIS467 4.1 18.6 1.0 CA B:CYS484 4.2 14.3 1.0 N B:HIS467 4.4 8.3 1.0 CA B:CYS481 4.5 11.8 1.0 CA B:HIS467 4.5 10.5 1.0 CA B:CYS465 4.6 10.0 1.0 CB B:MET483 4.8 19.2 1.0 C B:CYS465 4.8 11.8 1.0 C B:MET483 4.8 14.8 1.0 C B:CYS484 4.9 14.0 1.0 OG1 B:THR486 4.9 8.4 1.0 N B:TYR485 5.0 11.0 1.0 CB B:THR486 5.0 9.2 1.0 C B:CYS481 5.0 11.2 1.0

Q.Zhang, H.Sun. Crystal Structure of the Ring Domain of Human Xiap To Be Published.