Zinc in PDB 2opz: Avpf Bound to BIR3-Xiap

The structure of Avpf Bound to BIR3-Xiap, PDB code: 2opz was solved by A.D.Wist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	170.367, 170.367, 170.367, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27.7

The binding sites of Zinc atom in the Avpf Bound to BIR3-Xiap (pdb code 2opz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Avpf Bound to BIR3-Xiap, PDB code: 2opz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Avpf Bound to BIR3-Xiap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Avpf Bound to BIR3-Xiap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:46.8 occ:1.00 NE2 A:HIS320 2.2 59.2 1.0 SG A:CYS303 2.3 39.4 1.0 SG A:CYS327 2.4 59.5 1.0 SG A:CYS300 2.5 67.2 1.0 CE1 A:HIS320 2.7 52.6 1.0 CB A:CYS327 2.9 59.8 1.0 CB A:CYS300 3.1 61.9 1.0 CB A:CYS303 3.3 38.4 1.0 CD2 A:HIS320 3.5 51.1 1.0 N A:CYS303 3.6 51.5 1.0 ND1 A:HIS320 4.0 56.3 1.0 CA A:CYS303 4.0 52.9 1.0 CA A:CYS327 4.3 57.0 1.0 CG A:HIS320 4.4 52.2 1.0 CB A:HIS302 4.4 54.1 1.0 CA A:CYS300 4.6 58.4 1.0 C A:HIS302 4.7 70.2 1.0 N A:GLY304 4.7 52.0 1.0 C A:CYS303 4.8 52.9 1.0 N A:HIS302 4.9 77.8 1.0 CA A:HIS302 4.9 76.4 1.0 CB A:TYR324 5.0 49.0 1.0

Zinc binding site 2 out of 4 in the Avpf Bound to BIR3-Xiap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Avpf Bound to BIR3-Xiap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:46.8 occ:1.00 NE2 B:HIS320 2.2 62.4 1.0 SG B:CYS303 2.3 42.5 1.0 SG B:CYS300 2.4 67.2 1.0 SG B:CYS327 2.4 59.9 1.0 CE1 B:HIS320 2.7 55.8 1.0 CB B:CYS327 2.8 60.2 1.0 CB B:CYS300 3.1 62.0 1.0 CB B:CYS303 3.2 41.5 1.0 CD2 B:HIS320 3.5 54.2 1.0 N B:CYS303 3.6 53.9 1.0 ND1 B:HIS320 4.0 59.5 1.0 CA B:CYS303 4.0 55.2 1.0 CA B:CYS327 4.2 55.6 1.0 CG B:HIS320 4.4 55.3 1.0 CB B:HIS302 4.5 61.3 1.0 CA B:CYS300 4.6 61.2 1.0 C B:HIS302 4.7 73.5 1.0 N B:GLY304 4.7 54.8 1.0 C B:CYS303 4.8 55.2 1.0 CB B:TYR329 5.0 62.7 1.0 N B:HIS302 5.0 81.2 1.0 CA B:HIS302 5.0 79.7 1.0

Zinc binding site 3 out of 4 in the Avpf Bound to BIR3-Xiap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Avpf Bound to BIR3-Xiap within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:47.1 occ:1.00 NE2 C:HIS320 2.3 65.4 1.0 SG C:CYS303 2.4 49.2 1.0 SG C:CYS300 2.5 59.5 1.0 SG C:CYS327 2.5 56.5 1.0 CB C:CYS327 2.7 56.8 1.0 CE1 C:HIS320 2.9 58.8 1.0 CB C:CYS303 3.2 48.3 1.0 CB C:CYS300 3.2 54.3 1.0 CD2 C:HIS320 3.6 57.3 1.0 N C:CYS303 3.6 59.5 1.0 CA C:CYS303 4.0 60.8 1.0 CA C:CYS327 4.1 61.5 1.0 ND1 C:HIS320 4.1 62.5 1.0 CG C:HIS320 4.5 58.4 1.0 CA C:CYS300 4.6 52.6 1.0 N C:GLY304 4.7 51.1 1.0 C C:CYS303 4.7 60.8 1.0 C C:HIS302 4.8 74.6 1.0 CB C:HIS302 4.8 48.3 1.0 CB C:TYR324 4.8 59.1 1.0 N C:CYS327 4.9 63.6 1.0 N C:HIS302 4.9 82.3 1.0 C C:CYS327 5.0 62.1 1.0

Zinc binding site 4 out of 4 in the Avpf Bound to BIR3-Xiap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Avpf Bound to BIR3-Xiap within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn504 b:46.8 occ:1.00 NE2 D:HIS320 2.4 66.8 1.0 SG D:CYS300 2.4 61.2 1.0 SG D:CYS303 2.4 42.5 1.0 SG D:CYS327 2.5 52.2 1.0 CE1 D:HIS320 2.8 60.2 1.0 CB D:CYS327 2.8 52.5 1.0 CB D:CYS303 3.1 41.6 1.0 CB D:CYS300 3.3 55.9 1.0 N D:CYS303 3.6 56.3 1.0 CD2 D:HIS320 3.7 58.7 1.0 CA D:CYS303 4.0 57.6 1.0 ND1 D:HIS320 4.1 63.9 1.0 CA D:CYS327 4.3 67.4 1.0 CG D:HIS320 4.6 59.8 1.0 C D:HIS302 4.7 72.3 1.0 CB D:HIS302 4.7 50.5 1.0 CA D:CYS300 4.8 56.4 1.0 C D:CYS303 4.8 57.6 1.0 N D:GLY304 4.9 54.8 1.0 N D:HIS302 4.9 80.0 1.0 CB D:TYR329 5.0 66.4 1.0

A.D.Wist, L.Gu, S.J.Riedl, Y.Shi, G.L.Mclendon. Structure-Activity Based Study of the Smac-Binding Pocket Within the BIR3 Domain of Xiap. Bioorg.Med.Chem. V. 15 2935 2007.
ISSN: ISSN 0968-0896
PubMed: 17336535
DOI: 10.1016/J.BMC.2007.02.010