Zinc in PDB 3g76: Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound

The structure of Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound, PDB code: 3g76 was solved by F.Cossu, M.Milani, E.Mastrangelo, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.00
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	119.077, 119.077, 105.590, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 31.1

The binding sites of Zinc atom in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound (pdb code 3g76). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound, PDB code: 3g76:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


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 Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:41.9 occ:1.00 NE2 A:HIS320 2.1 26.8 1.0 SG A:CYS327 2.2 50.7 1.0 SG A:CYS300 2.3 41.0 1.0 SG A:CYS303 2.4 48.6 1.0 CE1 A:HIS320 2.7 39.1 1.0 CB A:CYS300 2.9 54.3 1.0 CB A:CYS327 3.0 40.0 1.0 CD2 A:HIS320 3.3 28.3 1.0 CB A:CYS303 3.3 49.5 1.0 N A:CYS303 3.9 59.1 1.0 ND1 A:HIS320 4.0 29.7 1.0 CA A:CYS303 4.2 51.6 1.0 CG A:HIS320 4.3 28.6 1.0 CA A:CYS327 4.3 48.1 1.0 CA A:CYS300 4.4 56.0 1.0 C A:CYS303 4.7 54.9 1.0 CB A:HIS302 4.9 58.1 1.0 CB A:TYR324 4.9 38.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


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 Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:44.1 occ:1.00 NE2 B:HIS320 2.0 45.7 1.0 SG B:CYS300 2.2 28.3 1.0 SG B:CYS303 2.3 29.9 1.0 SG B:CYS327 2.4 59.8 1.0 CE1 B:HIS320 2.7 52.4 1.0 CB B:CYS300 3.2 50.1 1.0 CB B:CYS327 3.2 47.0 1.0 CD2 B:HIS320 3.3 45.8 1.0 CB B:CYS303 3.6 42.7 1.0 N B:CYS303 3.8 43.0 1.0 ND1 B:HIS320 3.9 52.5 1.0 CG B:HIS320 4.2 48.5 1.0 CA B:CYS303 4.3 43.7 1.0 CA B:CYS327 4.6 48.7 1.0 CA B:CYS300 4.7 46.7 1.0 CB B:HIS302 4.7 47.7 1.0 C B:HIS302 4.9 43.4 1.0 N B:HIS302 5.0 45.6 1.0 CB B:TYR324 5.0 41.3 1.0 CB B:LEU330 5.0 48.7 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


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 Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:46.3 occ:1.00 NE2 C:HIS320 2.0 28.0 1.0 SG C:CYS327 2.2 48.2 1.0 SG C:CYS300 2.3 47.2 1.0 SG C:CYS303 2.4 46.0 1.0 CE1 C:HIS320 2.6 36.8 1.0 CB C:CYS327 3.0 43.4 1.0 CB C:CYS300 3.1 60.1 1.0 CD2 C:HIS320 3.3 25.0 1.0 CB C:CYS303 3.4 59.5 1.0 ND1 C:HIS320 3.8 38.1 1.0 N C:CYS303 3.9 62.8 1.0 CG C:HIS320 4.2 26.1 1.0 CA C:CYS303 4.2 58.5 1.0 CA C:CYS327 4.3 48.1 1.0 CA C:CYS300 4.6 56.5 1.0 CB C:HIS302 4.8 70.0 1.0 C C:CYS303 4.9 59.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


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 Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:41.7 occ:1.00 NE2 D:HIS320 2.1 48.1 1.0 SG D:CYS300 2.3 27.3 1.0 SG D:CYS303 2.3 30.6 1.0 SG D:CYS327 2.6 58.7 1.0 CE1 D:HIS320 2.7 43.7 1.0 CB D:CYS327 3.2 51.2 1.0 CB D:CYS300 3.2 40.5 1.0 CD2 D:HIS320 3.3 55.9 1.0 CB D:CYS303 3.4 38.0 1.0 N D:CYS303 3.9 40.4 1.0 ND1 D:HIS320 3.9 48.3 1.0 CA D:CYS303 4.2 40.0 1.0 CG D:HIS320 4.3 52.5 1.0 CA D:CYS327 4.6 52.2 1.0 CA D:CYS300 4.7 36.3 1.0 CB D:HIS302 4.8 48.1 1.0 CD2 D:TYR329 4.9 62.8 1.0 CB D:LEU330 5.0 43.1 1.0 C D:HIS302 5.0 39.6 1.0 C D:CYS303 5.0 34.5 1.0 N D:HIS302 5.0 47.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:75.2 occ:1.00 NE2 E:HIS320 2.1 43.9 1.0 SG E:CYS300 2.3 87.3 1.0 SG E:CYS327 2.5 73.0 1.0 SG E:CYS303 2.5 66.2 1.0 CB E:CYS327 2.8 80.3 1.0 CE1 E:HIS320 2.8 74.0 1.0 CB E:CYS303 3.2 75.5 1.0 CB E:CYS300 3.2 89.7 1.0 CD2 E:HIS320 3.3 59.2 1.0 N E:CYS303 3.8 85.2 1.0 ND1 E:HIS320 4.0 64.2 1.0 CA E:CYS303 4.1 80.2 1.0 CA E:CYS327 4.1 77.8 1.0 CG E:HIS320 4.3 64.1 1.0 CA E:CYS300 4.7 89.2 1.0 C E:CYS303 4.7 81.0 1.0 CB E:TYR324 4.8 71.0 1.0 CB E:HIS302 4.8 85.5 1.0 N E:GLY305 4.9 80.8 1.0 N E:GLY304 4.9 80.7 1.0 C E:HIS302 5.0 87.8 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:92.5 occ:1.00 SG F:CYS303 2.1 89.5 1.0 NE2 F:HIS320 2.2 0.1 1.0 SG F:CYS300 2.3 77.6 1.0 CE1 F:HIS320 2.6 0.9 1.0 SG F:CYS327 2.8 89.1 1.0 CB F:CYS303 3.2 79.5 1.0 CB F:CYS300 3.2 85.9 1.0 CB F:CYS327 3.2 0.8 1.0 N F:CYS303 3.4 85.1 1.0 CD2 F:HIS320 3.5 93.5 1.0 CA F:CYS303 3.9 81.8 1.0 ND1 F:HIS320 3.9 0.1 1.0 CB F:HIS302 4.3 90.3 1.0 CG F:HIS320 4.4 96.9 1.0 CA F:CYS327 4.4 0.1 1.0 C F:HIS302 4.5 90.3 1.0 CA F:CYS300 4.7 86.1 1.0 C F:CYS303 4.7 81.1 1.0 N F:GLY304 4.7 81.3 1.0 N F:HIS302 4.7 92.7 1.0 CA F:HIS302 4.8 90.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn502 b:80.2 occ:1.00 NE2 G:HIS320 2.1 37.8 1.0 SG G:CYS327 2.3 75.9 1.0 SG G:CYS300 2.3 81.6 1.0 SG G:CYS303 2.6 66.7 1.0 CE1 G:HIS320 2.7 59.8 1.0 CB G:CYS327 3.0 75.1 1.0 CB G:CYS300 3.2 89.2 1.0 CB G:CYS303 3.3 74.2 1.0 CD2 G:HIS320 3.3 46.6 1.0 N G:CYS303 3.8 82.2 1.0 ND1 G:HIS320 4.0 57.5 1.0 CA G:CYS303 4.1 78.9 1.0 CA G:CYS327 4.3 75.2 1.0 CG G:HIS320 4.3 63.8 1.0 CA G:CYS300 4.6 87.5 1.0 CB G:HIS302 4.6 81.1 1.0 C G:CYS303 4.8 82.7 1.0 C G:HIS302 4.9 85.4 1.0 N G:GLY305 4.9 83.9 1.0 N G:GLY304 5.0 82.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Xiap-BIR3 in Complex with A Bivalent Compound within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn502 b:0.5 occ:1.00 SG H:CYS303 1.8 90.5 1.0 NE2 H:HIS320 2.2 92.4 1.0 SG H:CYS300 2.6 87.6 1.0 CE1 H:HIS320 2.7 95.9 1.0 SG H:CYS327 2.9 96.3 1.0 CB H:CYS303 3.0 74.0 1.0 CB H:CYS327 3.2 0.5 1.0 CB H:CYS300 3.3 88.1 1.0 CD2 H:HIS320 3.4 86.8 1.0 N H:CYS303 3.5 79.4 1.0 CA H:CYS303 3.8 77.6 1.0 ND1 H:HIS320 4.0 95.9 1.0 CG H:HIS320 4.3 90.3 1.0 CA H:CYS327 4.5 0.4 1.0 CB H:HIS302 4.5 85.3 1.0 C H:CYS303 4.5 78.1 1.0 N H:GLY304 4.6 80.6 1.0 C H:HIS302 4.7 83.8 1.0 CA H:CYS300 4.8 87.5 1.0 N H:HIS302 4.9 88.1 1.0 CB H:TYR324 4.9 82.0 1.0 CA H:HIS302 4.9 84.7 1.0

F.Cossu, M.Milani, E.Mastrangelo, P.Vachette, F.Servida, D.Lecis, G.Canevari, D.Delia, C.Drago, V.Rizzo, L.Manzoni, P.Seneci, C.Scolastico, M.Bolognesi. Structural Basis For Bivalent Smac-Mimetics Recognition in the Iap Protein Family J.Mol.Biol. V. 392 630 2009.
ISSN: ISSN 0022-2836
PubMed: 19393243
DOI: 10.1016/J.JMB.2009.04.033