Zinc in PDB 3clx: Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005

The structure of Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005, PDB code: 3clx was solved by M.Milani, E.Mastrangelo, F.Cossu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.875, 115.280, 163.233, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 30.6

The binding sites of Zinc atom in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005 (pdb code 3clx). 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 Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005, PDB code: 3clx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005


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 Domain in Complex with A Smac-Mimetic Compound, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:27.2 occ:1.00 NE2 D:HIS320 2.1 31.8 1.0 SG D:CYS300 2.2 19.5 1.0 SG D:CYS303 2.3 22.7 1.0 SG D:CYS327 2.3 36.8 1.0 CE1 D:HIS320 2.9 27.9 1.0 CB D:CYS327 3.0 34.3 1.0 CB D:CYS300 3.1 22.9 1.0 CD2 D:HIS320 3.1 27.5 1.0 CB D:CYS303 3.5 30.3 1.0 N D:CYS303 4.0 28.9 1.0 ND1 D:HIS320 4.0 21.9 1.0 CG D:HIS320 4.1 24.6 1.0 CA D:CYS303 4.4 28.6 1.0 CA D:CYS327 4.5 32.6 1.0 CA D:CYS300 4.6 23.2 1.0 CB D:HIS302 4.8 30.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005


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 Domain in Complex with A Smac-Mimetic Compound, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:27.6 occ:1.00 SG A:CYS300 2.1 30.8 1.0 NE2 A:HIS320 2.3 27.0 1.0 SG A:CYS327 2.3 32.8 1.0 SG A:CYS303 2.4 22.9 1.0 CE1 A:HIS320 2.9 26.3 1.0 CB A:CYS327 3.2 26.6 1.0 CB A:CYS300 3.2 28.3 1.0 CB A:CYS303 3.2 27.3 1.0 CD2 A:HIS320 3.5 20.6 1.0 N A:CYS303 3.7 28.3 1.0 CA A:CYS303 4.0 25.8 1.0 ND1 A:HIS320 4.1 26.5 1.0 CG A:HIS320 4.5 20.6 1.0 CA A:CYS327 4.5 26.1 1.0 CA A:CYS300 4.6 25.9 1.0 C A:HIS302 4.8 30.6 1.0 CB A:HIS302 4.9 30.8 1.0 C A:CYS303 4.9 24.5 1.0 CB A:TYR324 4.9 24.4 1.0 N A:HIS302 4.9 30.6 1.0 O A:TYR324 4.9 21.8 1.0 N A:GLY304 5.0 24.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005


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 Domain in Complex with A Smac-Mimetic Compound, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:33.5 occ:1.00 SG B:CYS303 2.1 29.0 1.0 NE2 B:HIS320 2.2 36.9 1.0 SG B:CYS327 2.2 39.9 1.0 SG B:CYS300 2.3 33.1 1.0 CB B:CYS327 2.8 38.3 1.0 CE1 B:HIS320 2.9 32.1 1.0 CB B:CYS303 3.0 34.0 1.0 CB B:CYS300 3.3 31.3 1.0 CD2 B:HIS320 3.4 33.0 1.0 N B:CYS303 3.5 32.7 1.0 CA B:CYS303 3.9 34.3 1.0 ND1 B:HIS320 4.1 30.5 1.0 CA B:CYS327 4.3 37.1 1.0 CG B:HIS320 4.4 31.1 1.0 C B:HIS302 4.7 31.9 1.0 CB B:HIS302 4.7 31.9 1.0 CA B:CYS300 4.8 30.4 1.0 C B:CYS303 4.8 35.7 1.0 N B:GLY304 4.8 33.9 1.0 CA B:HIS302 5.0 32.4 1.0 N B:HIS302 5.0 30.7 1.0 O B:CYS300 5.0 34.8 1.0 CB B:TYR329 5.0 26.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC005


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 Domain in Complex with A Smac-Mimetic Compound, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:24.0 occ:1.00 NE2 C:HIS320 2.1 28.8 1.0 SG C:CYS300 2.3 39.1 1.0 SG C:CYS327 2.3 20.5 1.0 SG C:CYS303 2.4 30.2 1.0 CE1 C:HIS320 2.8 31.9 1.0 CB C:CYS303 3.1 29.0 1.0 CB C:CYS300 3.1 32.2 1.0 CB C:CYS327 3.3 22.4 1.0 CD2 C:HIS320 3.3 25.5 1.0 N C:CYS303 3.5 28.6 1.0 CA C:CYS303 3.9 29.3 1.0 ND1 C:HIS320 4.1 25.4 1.0 CG C:HIS320 4.3 20.1 1.0 CA C:CYS300 4.6 32.1 1.0 C C:HIS302 4.6 28.8 1.0 CB C:TYR329 4.6 28.9 1.0 CA C:CYS327 4.7 22.0 1.0 CB C:HIS302 4.7 26.2 1.0 N C:GLY304 4.8 31.2 1.0 C C:CYS303 4.8 30.8 1.0 CA C:HIS302 5.0 27.2 1.0 N C:HIS302 5.0 27.0 1.0

E.Mastrangelo, F.Cossu, M.Milani, G.Sorrentino, D.Lecis, D.Delia, L.Manzoni, C.Drago, P.Seneci, C.Scolastico, V.Rizzo, M.Bolognesi. Targeting the X-Linked Inhibitor of Apoptosis Protein Through 4-Substituted Azabicyclo[5.3.0]Alkane Smac Mimetics. Structure, Activity, and Recognition Principles. J.Mol.Biol. V. 384 673 2008.
ISSN: ISSN 0022-2836
PubMed: 18851976
DOI: 10.1016/J.JMB.2008.09.064