Zinc in PDB 3cm7: Crystal Structure of Xiap-BIR3 Domain in Complex with Smac- Mimetic Compuond, SMAC005

The structure of Crystal Structure of Xiap-BIR3 Domain in Complex with Smac- Mimetic Compuond, SMAC005, PDB code: 3cm7 was solved by E.Mastrangelo, F.Cossu, M.Milani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.390, 92.390, 175.151, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 30

The binding sites of Zinc atom in the Crystal Structure of Xiap-BIR3 Domain in Complex with Smac- Mimetic Compuond, SMAC005 (pdb code 3cm7). 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 Smac- Mimetic Compuond, SMAC005, PDB code: 3cm7:
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 Smac- Mimetic Compuond, 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 Smac- Mimetic Compuond, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn4 b:28.8 occ:1.00 SG C:CYS303 2.1 24.6 1.0 NE2 C:HIS320 2.1 21.4 1.0 SG C:CYS300 2.2 29.6 1.0 SG C:CYS327 2.2 23.9 1.0 CE1 C:HIS320 2.9 21.2 1.0 CB C:CYS300 3.1 29.4 1.0 CB C:CYS327 3.2 23.6 1.0 CB C:CYS303 3.3 26.1 1.0 CD2 C:HIS320 3.3 22.1 1.0 N C:CYS303 3.6 26.5 1.0 CA C:CYS303 4.0 26.3 1.0 ND1 C:HIS320 4.1 21.8 1.0 CG C:HIS320 4.3 22.5 1.0 CA C:CYS327 4.5 23.6 1.0 CA C:CYS300 4.5 29.4 1.0 C C:HIS302 4.7 26.8 1.0 CB C:HIS302 4.7 27.0 1.0 N C:HIS302 4.8 27.6 1.0 N C:GLY304 4.9 26.9 1.0 CB C:TYR324 4.9 19.6 1.0 C C:CYS303 4.9 26.6 1.0 CA C:HIS302 4.9 27.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Xiap-BIR3 Domain in Complex with Smac- Mimetic Compuond, 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 Smac- Mimetic Compuond, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn6 b:51.0 occ:1.00 SG A:CYS327 1.7 32.7 1.0 SG A:CYS303 1.8 33.6 1.0 SG A:CYS300 2.0 37.8 1.0 NE2 A:HIS320 2.2 27.6 1.0 CE1 A:HIS320 2.8 27.8 1.0 CB A:CYS300 2.9 37.3 1.0 CB A:CYS327 3.2 32.3 1.0 CD2 A:HIS320 3.3 27.2 1.0 CB A:CYS303 3.4 34.2 1.0 N A:CYS303 3.6 34.5 1.0 ND1 A:HIS320 4.0 27.7 1.0 CA A:CYS303 4.1 34.3 1.0 CG A:HIS320 4.3 27.0 1.0 CA A:CYS300 4.3 37.3 1.0 CA A:CYS327 4.4 32.1 1.0 CB A:HIS302 4.6 35.2 1.0 N A:HIS302 4.6 35.5 1.0 C A:HIS302 4.6 34.7 1.0 N A:GLY304 4.8 34.5 1.0 C A:CYS300 4.8 37.0 1.0 CA A:HIS302 4.8 35.1 1.0 C A:CYS303 4.9 34.3 1.0 N A:GLY305 4.9 35.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Xiap-BIR3 Domain in Complex with Smac- Mimetic Compuond, 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 Smac- Mimetic Compuond, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5 b:35.6 occ:1.00 NE2 B:HIS320 2.2 32.2 1.0 SG B:CYS327 2.2 32.9 1.0 SG B:CYS300 2.5 48.8 1.0 SG B:CYS303 2.5 41.6 1.0 CE1 B:HIS320 2.8 32.2 1.0 CB B:CYS327 2.9 33.2 1.0 CB B:CYS303 3.4 42.3 1.0 CD2 B:HIS320 3.4 32.4 1.0 CB B:CYS300 3.5 48.5 1.0 N B:CYS303 3.9 42.9 1.0 ND1 B:HIS320 4.0 32.2 1.0 CA B:CYS303 4.3 42.3 1.0 CA B:CYS327 4.3 33.5 1.0 CG B:HIS320 4.3 32.2 1.0 C B:HIS302 4.7 43.4 1.0 N B:HIS302 4.8 44.7 1.0 CD2 B:TYR329 4.9 38.7 1.0 CB B:HIS302 4.9 43.7 1.0 O B:TYR324 4.9 30.6 1.0 CB B:TYR324 4.9 30.7 1.0 CA B:CYS300 5.0 48.5 1.0 CA B:HIS302 5.0 43.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Xiap-BIR3 Domain in Complex with Smac- Mimetic Compuond, 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 Smac- Mimetic Compuond, SMAC005 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn3 b:28.4 occ:1.00 NE2 D:HIS320 2.0 26.5 1.0 SG D:CYS300 2.3 31.1 1.0 SG D:CYS327 2.4 24.6 1.0 SG D:CYS303 2.5 29.3 1.0 CE1 D:HIS320 2.7 26.6 1.0 CB D:CYS327 3.1 24.9 1.0 CB D:CYS300 3.2 31.3 1.0 CD2 D:HIS320 3.2 26.3 1.0 CB D:CYS303 3.5 30.1 1.0 N D:CYS303 3.9 30.4 1.0 ND1 D:HIS320 4.0 26.6 1.0 CG D:HIS320 4.2 26.2 1.0 CA D:CYS303 4.3 30.2 1.0 CA D:CYS327 4.4 25.1 1.0 CA D:CYS300 4.6 31.3 1.0 C D:HIS302 4.9 30.6 1.0 CB D:HIS302 5.0 30.7 1.0 N D:HIS302 5.0 30.9 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