Zinc in PDB 3cm2: Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010

The structure of Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010, PDB code: 3cm2 was solved by F.Cossu, E.Mastrangelo, M.Milani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.529, 108.349, 225.308, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.4

The binding sites of Zinc atom in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010 (pdb code 3cm2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010, PDB code: 3cm2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:30.7 occ:1.00 NE2 D:HIS320 2.1 27.8 1.0 SG D:CYS303 2.2 33.1 1.0 SG D:CYS327 2.3 29.7 1.0 SG D:CYS300 2.3 32.5 1.0 CE1 D:HIS320 2.7 32.3 1.0 CB D:CYS327 2.9 29.3 1.0 CB D:CYS300 3.2 29.0 1.0 CB D:CYS303 3.2 31.5 1.0 CD2 D:HIS320 3.3 28.5 1.0 N D:CYS303 3.6 33.4 1.0 ND1 D:HIS320 3.9 31.6 1.0 CA D:CYS303 4.0 32.6 1.0 CG D:HIS320 4.2 30.5 1.0 CA D:CYS327 4.3 32.5 1.0 CA D:CYS300 4.6 31.7 1.0 C D:HIS302 4.7 34.5 1.0 CB D:HIS302 4.7 34.6 1.0 C D:CYS303 4.8 33.2 1.0 N D:GLY304 4.9 32.5 1.0 N D:HIS302 4.9 37.5 1.0 CA D:HIS302 5.0 33.6 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:33.0 occ:1.00 NE2 A:HIS320 2.1 34.6 1.0 SG A:CYS327 2.2 30.1 1.0 SG A:CYS303 2.3 32.9 1.0 SG A:CYS300 2.4 36.8 1.0 CE1 A:HIS320 2.7 33.2 1.0 CB A:CYS327 3.0 29.2 1.0 CB A:CYS303 3.1 27.3 1.0 CB A:CYS300 3.3 35.6 1.0 CD2 A:HIS320 3.3 36.0 1.0 N A:CYS303 3.7 32.8 1.0 ND1 A:HIS320 4.0 31.2 1.0 CA A:CYS303 4.0 32.7 1.0 CG A:HIS320 4.3 32.3 1.0 CA A:CYS327 4.4 31.2 1.0 CB A:HIS302 4.7 33.7 1.0 CA A:CYS300 4.7 37.4 1.0 C A:HIS302 4.8 35.1 1.0 C A:CYS303 4.9 32.8 1.0 CB A:TYR324 5.0 26.2 1.0 N A:GLY304 5.0 34.5 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:39.0 occ:1.00 NE2 B:HIS320 2.1 36.6 1.0 SG B:CYS303 2.3 41.8 1.0 SG B:CYS327 2.3 39.4 1.0 SG B:CYS300 2.4 39.1 1.0 CE1 B:HIS320 2.7 40.1 1.0 CB B:CYS327 2.8 36.7 1.0 CB B:CYS300 3.2 39.2 1.0 CB B:CYS303 3.2 40.5 1.0 CD2 B:HIS320 3.4 34.4 1.0 N B:CYS303 3.7 44.1 1.0 ND1 B:HIS320 3.9 37.7 1.0 CA B:CYS303 4.0 43.5 1.0 CA B:CYS327 4.3 39.8 1.0 CG B:HIS320 4.3 35.3 1.0 CA B:CYS300 4.6 41.3 1.0 CB B:HIS302 4.7 43.0 1.0 C B:HIS302 4.8 45.4 1.0 C B:CYS303 4.9 42.4 1.0 N B:HIS302 4.9 46.7 1.0 O B:TYR324 5.0 32.3 1.0 N B:GLY304 5.0 44.1 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:30.4 occ:1.00 NE2 C:HIS320 2.1 34.3 1.0 SG C:CYS300 2.2 36.4 1.0 SG C:CYS327 2.3 26.8 1.0 SG C:CYS303 2.4 35.2 1.0 CE1 C:HIS320 2.7 35.9 1.0 CB C:CYS327 3.0 27.7 1.0 CB C:CYS303 3.2 28.9 1.0 CB C:CYS300 3.2 33.3 1.0 CD2 C:HIS320 3.3 31.0 1.0 N C:CYS303 3.7 30.8 1.0 ND1 C:HIS320 3.9 34.0 1.0 CA C:CYS303 4.0 31.0 1.0 CG C:HIS320 4.3 31.3 1.0 CA C:CYS327 4.4 28.9 1.0 CB C:HIS302 4.6 28.4 1.0 CA C:CYS300 4.7 33.9 1.0 C C:HIS302 4.7 29.7 1.0 C C:CYS303 4.9 30.4 1.0 N C:HIS302 4.9 30.1 1.0 CA C:HIS302 4.9 28.3 1.0 N C:GLY304 5.0 32.8 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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 Domain in Complex with A Smac-Mimetic Compound, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:32.2 occ:1.00 NE2 E:HIS320 2.1 33.1 1.0 SG E:CYS300 2.3 31.8 1.0 SG E:CYS303 2.3 32.8 1.0 SG E:CYS327 2.3 28.4 1.0 CE1 E:HIS320 2.7 34.2 1.0 CB E:CYS327 3.0 29.3 1.0 CB E:CYS300 3.1 28.8 1.0 CB E:CYS303 3.3 32.6 1.0 CD2 E:HIS320 3.3 31.8 1.0 N E:CYS303 3.6 34.6 1.0 ND1 E:HIS320 3.9 31.8 1.0 CA E:CYS303 4.0 35.4 1.0 CG E:HIS320 4.3 28.9 1.0 CA E:CYS327 4.4 31.5 1.0 CA E:CYS300 4.6 30.5 1.0 CB E:HIS302 4.6 31.0 1.0 C E:HIS302 4.7 35.0 1.0 N E:HIS302 4.9 34.7 1.0 CA E:HIS302 4.9 33.3 1.0 C E:CYS303 4.9 34.1 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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 Domain in Complex with A Smac-Mimetic Compound, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:39.6 occ:1.00 NE2 F:HIS320 2.2 36.8 1.0 SG F:CYS300 2.3 46.0 1.0 SG F:CYS327 2.4 42.8 1.0 SG F:CYS303 2.4 42.5 1.0 CE1 F:HIS320 2.9 32.9 1.0 CB F:CYS327 2.9 40.7 1.0 CB F:CYS303 3.1 38.6 1.0 CB F:CYS300 3.2 44.3 1.0 CD2 F:HIS320 3.4 35.3 1.0 N F:CYS303 3.6 42.7 1.0 CA F:CYS303 3.9 41.1 1.0 ND1 F:HIS320 4.1 38.8 1.0 CA F:CYS327 4.3 42.5 1.0 CG F:HIS320 4.4 36.9 1.0 CB F:HIS302 4.6 41.7 1.0 CA F:CYS300 4.7 45.5 1.0 C F:HIS302 4.7 43.7 1.0 C F:CYS303 4.9 42.8 1.0 N F:GLY304 5.0 44.3 1.0 N F:HIS302 5.0 43.9 1.0 O F:TYR324 5.0 38.9 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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 Domain in Complex with A Smac-Mimetic Compound, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn502 b:36.6 occ:1.00 NE2 G:HIS320 2.1 42.0 1.0 SG G:CYS300 2.2 42.9 1.0 SG G:CYS327 2.2 32.6 1.0 SG G:CYS303 2.4 42.0 1.0 CE1 G:HIS320 2.6 35.9 1.0 CB G:CYS327 2.9 37.3 1.0 CB G:CYS300 3.0 41.1 1.0 CB G:CYS303 3.3 39.5 1.0 CD2 G:HIS320 3.4 35.9 1.0 N G:CYS303 3.7 42.4 1.0 ND1 G:HIS320 3.9 39.6 1.0 CA G:CYS303 4.1 42.7 1.0 CG G:HIS320 4.3 38.4 1.0 CA G:CYS327 4.3 39.1 1.0 CA G:CYS300 4.5 42.5 1.0 CB G:HIS302 4.7 42.6 1.0 C G:HIS302 4.8 44.3 1.0 C G:CYS303 4.9 41.1 1.0 N G:HIS302 5.0 46.0 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


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 Domain in Complex with A Smac-Mimetic Compound, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn502 b:38.5 occ:1.00 SG H:CYS300 2.2 39.1 1.0 NE2 H:HIS320 2.2 34.8 1.0 SG H:CYS327 2.2 32.6 1.0 SG H:CYS303 2.3 35.3 1.0 CE1 H:HIS320 2.7 42.1 1.0 CB H:CYS327 2.8 31.9 1.0 CB H:CYS300 3.1 35.5 1.0 CB H:CYS303 3.2 37.6 1.0 CD2 H:HIS320 3.5 39.1 1.0 N H:CYS303 3.6 39.2 1.0 ND1 H:HIS320 4.0 40.4 1.0 CA H:CYS303 4.0 37.9 1.0 CA H:CYS327 4.2 34.8 1.0 CG H:HIS320 4.4 39.7 1.0 CA H:CYS300 4.5 36.9 1.0 CB H:HIS302 4.6 42.0 1.0 C H:HIS302 4.7 42.1 1.0 C H:CYS303 4.8 39.1 1.0 N H:HIS302 4.9 42.6 1.0 N H:GLY304 4.9 38.1 1.0 CA H:HIS302 5.0 41.8 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn502 b:38.8 occ:1.00 NE2 I:HIS320 2.2 38.8 1.0 SG I:CYS327 2.2 35.9 1.0 SG I:CYS300 2.2 41.7 1.0 SG I:CYS303 2.3 37.9 1.0 CE1 I:HIS320 2.8 39.4 1.0 CB I:CYS327 2.9 37.1 1.0 CB I:CYS300 3.2 37.3 1.0 CB I:CYS303 3.2 37.5 1.0 CD2 I:HIS320 3.4 38.1 1.0 N I:CYS303 3.7 41.7 1.0 CA I:CYS303 4.1 40.3 1.0 ND1 I:HIS320 4.1 41.8 1.0 CA I:CYS327 4.3 38.5 1.0 CG I:HIS320 4.3 40.3 1.0 CA I:CYS300 4.6 39.8 1.0 CB I:HIS302 4.6 44.2 1.0 C I:HIS302 4.7 44.1 1.0 N I:HIS302 4.9 44.9 1.0 C I:CYS303 4.9 39.9 1.0 CA I:HIS302 5.0 44.0 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Xiap BIR3 Domain in Complex with A Smac-Mimetic Compound, SMAC010 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn502 b:38.1 occ:1.00 NE2 J:HIS320 2.1 43.8 1.0 SG J:CYS327 2.2 37.1 1.0 SG J:CYS300 2.3 39.7 1.0 SG J:CYS303 2.3 41.8 1.0 CE1 J:HIS320 2.8 43.8 1.0 CB J:CYS327 2.8 40.0 1.0 CB J:CYS300 3.1 39.0 1.0 CB J:CYS303 3.2 42.7 1.0 CD2 J:HIS320 3.3 40.9 1.0 N J:CYS303 3.6 44.8 1.0 ND1 J:HIS320 4.0 41.4 1.0 CA J:CYS303 4.0 43.9 1.0 CA J:CYS327 4.2 42.5 1.0 CG J:HIS320 4.3 40.3 1.0 CB J:HIS302 4.5 46.4 1.0 CA J:CYS300 4.6 42.3 1.0 C J:HIS302 4.7 46.1 1.0 N J:HIS302 4.9 48.5 1.0 CA J:HIS302 4.9 46.6 1.0 C J:CYS303 4.9 43.2 1.0 N J:GLY304 5.0 41.9 1.0 C J:CYS327 5.0 45.0 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