Zinc in PDB 5h9m: Crystal Structure of SIAH2 Sbd Domain

The structure of Crystal Structure of SIAH2 Sbd Domain, PDB code: 5h9m was solved by A.Dong, Q.Zhang, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwards, Y.Tong, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.624, 68.753, 102.884, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.7

The structure of Crystal Structure of SIAH2 Sbd Domain also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of SIAH2 Sbd Domain (pdb code 5h9m). 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 SIAH2 Sbd Domain, PDB code: 5h9m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of SIAH2 Sbd Domain


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 SIAH2 Sbd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.6 occ:1.00 NE2 A:HIS157 2.1 21.4 1.0 SG A:CYS138 2.3 19.6 1.0 SG A:CYS145 2.3 22.2 1.0 SG A:CYS161 2.3 18.9 1.0 CD2 A:HIS157 3.0 21.3 1.0 CE1 A:HIS157 3.1 21.5 1.0 CB A:CYS145 3.1 24.6 1.0 CB A:CYS138 3.2 19.6 1.0 CB A:CYS161 3.2 19.6 1.0 O A:HOH646 3.8 36.4 1.0 ND1 A:HIS157 4.2 21.9 1.0 CG A:HIS157 4.2 20.9 1.0 CA A:CYS161 4.4 20.2 1.0 CD2 A:TYR140 4.5 21.1 1.0 CA A:CYS145 4.5 27.2 1.0 CB A:TYR140 4.6 21.9 1.0 CA A:CYS138 4.6 20.2 1.0 CD1 A:TYR163 4.9 32.9 1.0 CB A:LEU147 5.0 30.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of SIAH2 Sbd Domain


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 SIAH2 Sbd Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:18.4 occ:1.00 NE2 A:HIS187 2.0 15.6 1.0 NE2 A:HIS192 2.1 18.2 1.0 SG A:CYS168 2.3 19.1 1.0 SG A:CYS175 2.3 21.0 1.0 CE1 A:HIS187 3.0 15.3 1.0 CD2 A:HIS187 3.0 14.5 1.0 CE1 A:HIS192 3.0 20.3 1.0 CD2 A:HIS192 3.0 18.3 1.0 CB A:CYS175 3.2 24.7 1.0 CB A:CYS168 3.2 18.6 1.0 ND1 A:HIS187 4.1 15.5 1.0 ND1 A:HIS192 4.1 19.3 1.0 CG A:HIS187 4.1 14.8 1.0 CG A:HIS192 4.2 18.8 1.0 CB A:TRP177 4.3 17.7 1.0 CA A:CYS168 4.4 18.9 1.0 O A:HOH514 4.5 34.6 1.0 CA A:CYS175 4.6 27.0 1.0 CB A:CYS170 5.0 27.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of SIAH2 Sbd Domain


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 SIAH2 Sbd Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:20.2 occ:1.00 NE2 B:HIS157 2.0 22.2 1.0 SG B:CYS145 2.3 19.1 1.0 SG B:CYS161 2.3 19.5 1.0 SG B:CYS138 2.3 19.8 1.0 CE1 B:HIS157 3.0 23.9 1.0 CD2 B:HIS157 3.0 22.7 1.0 CB B:CYS145 3.1 18.8 1.0 CB B:CYS138 3.3 19.8 1.0 CB B:CYS161 3.3 20.7 1.0 ND1 B:HIS157 4.1 24.9 1.0 CG B:HIS157 4.1 23.4 1.0 O B:HOH652 4.2 27.4 1.0 CA B:CYS161 4.4 22.7 1.0 CA B:CYS145 4.5 19.7 1.0 CD2 B:TYR140 4.5 22.8 1.0 CB B:TYR140 4.6 21.9 1.0 CA B:CYS138 4.7 21.0 1.0 O B:HOH609 4.8 25.3 1.0 CD1 B:TYR163 4.9 17.8 1.0 CD1 B:LEU147 5.0 29.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of SIAH2 Sbd Domain


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 SIAH2 Sbd Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:18.6 occ:1.00 NE2 B:HIS187 2.0 17.4 1.0 NE2 B:HIS192 2.1 18.3 1.0 SG B:CYS168 2.3 19.0 1.0 SG B:CYS175 2.3 19.4 1.0 CE1 B:HIS187 3.0 16.7 1.0 CE1 B:HIS192 3.0 20.2 1.0 CD2 B:HIS187 3.0 17.0 1.0 CD2 B:HIS192 3.1 17.3 1.0 CB B:CYS168 3.1 19.0 1.0 CB B:CYS175 3.2 22.0 1.0 ND1 B:HIS187 4.1 17.4 1.0 ND1 B:HIS192 4.1 19.1 1.0 CG B:HIS187 4.1 17.3 1.0 CG B:HIS192 4.2 18.0 1.0 CB B:TRP177 4.3 16.7 1.0 CA B:CYS168 4.4 19.7 1.0 O B:HOH519 4.5 29.3 1.0 CA B:CYS175 4.7 24.0 1.0

Q.Zhang, A.Dong, J.R.Walker, C.Bountra, C.H.Arrowsmith, A.M.Edwards, Y.Tong, Structural Genomics Consortium (Sgc). Crystal Structure of SIAH2 Sbd Domain To Be Published.