Zinc in PDB 3ng2: Crystal Structure of the RNF4 Ring Domain Dimer

The structure of Crystal Structure of the RNF4 Ring Domain Dimer, PDB code: 3ng2 was solved by C.W.Liew, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.73 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.487, 85.922, 22.277, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 24.2

The binding sites of Zinc atom in the Crystal Structure of the RNF4 Ring Domain Dimer (pdb code 3ng2). 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 the RNF4 Ring Domain Dimer, PDB code: 3ng2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the RNF4 Ring Domain Dimer


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 the RNF4 Ring Domain Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:14.9 occ:1.00 SG A:CYS139 2.3 18.9 1.0 SG A:CYS163 2.3 16.3 1.0 SG A:CYS166 2.4 17.5 1.0 SG A:CYS136 2.4 15.1 1.0 CB A:CYS136 3.1 18.6 1.0 CB A:CYS166 3.1 16.6 1.0 CB A:CYS139 3.2 21.0 1.0 CB A:CYS163 3.4 14.5 1.0 N A:CYS139 3.6 20.8 1.0 NH2 A:ARG151 4.0 29.2 1.0 CA A:CYS139 4.0 21.3 1.0 N A:CYS163 4.1 14.3 1.0 N A:CYS166 4.2 16.3 1.0 CA A:CYS163 4.2 13.8 1.0 CA A:CYS166 4.3 16.9 1.0 CA A:CYS136 4.6 19.3 1.0 CB A:ILE138 4.7 21.0 1.0 O A:CYS163 4.7 13.6 1.0 C A:ILE138 4.8 21.6 1.0 C A:CYS163 4.8 14.3 1.0 C A:CYS139 4.9 22.9 1.0 N A:MET140 5.0 23.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the RNF4 Ring Domain Dimer


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 the RNF4 Ring Domain Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:12.7 occ:1.00 ND1 A:HIS160 2.1 15.9 1.0 SG A:CYS158 2.3 15.5 1.0 SG A:CYS180 2.3 16.1 1.0 SG A:CYS177 2.3 13.7 1.0 CE1 A:HIS160 2.9 15.2 1.0 CB A:CYS177 3.1 15.8 1.0 CG A:HIS160 3.2 13.5 1.0 CB A:CYS158 3.3 16.0 1.0 CB A:CYS180 3.4 19.2 1.0 CB A:HIS160 3.7 13.3 1.0 N A:CYS180 3.8 19.2 1.0 OG1 A:THR156 3.8 13.8 1.0 NE2 A:HIS160 4.1 15.6 1.0 CA A:CYS180 4.2 19.1 1.0 CD2 A:HIS160 4.2 15.0 1.0 CA A:CYS158 4.5 15.8 1.0 O A:HOH18 4.5 32.1 1.0 CA A:CYS177 4.6 15.6 1.0 C A:CYS158 4.6 16.8 1.0 O A:CYS158 4.6 17.1 1.0 CB A:THR156 4.7 14.3 1.0 CB A:THR179 4.8 18.9 1.0 N A:HIS160 4.8 12.5 1.0 C A:CYS180 4.8 19.7 1.0 N A:ARG181 4.8 19.6 1.0 CB A:LYS182 4.9 22.3 1.0 C A:THR179 4.9 19.1 1.0 CA A:HIS160 4.9 13.1 1.0 CG2 A:THR156 5.0 15.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the RNF4 Ring Domain Dimer


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 the RNF4 Ring Domain Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:17.0 occ:1.00 SG B:CYS139 2.3 21.1 1.0 SG B:CYS166 2.3 21.8 1.0 SG B:CYS136 2.4 16.6 1.0 SG B:CYS163 2.4 17.1 1.0 CB B:CYS166 3.1 19.6 1.0 CB B:CYS136 3.1 18.5 1.0 CB B:CYS139 3.2 23.2 1.0 CB B:CYS163 3.4 15.7 1.0 N B:CYS139 3.6 22.6 1.0 CA B:CYS139 4.0 23.1 1.0 NH1 B:ARG151 4.0 21.9 1.0 N B:CYS163 4.1 15.7 1.0 CA B:CYS163 4.2 15.7 1.0 CA B:CYS166 4.2 19.8 1.0 N B:CYS166 4.3 19.1 1.0 CB B:ILE138 4.5 22.0 1.0 CA B:CYS136 4.6 19.1 1.0 C B:ILE138 4.7 23.0 1.0 O B:CYS163 4.7 17.3 1.0 C B:CYS163 4.8 16.2 1.0 C B:CYS139 4.9 23.5 1.0 CA B:ILE138 5.0 21.9 1.0 N B:ILE138 5.0 20.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the RNF4 Ring Domain Dimer


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 the RNF4 Ring Domain Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:14.6 occ:1.00 ND1 B:HIS160 2.1 16.4 1.0 SG B:CYS158 2.4 17.8 1.0 SG B:CYS177 2.4 15.9 1.0 SG B:CYS180 2.4 18.2 1.0 CE1 B:HIS160 2.9 16.6 1.0 CB B:CYS177 3.1 18.6 1.0 CG B:HIS160 3.2 16.1 1.0 CB B:CYS158 3.4 17.2 1.0 CB B:CYS180 3.4 20.7 1.0 CB B:HIS160 3.7 14.7 1.0 OG1 B:THR156 3.8 15.4 1.0 N B:CYS180 3.8 20.5 1.0 NE2 B:HIS160 4.1 16.1 1.0 CA B:CYS180 4.2 20.3 1.0 CD2 B:HIS160 4.3 15.8 1.0 CA B:CYS158 4.5 16.8 1.0 O B:CYS158 4.5 18.3 1.0 C B:CYS158 4.5 17.3 1.0 CA B:CYS177 4.6 18.4 1.0 CB B:THR179 4.7 20.3 1.0 N B:HIS160 4.7 13.7 1.0 CB B:THR156 4.7 14.6 1.0 N B:ARG181 4.8 20.9 1.0 C B:CYS180 4.8 20.7 1.0 CB B:LYS182 4.8 25.5 1.0 O B:HOH70 4.8 29.8 1.0 CA B:HIS160 4.8 14.1 1.0 C B:THR179 4.9 20.0 1.0 CG2 B:THR156 5.0 16.2 1.0

C.W.Liew, H.Sun, T.Hunter, C.L.Day. Ring Domain Dimerization Is Essential For RNF4 Function Biochem.J. V. 431 23 2010.
ISSN: ISSN 0264-6021
PubMed: 20681948
DOI: 10.1042/BJ20100957