Zinc in PDB 3l11: Crystal Structure of the Ring Domain of RNF168

The structure of Crystal Structure of the Ring Domain of RNF168, PDB code: 3l11 was solved by D.Neculai, L.Yermekbayeva, L.Crombet, J.Weigelt, C.Bountra, A.M.Edwards, C.H.Arrowsmith, A.Bochkarev, S.Dhe-Paganon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.49 / 2.12
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.706, 49.706, 110.149, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.5

The binding sites of Zinc atom in the Crystal Structure of the Ring Domain of RNF168 (pdb code 3l11). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Ring Domain of RNF168, PDB code: 3l11:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Ring Domain of RNF168


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 Ring Domain of RNF168 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:24.9 occ:1.00 ND1 A:HIS33 2.0 25.5 1.0 SG A:CYS31 2.2 23.5 1.0 SG A:CYS54 2.2 23.4 1.0 SG A:CYS51 2.3 23.5 1.0 CE1 A:HIS33 2.9 27.6 1.0 CB A:CYS51 3.0 23.0 1.0 CG A:HIS33 3.1 26.6 1.0 CB A:CYS31 3.2 25.6 1.0 CB A:HIS33 3.5 24.2 1.0 CB A:CYS54 3.5 23.4 1.0 N A:CYS54 3.7 23.4 1.0 NE2 A:HIS33 4.1 30.4 1.0 CA A:CYS54 4.2 24.8 1.0 CD2 A:HIS33 4.2 27.1 1.0 CB A:PHE53 4.4 23.7 1.0 CB A:ARG56 4.4 24.4 1.0 N A:HIS33 4.5 26.5 1.0 CA A:CYS51 4.5 24.0 1.0 CA A:CYS31 4.5 23.9 1.0 C A:PHE53 4.5 25.4 1.0 CA A:HIS33 4.6 26.4 1.0 O A:CYS31 4.6 27.3 1.0 C A:CYS31 4.6 26.4 1.0 CA A:PHE53 4.8 24.9 1.0 C A:CYS54 4.8 23.1 1.0 N A:PHE53 4.8 23.8 1.0 N A:ARG55 4.9 23.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Ring Domain of RNF168


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 Ring Domain of RNF168 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:29.6 occ:1.00 SG A:CYS36 2.2 26.7 1.0 SG A:CYS16 2.3 27.0 1.0 SG A:CYS19 2.4 29.4 1.0 SG A:CYS39 2.4 30.2 1.0 CB A:CYS16 3.0 28.3 1.0 CB A:CYS39 3.2 29.2 1.0 CB A:CYS19 3.3 30.7 1.0 CB A:CYS36 3.5 25.3 1.0 N A:CYS19 3.8 30.6 1.0 N A:CYS36 3.9 24.3 1.0 CA A:CYS19 4.1 30.8 1.0 N A:CYS39 4.3 29.0 1.0 CA A:CYS39 4.3 28.5 1.0 CA A:CYS36 4.3 24.5 1.0 NH1 A:ARG91 4.3 29.1 1.0 CA A:CYS16 4.4 26.2 1.0 CB A:ILE18 4.5 29.8 1.0 NH2 A:ARG91 4.6 32.2 1.0 C A:ILE18 4.7 30.6 1.0 O A:CYS36 4.7 26.4 1.0 N A:ILE18 4.8 28.0 1.0 CA A:ILE18 4.9 29.4 1.0 C A:CYS36 4.9 27.8 1.0 C A:CYS16 4.9 27.7 1.0 C A:CYS19 4.9 32.5 1.0 CZ A:ARG91 4.9 35.8 1.0 CG2 A:ILE18 5.0 29.9 1.0

S.J.Campbell, R.A.Edwards, C.C.Leung, D.Neculai, C.D.Hodge, S.Dhe-Paganon, J.N.Glover. Molecular Insights Into the Function of Ring Finger (Rnf)-Containing Proteins HRNF8 and HRNF168 in UBC13/MMS2-Dependent Ubiquitylation. J.Biol.Chem. V. 287 23900 2012.
ISSN: ISSN 0021-9258
PubMed: 22589545
DOI: 10.1074/JBC.M112.359653