Zinc in PDB 5trb: Crystal Structure of the RNF20 Ring Domain

The structure of Crystal Structure of the RNF20 Ring Domain, PDB code: 5trb was solved by M.Foglizzo, A.J.Middleton, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 1.80
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.830, 61.290, 78.670, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 23.6

The binding sites of Zinc atom in the Crystal Structure of the RNF20 Ring Domain (pdb code 5trb). 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 RNF20 Ring Domain, PDB code: 5trb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the RNF20 Ring 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 the RNF20 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:22.5 occ:1.00 SG A:CYS922 2.3 21.1 1.0 SG A:CYS942 2.3 21.4 1.0 SG A:CYS925 2.3 24.1 1.0 SG A:CYS945 2.3 22.5 1.0 CB A:CYS922 3.1 23.5 1.0 CB A:CYS945 3.3 22.8 1.0 CB A:CYS925 3.3 25.6 1.0 CB A:CYS942 3.5 20.2 1.0 N A:CYS925 3.6 26.3 1.0 NH2 A:ARG928 3.8 26.6 1.0 N A:CYS942 4.0 19.3 1.0 CA A:CYS925 4.1 27.9 1.0 NE A:ARG928 4.1 26.4 1.0 CB A:CYS924 4.2 30.0 1.0 CA A:CYS942 4.3 19.9 1.0 CZ A:ARG928 4.4 29.4 1.0 N A:CYS945 4.4 22.2 1.0 CA A:CYS945 4.4 25.5 1.0 CA A:CYS922 4.5 21.8 1.0 C A:CYS924 4.6 29.4 1.0 CA A:CYS924 4.8 26.8 1.0 N A:CYS924 4.8 28.1 1.0 C A:CYS922 4.8 24.6 1.0 O A:CYS942 4.8 20.6 1.0 O A:CYS922 4.8 24.1 1.0 CB A:ARG928 4.8 27.7 1.0 C A:CYS942 4.9 23.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the RNF20 Ring 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 the RNF20 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:28.0 occ:1.00 ND1 A:HIS939 2.1 32.8 1.0 SG A:CYS957 2.2 28.3 1.0 SG A:CYS937 2.3 27.8 1.0 SG A:CYS960 2.4 29.8 1.0 CB A:CYS957 3.0 29.9 1.0 CE1 A:HIS939 3.0 33.0 1.0 CB A:CYS937 3.1 28.3 1.0 CG A:HIS939 3.2 29.2 1.0 CB A:CYS960 3.5 33.7 1.0 CB A:HIS939 3.5 26.9 1.0 N A:CYS960 3.8 33.1 1.0 NE2 A:HIS939 4.1 35.3 1.0 CA A:CYS960 4.2 33.4 1.0 CD2 A:HIS939 4.2 34.4 1.0 CB A:LYS959 4.4 34.2 1.0 CA A:CYS957 4.5 27.9 1.0 CA A:CYS937 4.5 28.6 1.0 N A:HIS939 4.6 26.5 1.0 O A:HOH1125 4.7 30.3 1.0 CB A:ALA962 4.7 32.8 1.0 CA A:HIS939 4.7 25.1 1.0 C A:CYS937 4.7 29.4 1.0 C A:CYS960 4.8 34.5 1.0 C A:LYS959 4.8 34.3 1.0 CG A:LYS959 4.8 38.9 1.0 CD1 A:LEU934 4.9 28.4 1.0 N A:ASN961 4.9 31.5 1.0 N A:LYS959 4.9 30.8 1.0 O A:CYS937 4.9 30.0 1.0 N A:ALA962 4.9 30.9 1.0 CA A:LYS959 5.0 34.3 1.0 C A:CYS957 5.0 30.7 1.0 O A:HOH1130 5.0 44.3 1.0

M.Foglizzo, A.J.Middleton, C.L.Day. Structure and Function of the Ring Domains of RNF20 and RNF40, Dimeric E3 Ligases That Monoubiquitylate Histone H2B. J.Mol.Biol. V. 428 4073 2016.
ISSN: ESSN 1089-8638
PubMed: 27569044
DOI: 10.1016/J.JMB.2016.07.025