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

Protein crystallography data

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

Zinc Binding Sites:

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 5trb

Go back to Zinc Binding Sites List in 5trb
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 5trb

Go back to Zinc Binding Sites List in 5trb
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

Reference:

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
Page generated: Wed Dec 16 10:56:27 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy