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Zinc in PDB 2xeu: Ring Domain

Protein crystallography data

The structure of Ring Domain, PDB code: 2xeu was solved by A.Plechanovova, S.A.Mcmahon, K.A.Johnson, I.Navratilova, J.H.Naismith, R.T.Hay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.15 / 1.50
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 72.616, 72.616, 72.616, 90.00, 90.00, 90.00
R / Rfree (%) 16.836 / 19.727

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 2xeu

Go back to Zinc Binding Sites List in 2xeu
Zinc binding site 1 out of 2 in the Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1065

b:23.3
occ:1.00
SG A:CYS9 2.4 25.6 1.0
SG A:CYS36 2.4 24.4 1.0
SG A:CYS6 2.4 19.7 1.0
SG A:CYS33 2.4 22.7 1.0
CB A:CYS6 3.2 20.3 1.0
CB A:CYS9 3.2 24.6 1.0
CB A:CYS36 3.2 21.8 1.0
CB A:CYS33 3.5 20.9 1.0
N A:CYS9 3.6 23.2 1.0
NH1 A:ARG21 4.0 30.2 1.0
N A:CYS33 4.0 17.0 1.0
CA A:CYS9 4.0 24.3 1.0
CA A:CYS33 4.3 18.5 1.0
CA A:CYS36 4.4 22.2 1.0
N A:CYS36 4.4 21.6 1.0
O A:HOH2022 4.4 33.8 1.0
CA A:CYS6 4.6 19.3 1.0
CB A:ILE8 4.6 21.8 1.0
C A:ILE8 4.7 22.7 1.0
O A:CYS33 4.7 19.6 1.0
C A:CYS33 4.8 19.3 1.0
C A:CYS9 5.0 23.5 1.0
N A:ILE8 5.0 20.2 1.0

Zinc binding site 2 out of 2 in 2xeu

Go back to Zinc Binding Sites List in 2xeu
Zinc binding site 2 out of 2 in the Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1066

b:17.5
occ:1.00
ND1 A:HIS30 2.1 17.0 1.0
SG A:CYS47 2.3 17.3 1.0
SG A:CYS28 2.4 17.8 1.0
SG A:CYS50 2.4 19.9 1.0
CE1 A:HIS30 2.9 18.8 1.0
CB A:CYS47 3.1 19.9 1.0
CG A:HIS30 3.2 15.1 1.0
CB A:CYS28 3.3 18.4 1.0
CB A:CYS50 3.5 22.2 1.0
CB A:HIS30 3.7 13.8 1.0
N A:CYS50 3.8 21.6 1.0
OG1 A:THR26 3.8 14.6 1.0
NE2 A:HIS30 4.1 19.0 1.0
CA A:CYS50 4.2 23.6 1.0
CD2 A:HIS30 4.2 16.6 1.0
O A:CYS28 4.4 17.4 1.0
CA A:CYS28 4.4 17.5 1.0
C A:CYS28 4.5 15.8 1.0
CA A:CYS47 4.5 20.8 1.0
CB A:THR49 4.6 20.7 1.0
CB A:THR26 4.7 13.8 1.0
N A:HIS30 4.7 13.1 1.0
C A:CYS50 4.8 24.8 1.0
C A:THR49 4.8 21.8 1.0
CA A:HIS30 4.9 12.8 1.0
N A:ARG51 4.9 33.3 1.0
CG2 A:THR26 5.0 15.0 1.0

Reference:

A.Plechanovova, E.G.Jaffray, S.A.Mcmahon, K.A.Johnson, I.Navratilova, J.H.Naismith, R.T.Hay. Mechanism of Ubiquitylation By Dimeric Ring Ligase RNF4 Nat.Struct.Mol.Biol. V. 18 1052 2011.
ISSN: ISSN 1545-9993
PubMed: 21857666
DOI: 10.1038/NSMB.2108
Page generated: Wed Dec 16 03:59:50 2020

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