Atomistry » Zinc » PDB 4pog-4q1l » 4ppe
Atomistry »
  Zinc »
    PDB 4pog-4q1l »
      4ppe »

Zinc in PDB 4ppe: Human RNF4 Ring Domain

Protein crystallography data

The structure of Human RNF4 Ring Domain, PDB code: 4ppe was solved by J.J.Perry, A.S.Arvai, C.Hitomi, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.34 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 59.938, 86.987, 22.869, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Human RNF4 Ring Domain (pdb code 4ppe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human RNF4 Ring Domain, PDB code: 4ppe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4ppe

Go back to Zinc Binding Sites List in 4ppe
Zinc binding site 1 out of 4 in the Human RNF4 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human RNF4 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:19.5
occ:1.00
SG A:CYS163 2.3 15.7 1.0
SG A:CYS136 2.4 13.3 1.0
SG A:CYS139 2.4 21.5 1.0
SG A:CYS166 2.4 18.1 1.0
CB A:CYS136 3.0 15.9 1.0
CB A:CYS166 3.0 12.7 1.0
CB A:CYS139 3.2 16.7 1.0
CB A:CYS163 3.4 13.3 1.0
N A:CYS139 3.7 18.1 1.0
NH2 A:ARG151 3.7 19.5 1.0
CA A:CYS139 4.1 18.4 1.0
N A:CYS163 4.1 13.6 1.0
N A:CYS166 4.2 16.5 1.0
CA A:CYS166 4.2 16.4 1.0
CA A:CYS163 4.3 14.0 1.0
O A:HOH311 4.3 26.5 1.0
CA A:CYS136 4.5 16.1 1.0
CB A:ILE138 4.6 14.4 1.0
O A:CYS163 4.7 12.3 1.0
C A:ILE138 4.8 18.7 1.0
C A:CYS163 4.8 12.9 1.0
CZ A:ARG151 4.8 18.7 1.0
C A:CYS139 4.9 20.9 1.0
C A:CYS136 5.0 16.2 1.0

Zinc binding site 2 out of 4 in 4ppe

Go back to Zinc Binding Sites List in 4ppe
Zinc binding site 2 out of 4 in the Human RNF4 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human RNF4 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:15.2
occ:1.00
ND1 A:HIS160 2.2 14.9 1.0
SG A:CYS158 2.4 14.2 1.0
SG A:CYS177 2.4 19.1 1.0
SG A:CYS180 2.5 16.6 1.0
CE1 A:HIS160 3.0 18.8 1.0
CB A:CYS177 3.1 16.2 1.0
CG A:HIS160 3.3 16.6 1.0
CB A:CYS158 3.3 14.8 1.0
CB A:CYS180 3.5 14.4 1.0
OG1 A:THR156 3.6 19.1 1.0
CB A:HIS160 3.8 15.0 1.0
N A:CYS180 3.9 15.1 1.0
NE2 A:HIS160 4.2 18.1 1.0
CA A:CYS180 4.2 14.2 1.0
CD2 A:HIS160 4.4 15.0 1.0
CA A:CYS158 4.5 18.8 1.0
CA A:CYS177 4.6 17.0 1.0
CB A:THR179 4.6 16.2 1.0
CB A:THR156 4.6 14.9 1.0
C A:CYS158 4.6 16.9 1.0
N A:HIS160 4.8 16.0 1.0
O A:CYS158 4.8 15.2 1.0
C A:THR179 4.9 13.0 1.0
CG2 A:THR156 4.9 15.0 1.0
C A:CYS180 4.9 21.5 1.0
CA A:HIS160 4.9 13.0 1.0
N A:ARG181 4.9 21.1 1.0
N A:CYS158 5.0 15.1 1.0
CG2 A:THR179 5.0 16.6 1.0

Zinc binding site 3 out of 4 in 4ppe

Go back to Zinc Binding Sites List in 4ppe
Zinc binding site 3 out of 4 in the Human RNF4 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human RNF4 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:25.1
occ:1.00
SG B:CYS136 2.4 20.2 1.0
SG B:CYS163 2.5 20.4 1.0
SG B:CYS139 2.5 19.9 1.0
SG B:CYS166 2.5 32.5 1.0
CB B:CYS136 3.0 17.1 1.0
CB B:CYS166 3.1 24.1 1.0
CB B:CYS139 3.2 19.5 1.0
CB B:CYS163 3.5 18.3 1.0
N B:CYS139 3.6 23.8 1.0
NH2 B:ARG151 3.9 20.8 1.0
CA B:CYS139 4.0 21.7 1.0
N B:CYS163 4.0 18.2 1.0
CA B:CYS163 4.3 20.2 1.0
N B:CYS166 4.3 27.9 1.0
CA B:CYS166 4.3 24.1 1.0
CA B:CYS136 4.5 17.4 1.0
CB B:ILE138 4.6 19.8 1.0
O B:CYS163 4.7 18.3 1.0
C B:ILE138 4.7 20.6 1.0
C B:CYS163 4.8 18.6 1.0
C B:CYS139 4.9 21.7 1.0
N B:ILE138 4.9 19.6 1.0
CZ B:ARG151 4.9 23.3 1.0
N B:MET140 4.9 19.3 1.0
C B:CYS136 5.0 18.5 1.0
CA B:ILE138 5.0 17.9 1.0

Zinc binding site 4 out of 4 in 4ppe

Go back to Zinc Binding Sites List in 4ppe
Zinc binding site 4 out of 4 in the Human RNF4 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human RNF4 Ring Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:22.8
occ:1.00
ND1 B:HIS160 2.1 14.5 1.0
SG B:CYS177 2.4 21.2 1.0
SG B:CYS180 2.4 25.3 1.0
SG B:CYS158 2.4 20.3 1.0
CE1 B:HIS160 2.9 17.0 1.0
CB B:CYS177 3.1 17.1 1.0
CG B:HIS160 3.2 13.8 1.0
CB B:CYS180 3.4 23.4 1.0
CB B:CYS158 3.4 20.4 1.0
CB B:HIS160 3.7 16.7 1.0
OG1 B:THR156 3.8 18.8 1.0
N B:CYS180 3.8 27.0 1.0
NE2 B:HIS160 4.1 16.3 1.0
CA B:CYS180 4.2 22.6 1.0
CD2 B:HIS160 4.3 12.8 1.0
O B:CYS158 4.4 22.0 1.0
C B:CYS158 4.5 18.9 1.0
CA B:CYS158 4.5 22.6 1.0
CA B:CYS177 4.6 25.9 1.0
CB B:THR179 4.7 21.4 1.0
N B:HIS160 4.7 14.2 1.0
CB B:THR156 4.7 16.8 1.0
C B:CYS180 4.9 22.9 1.0
CA B:HIS160 4.9 16.5 1.0
C B:THR179 4.9 24.1 1.0
N B:ARG181 4.9 26.6 1.0

Reference:

L.M.Groocock, J.Prudden, Minghua N., D.Moiani, T.Wang, A.Cheltsov, R.P.Rambo, A.S.Arvai, C.Hitomi, J.A.Tainer, J.J.P.Perry, E.Lazzerini-Denchi, M.N.Boddy. RNF4 Requires Both Its Sumo and Nucleosome Interacting Abilities to Promote the Dna Damage Response To Be Published.
Page generated: Sun Oct 27 06:02:30 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy