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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

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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

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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

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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

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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: Wed Dec 16 05:41:19 2020

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