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Zinc in PDB 5aiu: A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink)

Enzymatic activity of A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink)

All present enzymatic activity of A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink):
6.3.2.19;

Protein crystallography data

The structure of A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink), PDB code: 5aiu was solved by E.Branigan, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.02 / 2.21
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.190, 169.210, 52.620, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink) (pdb code 5aiu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink), PDB code: 5aiu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5aiu

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Zinc binding site 1 out of 4 in the A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn800

b:18.1
occ:1.00
SG A:CYS139 2.3 14.4 1.0
SG A:CYS136 2.3 18.1 1.0
SG A:CYS166 2.3 20.8 1.0
SG A:CYS163 2.3 19.8 1.0
CB A:CYS166 3.0 20.7 1.0
CB A:CYS136 3.2 18.2 1.0
CB A:CYS163 3.3 19.6 1.0
CB A:CYS139 3.3 17.0 1.0
N A:CYS139 3.5 17.8 1.0
CA A:CYS139 4.0 17.0 1.0
NH1 A:ARG151 4.1 25.8 1.0
N A:CYS163 4.1 19.2 1.0
CA A:CYS166 4.2 21.6 1.0
CA A:CYS163 4.2 19.2 1.0
N A:CYS166 4.3 22.3 1.0
CB A:ILE138 4.5 20.9 1.0
O A:CYS163 4.5 19.4 1.0
C A:ILE138 4.6 19.3 1.0
CA A:CYS136 4.6 18.3 1.0
C A:CYS163 4.7 19.6 1.0
N A:ILE138 4.8 20.5 1.0
CA A:ILE138 4.9 20.1 1.0
C A:CYS139 4.9 18.5 1.0
O A:CYS136 4.9 20.1 1.0
N A:MET140 5.0 19.0 1.0
C A:CYS136 5.0 18.1 1.0

Zinc binding site 2 out of 4 in 5aiu

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Zinc binding site 2 out of 4 in the A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:16.9
occ:1.00
ND1 A:HIS160 2.1 17.1 1.0
SG A:CYS177 2.3 16.6 1.0
SG A:CYS180 2.3 18.6 1.0
SG A:CYS158 2.3 16.3 1.0
CE1 A:HIS160 3.0 16.4 1.0
CG A:HIS160 3.1 15.4 1.0
CB A:CYS177 3.1 18.1 1.0
CB A:CYS180 3.3 17.3 1.0
CB A:CYS158 3.4 16.9 1.0
CB A:HIS160 3.6 15.3 1.0
N A:CYS180 3.8 16.8 1.0
OG1 A:THR156 4.0 16.8 1.0
CA A:CYS180 4.1 17.2 1.0
NE2 A:HIS160 4.1 16.4 1.0
CD2 A:HIS160 4.2 15.0 1.0
O A:CYS158 4.5 14.5 1.0
CA A:CYS158 4.5 17.0 1.0
C A:CYS158 4.6 16.8 1.0
CA A:CYS177 4.6 19.8 1.0
C A:CYS180 4.6 17.2 1.0
CB A:THR179 4.7 15.5 1.0
N A:HIS160 4.7 15.5 1.0
CB A:LYS182 4.8 27.9 1.0
C A:THR179 4.8 16.0 1.0
CA A:HIS160 4.8 15.4 1.0
N A:ARG181 4.8 18.1 1.0
N A:LYS182 4.9 23.0 1.0
CB A:THR156 5.0 15.4 1.0

Zinc binding site 3 out of 4 in 5aiu

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Zinc binding site 3 out of 4 in the A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:17.6
occ:1.00
SG A:CYS231 2.3 19.3 1.0
SG A:CYS204 2.3 19.3 1.0
SG A:CYS201 2.3 19.7 1.0
SG A:CYS228 2.3 16.3 1.0
CB A:CYS231 3.1 17.4 1.0
CB A:CYS204 3.2 19.6 1.0
CB A:CYS201 3.2 20.3 1.0
CB A:CYS228 3.4 16.1 1.0
N A:CYS204 3.5 19.0 1.0
CA A:CYS204 3.9 20.1 1.0
NH1 A:ARG216 4.1 18.8 1.0
N A:CYS228 4.1 14.8 1.0
CA A:CYS228 4.3 15.9 1.0
CA A:CYS231 4.3 18.4 1.0
N A:CYS231 4.3 18.1 1.0
C A:ILE203 4.6 19.6 1.0
CB A:ILE203 4.6 18.8 1.0
CA A:CYS201 4.6 21.7 1.0
O A:CYS228 4.7 17.0 1.0
C A:CYS228 4.8 16.9 1.0
C A:CYS204 4.9 20.1 1.0
CA A:ILE203 4.9 19.4 1.0
N A:ILE203 4.9 20.1 1.0
N A:MET205 4.9 19.9 1.0
O A:CYS201 5.0 20.6 1.0
C A:CYS201 5.0 20.4 1.0

Zinc binding site 4 out of 4 in 5aiu

Go back to Zinc Binding Sites List in 5aiu
Zinc binding site 4 out of 4 in the A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Complex of RNF4-Ring Domain, UBC13-Ub (Isopeptide Crosslink) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:17.0
occ:1.00
ND1 A:HIS225 2.1 15.6 1.0
SG A:CYS242 2.3 18.6 1.0
SG A:CYS223 2.3 15.8 1.0
SG A:CYS245 2.4 17.3 1.0
CE1 A:HIS225 2.9 15.1 1.0
CB A:CYS242 3.1 18.2 1.0
CG A:HIS225 3.3 14.8 1.0
CB A:CYS223 3.4 15.2 1.0
CB A:CYS245 3.5 18.5 1.0
N A:CYS245 3.7 16.8 1.0
CB A:HIS225 3.8 15.8 1.0
OG1 A:THR221 4.0 18.8 1.0
NE2 A:HIS225 4.1 15.3 1.0
CA A:CYS245 4.1 17.0 1.0
CD2 A:HIS225 4.3 15.0 1.0
O A:CYS223 4.3 14.2 1.0
CA A:CYS223 4.5 15.8 1.0
C A:CYS223 4.5 15.4 1.0
CA A:CYS242 4.6 18.5 1.0
C A:THR244 4.6 16.3 1.0
CB A:THR244 4.6 14.8 1.0
N A:HIS225 4.8 15.8 1.0
C A:CYS245 4.8 18.0 1.0
CB A:THR221 4.8 18.9 1.0
CA A:HIS225 4.9 15.6 1.0
CA A:THR244 4.9 15.5 1.0
N A:THR244 4.9 14.7 1.0
CB A:LYS247 4.9 21.0 1.0
CG2 A:THR221 5.0 19.2 1.0
N A:ARG246 5.0 17.5 1.0

Reference:

E.Branigan, A.Plechanovova, E.Jaffray, J.H.Naismith, R.T.Hay. Structural Basis For the Ring Catalyzed Synthesis of K63 Linked Ubiquitin Chains Nat.Struct.Mol.Biol. V. 22 597 2015.
ISSN: ISSN 1545-9993
PubMed: 26148049
DOI: 10.1038/NSMB.3052
Page generated: Wed Dec 16 06:03:12 2020

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