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Zinc in PDB 4qpl: Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex

Enzymatic activity of Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex

All present enzymatic activity of Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex, PDB code: 4qpl was solved by Z.Wang, P.A.Darosa, R.E.Klevit, W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.665, 61.688, 94.346, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex (pdb code 4qpl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex, PDB code: 4qpl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4qpl

Go back to Zinc Binding Sites List in 4qpl
Zinc binding site 1 out of 4 in the Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex


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 RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:31.0
occ:1.00
SG A:CYS39 2.3 31.1 1.0
SG A:CYS36 2.3 27.6 1.0
SG A:CYS59 2.3 27.7 1.0
SG A:CYS56 2.3 31.8 1.0
CB A:CYS36 3.1 30.3 1.0
CB A:CYS56 3.2 29.0 1.0
CB A:CYS39 3.3 28.5 1.0
CB A:CYS59 3.4 26.1 1.0
N A:CYS39 3.8 27.6 1.0
O A:HOH341 3.9 48.1 1.0
N A:CYS56 4.0 27.4 1.0
CA A:CYS39 4.1 28.8 1.0
CA A:CYS56 4.2 28.7 1.0
O A:HOH311 4.4 35.6 1.0
CA A:CYS36 4.6 30.6 1.0
CB A:ILE38 4.7 24.4 1.0
CA A:CYS59 4.7 24.6 1.0
C A:ILE38 4.9 26.2 1.0
N A:CYS59 5.0 24.8 1.0

Zinc binding site 2 out of 4 in 4qpl

Go back to Zinc Binding Sites List in 4qpl
Zinc binding site 2 out of 4 in the Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex


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 RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:33.9
occ:1.00
ND1 A:HIS53 2.1 37.8 1.0
SG A:CYS51 2.3 35.9 1.0
SG A:CYS70 2.3 30.3 1.0
SG A:CYS73 2.3 33.5 1.0
CE1 A:HIS53 3.0 39.0 1.0
CG A:HIS53 3.1 34.0 1.0
CB A:CYS70 3.2 30.7 1.0
CB A:CYS51 3.3 38.0 1.0
CB A:CYS73 3.4 33.3 1.0
CB A:HIS53 3.5 31.3 1.0
N A:CYS73 3.8 29.2 1.0
NE2 A:HIS53 4.1 38.1 1.0
CA A:CYS73 4.1 31.9 1.0
CD2 A:HIS53 4.2 37.1 1.0
O A:HOH370 4.3 44.2 1.0
N A:HIS53 4.5 34.1 1.0
CA A:CYS51 4.6 38.4 1.0
CB A:LEU72 4.6 29.9 1.0
CA A:CYS70 4.6 29.5 1.0
C A:LEU72 4.7 30.4 1.0
CA A:HIS53 4.7 32.8 1.0
C A:CYS51 4.7 39.0 1.0
O A:CYS51 4.8 37.7 1.0
C A:CYS73 4.8 31.4 1.0
CD1 A:LEU49 4.9 36.7 1.0
CA A:LEU72 4.9 29.1 1.0
N A:LEU72 5.0 27.6 1.0
N A:ARG74 5.0 32.6 1.0

Zinc binding site 3 out of 4 in 4qpl

Go back to Zinc Binding Sites List in 4qpl
Zinc binding site 3 out of 4 in the Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:28.3
occ:1.00
SG C:CYS36 2.3 23.7 1.0
SG C:CYS39 2.3 25.7 1.0
SG C:CYS56 2.3 26.4 1.0
SG C:CYS59 2.4 25.3 1.0
CB C:CYS36 3.0 25.2 1.0
CB C:CYS56 3.3 24.0 1.0
CB C:CYS39 3.3 24.8 1.0
CB C:CYS59 3.4 22.9 1.0
N C:CYS39 3.8 23.6 1.0
N C:CYS56 3.9 24.7 1.0
O C:HOH318 4.0 38.9 1.0
CA C:CYS39 4.1 24.9 1.0
CA C:CYS56 4.2 25.4 1.0
O C:HOH333 4.4 27.9 1.0
CA C:CYS36 4.5 26.7 1.0
CB C:ILE38 4.7 23.5 1.0
CA C:CYS59 4.8 21.7 1.0
C C:ILE38 4.9 24.5 1.0
C C:CYS36 5.0 25.5 1.0

Zinc binding site 4 out of 4 in 4qpl

Go back to Zinc Binding Sites List in 4qpl
Zinc binding site 4 out of 4 in the Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of RNF146(Ring-Wwe)/UBCH5A/Iso-Adpr Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:32.9
occ:1.00
ND1 C:HIS53 2.1 35.0 1.0
SG C:CYS51 2.3 34.8 1.0
SG C:CYS73 2.3 36.1 1.0
SG C:CYS70 2.3 32.4 1.0
CE1 C:HIS53 3.0 37.8 1.0
CG C:HIS53 3.1 32.9 1.0
CB C:CYS70 3.3 33.2 1.0
CB C:CYS51 3.3 38.0 1.0
CB C:CYS73 3.4 34.8 1.0
CB C:HIS53 3.5 29.9 1.0
N C:CYS73 3.7 31.2 1.0
NE2 C:HIS53 4.1 37.9 1.0
CA C:CYS73 4.1 33.4 1.0
CD2 C:HIS53 4.2 34.8 1.0
N C:HIS53 4.5 31.9 1.0
CA C:HIS53 4.6 30.2 1.0
CB C:LEU72 4.6 31.7 1.0
CA C:CYS51 4.6 37.8 1.0
C C:LEU72 4.7 32.3 1.0
CA C:CYS70 4.7 32.4 1.0
C C:CYS51 4.8 38.8 1.0
O C:CYS51 4.8 38.3 1.0
C C:CYS73 4.8 33.2 1.0
N C:ARG74 4.9 33.4 1.0
CA C:LEU72 5.0 31.5 1.0

Reference:

P.A.Darosa, Z.Wang, X.Jiang, J.N.Pruneda, F.Cong, R.E.Klevit, W.Xu. Allosteric Activation of the RNF146 Ubiquitin Ligase By A Poly(Adp-Ribosyl)Ation Signal. Nature 2014.
ISSN: ESSN 1476-4687
PubMed: 25327252
DOI: 10.1038/NATURE13826
Page generated: Wed Dec 16 05:44:13 2020

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