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Zinc in PDB 5dka: A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125

Protein crystallography data

The structure of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125, PDB code: 5dka was solved by D.R.Boer, M.Coll, M.J.Bijlmakers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.71 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.670, 52.320, 73.970, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.9

Other elements in 5dka:

The structure of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 (pdb code 5dka). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125, PDB code: 5dka:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5dka

Go back to Zinc Binding Sites List in 5dka
Zinc binding site 1 out of 6 in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:19.2
occ:1.00
 SG A:CYS40 2.3 23.4 1.0
SG A:CYS60 2.4 21.9 1.0
SG A:CYS37 2.4 23.1 1.0
SG A:CYS57 2.4 18.1 1.0
CB A:CYS37 3.1 24.3 1.0
CB A:CYS57 3.2 17.9 1.0
CB A:CYS40 3.3 25.1 1.0
CB A:CYS60 3.4 20.5 1.0
N A:CYS40 3.8 26.3 1.0
O A:HOH428 3.8 36.2 1.0
N A:CYS57 3.9 17.7 1.0
CA A:CYS40 4.1 26.1 1.0
CA A:CYS57 4.2 18.1 1.0
O A:HOH455 4.3 37.1 1.0
NH2 A:ARG113 4.4 20.7 1.0
CA A:CYS37 4.5 25.3 1.0
CA A:CYS60 4.7 20.1 1.0
CB A:VAL39 4.8 27.8 1.0
C A:CYS40 4.9 27.1 1.0
N A:LEU41 5.0 27.3 1.0
C A:VAL39 5.0 28.3 1.0

Zinc binding site 2 out of 6 in 5dka

Go back to Zinc Binding Sites List in 5dka
Zinc binding site 2 out of 6 in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:25.8
occ:1.00
 NE2 A:HIS115 2.1 27.0 1.0
SG A:CYS119 2.3 26.5 1.0
SG A:CYS103 2.3 28.4 1.0
SG A:CYS100 2.3 28.2 1.0
CD2 A:HIS115 3.0 25.3 1.0
CE1 A:HIS115 3.1 24.3 1.0
CB A:CYS100 3.2 28.1 1.0
CB A:CYS119 3.3 25.7 1.0
CB A:CYS103 3.3 31.5 1.0
N A:CYS103 3.7 33.0 1.0
O A:HOH457 3.9 51.0 1.0
CA A:CYS103 4.1 31.4 1.0
ND1 A:HIS115 4.2 25.2 1.0
CG A:HIS115 4.2 23.5 1.0
CA A:CYS119 4.5 26.0 1.0
CA A:CYS100 4.6 29.3 1.0
C A:GLU102 4.7 32.8 1.0
C A:CYS103 4.9 34.7 1.0
CB A:GLU102 4.9 34.5 1.0
N A:GLU102 5.0 33.3 1.0

Zinc binding site 3 out of 6 in 5dka

Go back to Zinc Binding Sites List in 5dka
Zinc binding site 3 out of 6 in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:20.1
occ:1.00
 ND1 A:HIS54 2.1 21.9 1.0
SG A:CYS72 2.3 19.5 1.0
SG A:CYS75 2.3 20.7 1.0
SG A:CYS52 2.3 24.7 1.0
CE1 A:HIS54 3.0 21.0 1.0
CG A:HIS54 3.2 20.6 1.0
CB A:CYS72 3.2 20.3 1.0
CB A:CYS52 3.4 23.3 1.0
CB A:CYS75 3.4 22.0 1.0
CB A:HIS54 3.6 18.7 1.0
N A:CYS75 3.8 20.7 1.0
NE2 A:HIS54 4.2 22.9 1.0
CA A:CYS75 4.2 21.3 1.0
OG1 A:THR50 4.2 27.3 1.0
CD2 A:HIS54 4.3 20.8 1.0
CA A:CYS52 4.6 24.4 1.0
N A:HIS54 4.6 19.7 1.0
O A:CYS52 4.6 24.9 1.0
CB A:TYR74 4.6 21.6 1.0
CA A:CYS72 4.6 20.1 1.0
C A:CYS52 4.7 24.8 1.0
CB A:ALA77 4.7 24.7 1.0
CA A:HIS54 4.7 19.1 1.0
C A:CYS75 4.9 21.9 1.0
C A:TYR74 4.9 21.6 1.0
CD2 A:TYR74 5.0 21.9 1.0
N A:ARG76 5.0 21.9 1.0

Zinc binding site 4 out of 6 in 5dka

Go back to Zinc Binding Sites List in 5dka
Zinc binding site 4 out of 6 in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:20.1
occ:1.00
 SG B:CYS60 2.3 22.9 1.0
SG B:CYS57 2.3 19.5 1.0
SG B:CYS40 2.4 21.9 1.0
SG B:CYS37 2.4 20.4 1.0
CB B:CYS37 3.1 20.5 1.0
CB B:CYS57 3.1 19.8 1.0
CB B:CYS40 3.3 22.8 1.0
CB B:CYS60 3.4 22.0 1.0
N B:CYS40 3.8 22.9 1.0
O B:HOH447 3.9 33.1 1.0
N B:CYS57 4.0 19.4 1.0
CA B:CYS57 4.2 19.1 1.0
CA B:CYS40 4.2 23.6 1.0
O B:HOH463 4.3 38.6 1.0
NH2 B:ARG113 4.4 21.3 1.0
CA B:CYS37 4.5 21.2 1.0
CA B:CYS60 4.8 22.1 1.0
CB B:VAL39 4.8 25.6 1.0
C B:VAL39 4.9 25.0 1.0

Zinc binding site 5 out of 6 in 5dka

Go back to Zinc Binding Sites List in 5dka
Zinc binding site 5 out of 6 in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:23.4
occ:1.00
 NE2 B:HIS115 2.1 23.8 1.0
SG B:CYS119 2.3 22.9 1.0
SG B:CYS103 2.3 24.9 1.0
SG B:CYS100 2.4 24.9 1.0
CE1 B:HIS115 3.1 23.5 1.0
CD2 B:HIS115 3.1 21.7 1.0
CB B:CYS100 3.2 24.7 1.0
CB B:CYS103 3.3 27.5 1.0
CB B:CYS119 3.3 23.0 1.0
N B:CYS103 3.8 28.6 1.0
CA B:CYS103 4.1 28.4 1.0
ND1 B:HIS115 4.2 23.4 1.0
CG B:HIS115 4.2 22.0 1.0
CA B:CYS119 4.6 22.3 1.0
CA B:CYS100 4.6 24.5 1.0
C B:GLU102 4.8 31.0 1.0
O B:HOH457 4.8 31.1 1.0
C B:CYS103 4.9 29.1 1.0
CB B:GLU102 5.0 30.0 1.0

Zinc binding site 6 out of 6 in 5dka

Go back to Zinc Binding Sites List in 5dka
Zinc binding site 6 out of 6 in the A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A C2HC Zinc Finger Is Essential For the Activity of the Ring Ubiquitin Ligase RNF125 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:22.2
occ:1.00
 ND1 B:HIS54 2.1 23.9 1.0
SG B:CYS75 2.3 24.1 1.0
SG B:CYS72 2.3 22.2 1.0
SG B:CYS52 2.3 26.9 1.0
CE1 B:HIS54 3.0 24.3 1.0
CB B:CYS72 3.1 20.8 1.0
CG B:HIS54 3.2 25.1 1.0
CB B:CYS52 3.3 30.2 1.0
CB B:CYS75 3.4 26.7 1.0
CB B:HIS54 3.6 23.7 1.0
N B:CYS75 3.9 26.6 1.0
NE2 B:HIS54 4.2 26.1 1.0
CA B:CYS75 4.2 26.1 1.0
CD2 B:HIS54 4.3 25.8 1.0
N B:HIS54 4.4 24.7 1.0
OG1 B:THR50 4.6 25.7 1.0
CA B:CYS72 4.6 21.7 1.0
CA B:CYS52 4.7 28.6 1.0
CA B:HIS54 4.7 23.4 1.0
C B:CYS52 4.8 28.6 1.0
CB B:TYR74 4.8 24.8 1.0
O B:CYS52 4.8 30.4 1.0
C B:CYS75 4.9 25.0 1.0
C B:TYR74 4.9 26.2 1.0
CB B:ALA77 5.0 25.7 1.0
N B:ARG76 5.0 23.5 1.0

Reference:

M.J.Bijlmakers, J.M.Teixeira, R.Boer, M.Mayzel, P.Puig-Sarries, G.Karlsson, M.Coll, M.Pons, B.Crosas. A C2HC Zinc Finger Is Essential For the Ring-E2 Interaction of the Ubiquitin Ligase RNF125. Sci Rep V. 6 29232 2016.
ISSN: ESSN 2045-2322
PubMed: 27411375
DOI: 10.1038/SREP29232
Page generated: Sun Oct 27 14:47:22 2024

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