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Zinc in PDB 4whv: E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B

Enzymatic activity of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B

All present enzymatic activity of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B:
6.3.2.19;

Protein crystallography data

The structure of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B, PDB code: 4whv was solved by C.D.Hodge, R.A.Edwards, J.N.M.Glover, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 8.30
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 341.379, 341.379, 113.447, 90.00, 90.00, 120.00
R / Rfree (%) 32.9 / 33.7

Zinc Binding Sites:

The binding sites of Zinc atom in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B (pdb code 4whv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B, PDB code: 4whv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4whv

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Zinc binding site 1 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:0.8
occ:1.01
 ND1 C:HIS420 2.1 0.9 1.0
SG C:CYS418 2.3 0.5 1.0
SG C:CYS440 2.3 1.0 1.0
SG C:CYS437 2.3 0.5 1.0
CE1 C:HIS420 3.0 0.8 1.0
CB C:CYS437 3.0 0.7 1.0
CG C:HIS420 3.1 0.9 1.0
CB C:CYS418 3.2 0.8 1.0
CB C:CYS440 3.5 0.1 1.0
CB C:HIS420 3.5 0.5 1.0
N C:CYS440 3.7 0.2 1.0
NE2 C:HIS420 4.1 0.4 1.0
CA C:CYS440 4.1 0.7 1.0
CD2 C:HIS420 4.2 1.0 1.0
O C:CYS418 4.4 0.5 1.0
CA C:CYS418 4.5 0.5 1.0
CA C:CYS437 4.5 0.2 1.0
C C:CYS418 4.5 0.1 1.0
CB C:ILE439 4.5 0.0 1.0
N C:HIS420 4.5 0.4 1.0
CA C:HIS420 4.7 0.7 1.0
C C:ILE439 4.8 0.7 1.0
C C:CYS440 4.9 0.2 1.0
N C:ARG441 4.9 0.1 1.0
CA C:ILE439 5.0 0.3 1.0
N C:ILE439 5.0 0.2 1.0

Zinc binding site 2 out of 8 in 4whv

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Zinc binding site 2 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:0.8
occ:1.01
 SG C:CYS426 2.3 0.2 1.0
SG C:CYS406 2.3 0.4 1.0
SG C:CYS423 2.4 0.8 1.0
SG C:CYS403 2.4 0.9 1.0
CB C:CYS403 2.9 0.2 1.0
CB C:CYS423 3.1 0.4 1.0
CB C:CYS406 3.3 0.1 1.0
CB C:CYS426 3.3 0.7 1.0
N C:CYS406 3.8 0.3 1.0
NH2 C:ARG479 3.8 0.6 1.0
NH1 C:ARG479 4.0 0.8 1.0
N C:CYS423 4.0 0.1 1.0
CA C:CYS423 4.2 0.9 1.0
CA C:CYS406 4.2 0.9 1.0
CZ C:ARG479 4.3 0.8 1.0
CA C:CYS403 4.4 0.0 1.0
CB C:ILE405 4.6 0.6 1.0
CA C:CYS426 4.7 0.7 1.0
C C:ILE405 4.8 0.5 1.0
C C:CYS403 4.8 0.6 1.0
O C:CYS403 4.9 0.8 1.0
N C:CYS426 4.9 0.8 1.0
N C:ILE405 4.9 0.0 1.0
CA C:ILE405 5.0 0.0 1.0

Zinc binding site 3 out of 8 in 4whv

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Zinc binding site 3 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:0.6
occ:1.01
 ND1 D:HIS420 2.2 0.7 1.0
SG D:CYS418 2.2 0.3 1.0
SG D:CYS440 2.2 1.0 1.0
SG D:CYS437 2.3 0.0 1.0
CB D:CYS437 3.0 0.4 1.0
CE1 D:HIS420 3.2 0.3 1.0
CB D:CYS418 3.2 0.2 1.0
CG D:HIS420 3.2 0.6 1.0
CB D:CYS440 3.5 0.4 1.0
CB D:HIS420 3.5 0.3 1.0
N D:CYS440 3.8 0.7 1.0
CA D:CYS440 4.2 0.9 1.0
NE2 D:HIS420 4.3 0.5 1.0
O D:CYS418 4.3 0.1 1.0
CD2 D:HIS420 4.3 0.2 1.0
CA D:CYS418 4.4 0.0 1.0
CA D:CYS437 4.5 0.9 1.0
C D:CYS418 4.5 0.6 1.0
N D:HIS420 4.5 0.8 1.0
CB D:ILE439 4.7 0.5 1.0
CA D:HIS420 4.7 0.1 1.0
C D:ILE439 4.8 0.6 1.0
C D:CYS440 4.9 0.3 1.0
N D:ARG441 4.9 0.6 1.0
N D:ILE439 5.0 0.8 1.0

Zinc binding site 4 out of 8 in 4whv

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Zinc binding site 4 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:0.6
occ:1.01
 SG D:CYS426 2.3 0.4 1.0
SG D:CYS406 2.3 0.3 1.0
SG D:CYS403 2.3 0.8 1.0
SG D:CYS423 2.3 0.0 1.0
CB D:CYS403 3.0 0.8 1.0
CB D:CYS423 3.1 0.5 1.0
CB D:CYS426 3.2 0.7 1.0
CB D:CYS406 3.3 0.8 1.0
N D:CYS406 3.8 0.8 1.0
N D:CYS423 4.0 0.6 1.0
NH2 D:ARG479 4.0 0.7 1.0
NH1 D:ARG479 4.0 0.7 1.0
CA D:CYS423 4.1 0.5 1.0
CA D:CYS406 4.2 0.7 1.0
CA D:CYS403 4.4 0.4 1.0
CZ D:ARG479 4.5 0.1 1.0
CA D:CYS426 4.6 0.3 1.0
CB D:ILE405 4.6 0.8 1.0
C D:ILE405 4.8 0.3 1.0
N D:CYS426 4.8 0.9 1.0
C D:CYS403 4.9 0.7 1.0
N D:ILE405 5.0 0.2 1.0

Zinc binding site 5 out of 8 in 4whv

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Zinc binding site 5 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn501

b:0.3
occ:1.00
 ND1 I:HIS420 2.1 0.9 1.0
SG I:CYS440 2.3 0.7 1.0
SG I:CYS418 2.3 0.1 1.0
SG I:CYS437 2.3 0.7 1.0
CE1 I:HIS420 3.0 0.9 1.0
CB I:CYS437 3.0 0.6 1.0
CG I:HIS420 3.1 0.9 1.0
CB I:CYS418 3.2 0.8 1.0
CB I:CYS440 3.5 0.1 1.0
CB I:HIS420 3.5 0.5 1.0
N I:CYS440 3.7 0.7 1.0
NE2 I:HIS420 4.1 0.5 1.0
CA I:CYS440 4.1 0.4 1.0
CD2 I:HIS420 4.2 0.1 1.0
O I:CYS418 4.4 0.1 1.0
CA I:CYS418 4.5 0.6 1.0
CA I:CYS437 4.5 0.3 1.0
C I:CYS418 4.5 0.2 1.0
CB I:ILE439 4.5 0.9 1.0
N I:HIS420 4.6 0.2 1.0
CA I:HIS420 4.7 0.2 1.0
C I:ILE439 4.8 0.6 1.0
C I:CYS440 4.9 1.0 1.0
N I:ARG441 4.9 0.5 1.0
CA I:ILE439 5.0 0.1 1.0
N I:ILE439 5.0 0.1 1.0

Zinc binding site 6 out of 8 in 4whv

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Zinc binding site 6 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn502

b:0.3
occ:1.00
 SG I:CYS426 2.3 0.8 1.0
SG I:CYS406 2.3 0.9 1.0
SG I:CYS423 2.4 0.9 1.0
SG I:CYS403 2.4 0.1 1.0
CB I:CYS403 2.9 0.4 1.0
CB I:CYS423 3.1 0.8 1.0
CB I:CYS406 3.3 0.4 1.0
CB I:CYS426 3.3 0.6 1.0
N I:CYS406 3.8 0.5 1.0
NH2 I:ARG479 3.8 0.7 1.0
NH1 I:ARG479 4.0 0.1 1.0
N I:CYS423 4.0 0.4 1.0
CA I:CYS423 4.2 0.9 1.0
CA I:CYS406 4.2 0.6 1.0
CZ I:ARG479 4.3 0.3 1.0
CA I:CYS403 4.4 0.9 1.0
CB I:ILE405 4.6 0.3 1.0
CA I:CYS426 4.7 0.1 1.0
C I:ILE405 4.8 0.8 1.0
C I:CYS403 4.8 0.8 1.0
O I:CYS403 4.9 0.7 1.0
N I:CYS426 4.9 1.0 1.0
N I:ILE405 4.9 0.6 1.0
CA I:ILE405 5.0 0.7 1.0

Zinc binding site 7 out of 8 in 4whv

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Zinc binding site 7 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn501

b:0.1
occ:1.00
 ND1 J:HIS420 2.2 0.4 1.0
SG J:CYS418 2.2 0.3 1.0
SG J:CYS440 2.2 0.9 1.0
SG J:CYS437 2.3 0.0 1.0
CB J:CYS437 3.0 0.0 1.0
CE1 J:HIS420 3.2 0.7 1.0
CB J:CYS418 3.2 0.5 1.0
CG J:HIS420 3.2 0.9 1.0
CB J:CYS440 3.5 0.4 1.0
CB J:HIS420 3.5 0.8 1.0
N J:CYS440 3.8 0.7 1.0
CA J:CYS440 4.2 0.4 1.0
NE2 J:HIS420 4.3 0.1 1.0
O J:CYS418 4.3 0.6 1.0
CD2 J:HIS420 4.3 0.5 1.0
CA J:CYS418 4.4 0.9 1.0
CA J:CYS437 4.5 0.0 1.0
C J:CYS418 4.5 1.0 1.0
N J:HIS420 4.5 0.8 1.0
CB J:ILE439 4.7 0.3 1.0
CA J:HIS420 4.7 0.6 1.0
C J:ILE439 4.8 0.8 1.0
C J:CYS440 4.9 0.4 1.0
N J:ARG441 4.9 0.3 1.0
N J:ILE439 5.0 0.1 1.0

Zinc binding site 8 out of 8 in 4whv

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Zinc binding site 8 out of 8 in the E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of E3 Ubiquitin-Protein Ligase RNF8 in Complex with Ubiquitin-Conjugating Enzyme E2 N and Polyubiquitin-B within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn502

b:0.1
occ:1.00
 SG J:CYS426 2.3 0.8 1.0
SG J:CYS406 2.3 0.6 1.0
SG J:CYS403 2.3 0.1 1.0
SG J:CYS423 2.3 0.3 1.0
CB J:CYS403 3.0 0.1 1.0
CB J:CYS423 3.1 0.3 1.0
CB J:CYS426 3.2 0.9 1.0
CB J:CYS406 3.3 0.6 1.0
N J:CYS406 3.8 0.8 1.0
N J:CYS423 4.0 0.2 1.0
NH2 J:ARG479 4.0 0.2 1.0
NH1 J:ARG479 4.0 0.9 1.0
CA J:CYS423 4.1 0.1 1.0
CA J:CYS406 4.2 0.1 1.0
CA J:CYS403 4.4 0.1 1.0
CZ J:ARG479 4.5 0.0 1.0
CA J:CYS426 4.6 0.7 1.0
CB J:ILE405 4.6 0.6 1.0
C J:ILE405 4.8 0.5 1.0
N J:CYS426 4.8 0.8 1.0
C J:CYS403 4.9 0.8 1.0
N J:ILE405 5.0 0.6 1.0

Reference:

C.D.Hodge, I.H.Ismail, R.A.Edwards, G.L.Hura, A.T.Xiao, J.A.Tainer, M.J.Hendzel, J.N.Glover. RNF8 E3 Ubiquitin Ligase Stimulates UBC13 E2 Conjugating Activity That Is Essential For Dna Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment. J.Biol.Chem. V. 291 9396 2016.
ISSN: ESSN 1083-351X
PubMed: 26903517
DOI: 10.1074/JBC.M116.715698
Page generated: Sun Oct 27 09:55:35 2024

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