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Zinc in PDB 4orh: Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer

Enzymatic activity of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer

All present enzymatic activity of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer:
6.3.2.19;

Protein crystallography data

The structure of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer, PDB code: 4orh was solved by S.J.Campbell, 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) 123.54 / 4.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 205.258, 205.258, 235.372, 90.00, 90.00, 90.00
R / Rfree (%) 27.6 / 28.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer (pdb code 4orh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer, PDB code: 4orh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4orh

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Zinc binding site 1 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

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

Zinc binding site 2 out of 10 in 4orh

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Zinc binding site 2 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:0.5
occ:1.00
 SG C:CYS426 2.3 0.0 1.0
SG C:CYS406 2.3 0.9 1.0
SG C:CYS403 2.3 0.9 1.0
SG C:CYS423 2.3 0.6 1.0
CB C:CYS403 3.0 0.8 1.0
CB C:CYS423 3.1 0.4 1.0
CB C:CYS426 3.2 0.4 1.0
CB C:CYS406 3.3 0.2 1.0
N C:CYS406 3.8 0.2 1.0
N C:CYS423 4.0 0.1 1.0
NH2 C:ARG479 4.0 0.4 1.0
NH1 C:ARG479 4.0 0.3 1.0
CA C:CYS423 4.1 0.5 1.0
CA C:CYS406 4.2 0.3 1.0
CA C:CYS403 4.4 0.4 1.0
CZ C:ARG479 4.5 0.0 1.0
CB C:ILE405 4.5 1.0 1.0
CA C:CYS426 4.6 1.0 1.0
C C:ILE405 4.8 0.6 1.0
N C:CYS426 4.8 0.2 1.0
C C:CYS403 4.9 0.3 1.0
N C:ILE405 5.0 0.4 1.0

Zinc binding site 3 out of 10 in 4orh

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Zinc binding site 3 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


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 RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:0.2
occ:1.00
 ND1 G:HIS420 2.1 0.5 1.0
SG G:CYS440 2.3 0.3 1.0
SG G:CYS418 2.3 0.1 1.0
SG G:CYS437 2.3 0.4 1.0
CE1 G:HIS420 3.0 0.6 1.0
CB G:CYS437 3.0 0.7 1.0
CG G:HIS420 3.1 0.5 1.0
CB G:CYS418 3.2 0.0 1.0
CB G:CYS440 3.5 0.6 1.0
CB G:HIS420 3.5 0.8 1.0
N G:CYS440 3.7 0.7 1.0
NE2 G:HIS420 4.1 0.2 1.0
CA G:CYS440 4.1 0.9 1.0
CD2 G:HIS420 4.2 0.6 1.0
O G:CYS418 4.4 0.8 1.0
CA G:CYS418 4.5 0.1 1.0
CA G:CYS437 4.5 0.9 1.0
C G:CYS418 4.5 0.0 1.0
CB G:ILE439 4.5 0.1 1.0
N G:HIS420 4.6 0.3 1.0
CA G:HIS420 4.7 0.5 1.0
C G:ILE439 4.8 0.5 1.0
C G:CYS440 4.9 0.8 1.0
N G:ARG441 4.9 0.3 1.0
CA G:ILE439 5.0 0.3 1.0
N G:ILE439 5.0 0.8 1.0

Zinc binding site 4 out of 10 in 4orh

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Zinc binding site 4 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


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 RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn502

b:0.2
occ:1.00
 SG G:CYS426 2.3 0.0 1.0
SG G:CYS406 2.3 0.3 1.0
SG G:CYS423 2.4 0.5 1.0
SG G:CYS403 2.4 0.2 1.0
CB G:CYS403 2.9 0.6 1.0
CB G:CYS423 3.1 0.3 1.0
CB G:CYS406 3.3 0.3 1.0
CB G:CYS426 3.3 0.1 1.0
N G:CYS406 3.8 0.2 1.0
NH2 G:ARG479 3.8 0.5 1.0
NH1 G:ARG479 4.0 0.6 1.0
N G:CYS423 4.0 0.0 1.0
CA G:CYS423 4.2 0.6 1.0
CA G:CYS406 4.2 0.3 1.0
CZ G:ARG479 4.3 0.6 1.0
CA G:CYS403 4.4 0.4 1.0
CB G:ILE405 4.6 0.5 1.0
CA G:CYS426 4.7 0.3 1.0
C G:ILE405 4.8 0.7 1.0
C G:CYS403 4.8 0.1 1.0
O G:CYS403 4.9 0.6 1.0
N G:CYS426 4.9 0.5 1.0
N G:ILE405 4.9 0.7 1.0
CA G:ILE405 5.0 0.6 1.0

Zinc binding site 5 out of 10 in 4orh

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Zinc binding site 5 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn501

b:1.0
occ:1.00
 ND1 H:HIS420 2.2 0.1 1.0
SG H:CYS418 2.2 0.3 1.0
SG H:CYS440 2.2 0.1 1.0
SG H:CYS437 2.3 0.1 1.0
CB H:CYS437 3.0 0.8 1.0
CE1 H:HIS420 3.2 0.7 1.0
CB H:CYS418 3.2 0.8 1.0
CG H:HIS420 3.2 0.6 1.0
CB H:CYS440 3.5 0.5 1.0
CB H:HIS420 3.5 0.3 1.0
N H:CYS440 3.8 0.5 1.0
CA H:CYS440 4.2 0.3 1.0
NE2 H:HIS420 4.3 0.2 1.0
O H:CYS418 4.3 0.6 1.0
CD2 H:HIS420 4.3 0.1 1.0
CA H:CYS418 4.4 1.0 1.0
CA H:CYS437 4.5 0.6 1.0
C H:CYS418 4.5 0.8 1.0
N H:HIS420 4.5 0.7 1.0
CB H:ILE439 4.7 0.7 1.0
CA H:HIS420 4.7 0.7 1.0
C H:ILE439 4.8 0.3 1.0
C H:CYS440 4.9 0.2 1.0
N H:ARG441 4.9 0.2 1.0
N H:ILE439 5.0 0.0 1.0

Zinc binding site 6 out of 10 in 4orh

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Zinc binding site 6 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn502

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

Zinc binding site 7 out of 10 in 4orh

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Zinc binding site 7 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn501

b:0.0
occ:1.00
 ND1 K:HIS420 2.1 0.3 1.0
SG K:CYS440 2.3 0.2 1.0
SG K:CYS418 2.3 0.4 1.0
SG K:CYS437 2.3 0.7 1.0
CE1 K:HIS420 3.0 0.3 1.0
CB K:CYS437 3.0 0.4 1.0
CG K:HIS420 3.1 0.3 1.0
CB K:CYS418 3.2 0.1 1.0
CB K:CYS440 3.5 0.5 1.0
CB K:HIS420 3.5 0.9 1.0
N K:CYS440 3.7 0.1 1.0
NE2 K:HIS420 4.1 0.3 1.0
CA K:CYS440 4.1 0.0 1.0
CD2 K:HIS420 4.2 0.7 1.0
O K:CYS418 4.4 0.5 1.0
CA K:CYS418 4.5 0.9 1.0
CA K:CYS437 4.5 0.6 1.0
C K:CYS418 4.5 0.9 1.0
CB K:ILE439 4.5 0.5 1.0
N K:HIS420 4.6 0.5 1.0
CA K:HIS420 4.7 0.1 1.0
C K:ILE439 4.8 0.2 1.0
C K:CYS440 4.9 0.9 1.0
N K:ARG441 4.9 0.8 1.0
CA K:ILE439 5.0 0.8 1.0
N K:ILE439 5.0 0.8 1.0

Zinc binding site 8 out of 10 in 4orh

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Zinc binding site 8 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn502

b:0.0
occ:1.00
 SG K:CYS426 2.3 0.9 1.0
SG K:CYS406 2.3 0.0 1.0
SG K:CYS423 2.4 0.5 1.0
SG K:CYS403 2.4 0.8 1.0
CB K:CYS403 2.9 0.5 1.0
CB K:CYS423 3.1 0.2 1.0
CB K:CYS406 3.3 0.6 1.0
CB K:CYS426 3.3 0.4 1.0
NH2 K:ARG479 3.8 0.5 1.0
N K:CYS406 3.8 0.4 1.0
NH1 K:ARG479 4.0 0.4 1.0
N K:CYS423 4.0 0.8 1.0
CA K:CYS423 4.2 0.5 1.0
CA K:CYS406 4.2 0.2 1.0
CZ K:ARG479 4.3 0.1 1.0
CA K:CYS403 4.4 0.5 1.0
CB K:ILE405 4.6 0.6 1.0
CA K:CYS426 4.7 0.1 1.0
C K:ILE405 4.8 0.0 1.0
C K:CYS403 4.8 0.8 1.0
O K:CYS403 4.9 0.2 1.0
N K:CYS426 4.9 0.5 1.0
N K:ILE405 4.9 0.2 1.0
CA K:ILE405 5.0 0.8 1.0

Zinc binding site 9 out of 10 in 4orh

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Zinc binding site 9 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn501

b:0.9
occ:1.00
 ND1 L:HIS420 2.2 0.8 1.0
SG L:CYS418 2.2 0.3 1.0
SG L:CYS440 2.2 0.3 1.0
SG L:CYS437 2.3 0.3 1.0
CB L:CYS437 3.0 0.0 1.0
CE1 L:HIS420 3.2 0.2 1.0
CB L:CYS418 3.2 0.8 1.0
CG L:HIS420 3.2 0.9 1.0
CB L:CYS440 3.5 0.1 1.0
CB L:HIS420 3.5 0.7 1.0
N L:CYS440 3.8 0.7 1.0
CA L:CYS440 4.2 1.0 1.0
NE2 L:HIS420 4.3 0.4 1.0
O L:CYS418 4.3 0.9 1.0
CD2 L:HIS420 4.3 0.5 1.0
CA L:CYS418 4.4 0.1 1.0
CA L:CYS437 4.5 0.6 1.0
C L:CYS418 4.5 0.9 1.0
N L:HIS420 4.5 0.7 1.0
CB L:ILE439 4.7 0.8 1.0
CA L:HIS420 4.7 0.0 1.0
C L:ILE439 4.8 0.4 1.0
C L:CYS440 4.9 0.5 1.0
N L:ARG441 4.9 0.6 1.0
N L:ILE439 5.0 0.5 1.0

Zinc binding site 10 out of 10 in 4orh

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Zinc binding site 10 out of 10 in the Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of RNF8 Bound to the UBC13/MMS2 Heterodimer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn502

b:0.9
occ:1.00
 SG L:CYS426 2.3 0.7 1.0
SG L:CYS406 2.3 0.3 1.0
SG L:CYS403 2.3 0.6 1.0
SG L:CYS423 2.3 0.7 1.0
CB L:CYS403 3.0 0.8 1.0
CB L:CYS423 3.1 0.5 1.0
CB L:CYS426 3.2 0.6 1.0
CB L:CYS406 3.3 0.4 1.0
N L:CYS406 3.8 0.0 1.0
N L:CYS423 4.0 0.3 1.0
NH2 L:ARG479 4.0 0.1 1.0
NH1 L:ARG479 4.0 0.1 1.0
CA L:CYS423 4.1 0.2 1.0
CA L:CYS406 4.2 0.5 1.0
CA L:CYS403 4.4 0.4 1.0
CZ L:ARG479 4.5 0.2 1.0
CA L:CYS426 4.6 0.3 1.0
CB L:ILE405 4.6 0.5 1.0
C L:ILE405 4.8 0.1 1.0
N L:CYS426 4.8 0.4 1.0
C L:CYS403 4.9 0.8 1.0
N L:ILE405 5.0 0.4 1.0

Reference:

S.J.Campbell, R.A.Edwards, C.C.Leung, D.Neculai, C.D.Hodge, S.Dhe-Paganon, J.N.Glover. Molecular Insights Into the Function of Ring Finger (Rnf)-Containing Proteins HRNF8 and HRNF168 in UBC13/MMS2-Dependent Ubiquitylation. J.Biol.Chem. V. 287 23900 2012.
ISSN: ISSN 0021-9258
PubMed: 22589545
DOI: 10.1074/JBC.M112.359653
Page generated: Sun Oct 27 04:00:07 2024

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