Atomistry » Zinc » PDB 4ojx-4ox3 » 4orh
Atomistry »
  Zinc »
    PDB 4ojx-4ox3 »
      4orh »

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

Go back to Zinc Binding Sites List in 4orh
Zinc binding site 1 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 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

Go back to Zinc Binding Sites List in 4orh
Zinc binding site 2 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 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

Go back to Zinc Binding Sites List in 4orh
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

Go back to Zinc Binding Sites List in 4orh
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

Go back to Zinc Binding Sites List in 4orh
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

Go back to Zinc Binding Sites List in 4orh
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

Go back to Zinc Binding Sites List in 4orh
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

Go back to Zinc Binding Sites List in 4orh
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

Go back to Zinc Binding Sites List in 4orh
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

Go back to Zinc Binding Sites List in 4orh
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy