Zinc in PDB 7m4n: Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin

Enzymatic activity of Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin

All present enzymatic activity of Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin, PDB code: 7m4n was solved by T.R.Cotton, B.C.Lechtenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.21 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.791, 84.414, 96.418, 90, 102.15, 90
R / Rfree (%) 21.6 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin (pdb code 7m4n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin, PDB code: 7m4n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7m4n

Go back to Zinc Binding Sites List in 7m4n
Zinc binding site 1 out of 6 in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:47.9
occ:1.00
SG A:CYS695 2.2 40.9 1.0
SG A:CYS693 2.3 47.1 1.0
SG A:CYS678 2.4 52.7 1.0
SG A:CYS675 2.4 57.4 1.0
CB A:CYS693 3.2 43.8 1.0
CB A:CYS675 3.3 44.9 1.0
CB A:CYS695 3.3 47.9 1.0
CB A:CYS678 3.6 44.1 1.0
N A:CYS678 3.8 54.7 1.0
N A:CYS695 4.0 50.5 1.0
CA A:CYS695 4.2 52.9 1.0
CA A:CYS678 4.3 58.4 1.0
CB A:LYS677 4.4 67.8 1.0
CA A:CYS693 4.6 41.7 1.0
N A:ARG694 4.7 49.9 1.0
CA A:CYS675 4.7 53.0 1.0
CB A:ALA697 4.8 47.1 1.0
C A:CYS693 4.8 49.4 1.0
C A:LYS677 4.8 65.3 1.0
OG1 A:THR680 4.9 59.4 1.0
N A:GLY679 4.9 48.4 1.0
N A:LYS677 4.9 67.1 1.0
C A:CYS695 4.9 57.5 1.0
CA A:LYS677 5.0 65.3 1.0
C A:CYS678 5.0 51.9 1.0

Zinc binding site 2 out of 6 in 7m4n

Go back to Zinc Binding Sites List in 7m4n
Zinc binding site 2 out of 6 in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:36.8
occ:1.00
NE2 A:HIS712 2.1 33.6 1.0
SG A:CYS700 2.1 30.5 1.0
SG A:CYS703 2.3 36.0 1.0
SG A:CYS730 2.4 41.2 1.0
CE1 A:HIS712 3.0 39.8 1.0
CB A:CYS700 3.1 30.7 1.0
CD2 A:HIS712 3.1 34.5 1.0
CB A:CYS730 3.3 37.8 1.0
CB A:CYS703 3.5 33.0 1.0
N A:CYS703 3.8 35.4 1.0
ND1 A:HIS712 4.2 37.7 1.0
CA A:CYS703 4.2 38.7 1.0
CG A:HIS712 4.2 37.1 1.0
CA A:CYS700 4.5 37.7 1.0
CB A:LEU702 4.6 32.8 1.0
CE1 A:PHE713 4.6 34.0 1.0
CA A:CYS730 4.7 28.9 1.0
C A:LEU702 4.8 38.5 1.0
C A:CYS700 5.0 32.4 1.0
N A:LEU702 5.0 35.6 1.0
C A:CYS703 5.0 31.9 1.0

Zinc binding site 3 out of 6 in 7m4n

Go back to Zinc Binding Sites List in 7m4n
Zinc binding site 3 out of 6 in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:28.5
occ:1.00
ND1 A:HIS716 2.1 32.1 1.0
SG A:CYS724 2.2 34.5 1.0
SG A:CYS727 2.4 40.2 1.0
SG A:CYS714 2.4 30.4 1.0
CE1 A:HIS716 3.0 45.8 1.0
CG A:HIS716 3.1 37.0 1.0
CB A:CYS714 3.4 23.3 1.0
CB A:CYS724 3.4 35.0 1.0
CB A:HIS716 3.5 35.3 1.0
CB A:CYS727 3.6 30.6 1.0
N A:CYS727 3.8 35.5 1.0
CA A:CYS714 4.0 29.4 1.0
N A:HIS716 4.1 31.0 1.0
NE2 A:HIS716 4.1 46.1 1.0
CA A:CYS727 4.1 36.5 1.0
CD2 A:HIS716 4.2 39.0 1.0
O A:CYS727 4.4 36.6 1.0
CA A:HIS716 4.4 34.6 1.0
CB A:GLU726 4.4 43.3 1.0
O A:HOH905 4.4 28.3 1.0
C A:CYS727 4.5 36.5 1.0
C A:GLU726 4.5 40.8 1.0
N A:GLN715 4.5 33.8 1.0
O A:HOH914 4.5 33.0 1.0
C A:CYS714 4.5 30.3 1.0
NH2 A:ARG718 4.8 37.3 1.0
CA A:CYS724 4.8 36.1 1.0
N A:GLU726 4.8 55.8 1.0
CA A:GLU726 4.8 42.9 1.0
NE A:ARG718 5.0 46.0 1.0

Zinc binding site 4 out of 6 in 7m4n

Go back to Zinc Binding Sites List in 7m4n
Zinc binding site 4 out of 6 in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:103.1
occ:1.00
SG B:CYS695 2.3 79.9 1.0
SG B:CYS678 2.3 87.9 1.0
SG B:CYS693 2.4 82.8 1.0
SG B:CYS675 2.4 98.3 1.0
CB B:CYS675 3.1 57.0 1.0
CB B:CYS693 3.2 73.4 1.0
CB B:CYS695 3.4 83.8 1.0
CB B:CYS678 3.5 87.3 1.0
N B:CYS678 3.6 91.2 1.0
N B:CYS695 4.0 87.6 1.0
CA B:CYS678 4.2 92.1 1.0
CA B:CYS695 4.3 87.2 1.0
CB B:LYS677 4.3 85.4 1.0
CA B:CYS675 4.6 56.3 1.0
CA B:CYS693 4.6 66.5 1.0
C B:LYS677 4.7 90.6 1.0
N B:LYS677 4.7 76.7 1.0
N B:ARG694 4.8 93.8 1.0
N B:GLY679 4.8 77.5 1.0
CA B:LYS677 4.8 86.8 1.0
C B:CYS693 4.8 76.5 1.0
C B:CYS678 4.9 85.0 1.0
C B:CYS675 4.9 73.7 1.0
CB B:ALA697 5.0 90.9 1.0

Zinc binding site 5 out of 6 in 7m4n

Go back to Zinc Binding Sites List in 7m4n
Zinc binding site 5 out of 6 in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:34.4
occ:1.00
NE2 B:HIS712 2.0 36.2 1.0
SG B:CYS700 2.1 37.1 1.0
SG B:CYS703 2.3 39.1 1.0
SG B:CYS730 2.4 36.4 1.0
CE1 B:HIS712 3.0 39.4 1.0
CB B:CYS700 3.0 38.4 1.0
CD2 B:HIS712 3.1 38.2 1.0
CB B:CYS730 3.3 35.0 1.0
CB B:CYS703 3.4 36.2 1.0
N B:CYS703 3.7 34.1 1.0
ND1 B:HIS712 4.1 43.4 1.0
CA B:CYS703 4.2 39.0 1.0
CG B:HIS712 4.2 42.7 1.0
CA B:CYS700 4.5 43.0 1.0
CB B:LEU702 4.5 40.1 1.0
CA B:CYS730 4.8 36.4 1.0
C B:LEU702 4.8 35.5 1.0
CE1 B:PHE713 4.9 32.9 1.0
C B:CYS700 4.9 39.9 1.0
N B:LEU702 5.0 40.4 1.0
C B:CYS703 5.0 31.9 1.0
CA B:LEU702 5.0 37.1 1.0

Zinc binding site 6 out of 6 in 7m4n

Go back to Zinc Binding Sites List in 7m4n
Zinc binding site 6 out of 6 in the Crystal Structure of Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin


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 Rbr E3 Ligase RNF216 in Complex with K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn803

b:35.2
occ:1.00
ND1 B:HIS716 2.1 43.2 1.0
SG B:CYS724 2.2 35.5 1.0
SG B:CYS727 2.3 45.1 1.0
SG B:CYS714 2.4 39.5 1.0
CE1 B:HIS716 3.0 54.2 1.0
CG B:HIS716 3.2 44.8 1.0
CB B:CYS714 3.3 33.6 1.0
CB B:CYS724 3.4 41.4 1.0
CB B:CYS727 3.5 33.0 1.0
CB B:HIS716 3.6 42.6 1.0
N B:CYS727 3.8 45.2 1.0
CA B:CYS714 3.9 37.3 1.0
CA B:CYS727 4.1 39.5 1.0
NE2 B:HIS716 4.2 54.6 1.0
N B:HIS716 4.2 42.4 1.0
CD2 B:HIS716 4.3 48.9 1.0
O B:CYS727 4.3 43.7 1.0
C B:CYS727 4.4 38.0 1.0
C B:CYS714 4.5 38.6 1.0
O B:HOH906 4.5 36.9 1.0
N B:GLN715 4.5 42.1 1.0
C B:GLU726 4.5 42.5 1.0
CB B:GLU726 4.5 47.8 1.0
CA B:HIS716 4.6 46.4 1.0
CA B:CYS724 4.8 40.9 1.0
N B:GLU726 4.8 50.2 1.0
CA B:GLU726 4.9 43.3 1.0
NH2 B:ARG718 4.9 51.7 1.0

Reference:

T.R.Cotton, S.A.Cobbold, J.P.Bernardini, L.W.Richardson, X.S.Wang, B.C.Lechtenberg. Structural Basis of K63-Ubiquitin Chain Formation By the Gordon-Holmes Syndrome Rbr E3 Ubiquitin Ligase RNF216 Mol.Cell 2022.
ISSN: ISSN 1097-2765
Page generated: Tue Oct 29 23:08:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy