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

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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

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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

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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

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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

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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

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