Zinc in PDB 7m4m: Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin

Enzymatic activity of Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin

All present enzymatic activity of Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin:
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin, PDB code: 7m4m 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) 47.46 / 2.39
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.871, 81.871, 248.656, 90, 90, 90
R / Rfree (%) 20 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin (pdb code 7m4m). 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 Rbr E3 Ligase RNF216 with Ubiquitin, PDB code: 7m4m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7m4m

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Zinc binding site 1 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with 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 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.0
occ:1.00
 SG A:CYS623 2.2 43.7 1.0
SG A:CYS605 2.2 45.6 1.0
SG A:CYS628 2.3 43.4 1.0
SG A:CYS608 2.3 45.8 1.0
CB A:CYS605 3.0 30.0 1.0
CB A:CYS628 3.0 45.5 1.0
CB A:CYS623 3.1 33.9 1.0
CB A:CYS608 3.7 44.0 1.0
N A:CYS608 3.9 54.2 1.0
CA A:CYS608 4.3 32.7 1.0
CA A:CYS628 4.4 38.5 1.0
CA A:CYS605 4.5 37.5 1.0
CA A:CYS623 4.5 30.1 1.0
CB A:ASN625 4.5 44.6 1.0
CB A:PHE610 4.7 29.2 1.0
CB A:SER607 4.7 35.7 1.0
N A:ARG629 4.7 53.7 1.0
C A:CYS628 4.8 43.8 1.0
C A:CYS608 4.9 42.7 1.0
N A:PHE610 4.9 42.6 1.0
N A:SER609 4.9 40.5 1.0
N A:LYS630 4.9 41.9 1.0
C A:SER607 5.0 40.9 1.0

Zinc binding site 2 out of 10 in 7m4m

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Zinc binding site 2 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with 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 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:59.0
occ:1.00
 NE2 A:HIS643 2.1 50.9 1.0
SG A:CYS636 2.3 45.6 1.0
SG A:CYS648 2.3 56.5 1.0
SG A:CYS633 2.4 58.0 1.0
CD2 A:HIS643 2.9 49.6 1.0
CB A:CYS633 3.2 45.2 1.0
CE1 A:HIS643 3.2 50.5 1.0
CB A:CYS648 3.5 61.5 1.0
CB A:CYS636 3.6 55.2 1.0
CA A:CYS648 3.8 62.8 1.0
N A:CYS636 4.0 61.7 1.0
CG A:HIS643 4.1 50.7 1.0
ND1 A:HIS643 4.2 51.7 1.0
N A:CYS648 4.3 54.9 1.0
CA A:CYS636 4.4 46.6 1.0
CA A:CYS633 4.7 41.4 1.0
CB A:LYS635 4.8 56.2 1.0
N A:GLY638 5.0 33.4 1.0
C A:CYS636 5.0 41.6 1.0
N A:LYS635 5.0 50.4 1.0

Zinc binding site 3 out of 10 in 7m4m

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Zinc binding site 3 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with 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 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:49.7
occ:1.00
 SG A:CYS678 2.3 56.8 1.0
SG A:CYS695 2.3 50.2 1.0
SG A:CYS675 2.3 33.4 1.0
SG A:CYS693 2.3 46.1 1.0
CB A:CYS675 3.1 35.8 1.0
CB A:CYS695 3.2 33.9 1.0
CB A:CYS678 3.3 40.3 1.0
CB A:CYS693 3.3 43.1 1.0
N A:CYS678 3.7 45.2 1.0
N A:CYS695 4.1 47.5 1.0
CA A:CYS678 4.1 40.2 1.0
CA A:CYS695 4.3 41.0 1.0
CA A:CYS675 4.5 32.8 1.0
CB A:LYS677 4.7 38.7 1.0
CA A:CYS693 4.7 33.9 1.0
C A:CYS678 4.7 39.1 1.0
N A:GLY679 4.8 41.6 1.0
OG1 A:THR680 4.8 45.0 1.0
C A:LYS677 4.8 43.7 1.0
CB A:THR680 4.9 39.0 1.0
N A:ARG694 4.9 44.0 1.0
CB A:ALA697 4.9 33.3 1.0
C A:CYS693 5.0 48.0 1.0
N A:THR680 5.0 33.8 1.0

Zinc binding site 4 out of 10 in 7m4m

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Zinc binding site 4 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with 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 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn804

b:51.9
occ:1.00
 SG A:CYS700 2.1 57.6 1.0
NE2 A:HIS712 2.1 33.0 1.0
SG A:CYS703 2.3 43.2 1.0
SG A:CYS730 2.3 55.7 1.0
CB A:CYS700 2.9 51.4 1.0
CD2 A:HIS712 2.9 43.4 1.0
CB A:CYS730 3.1 47.8 1.0
CE1 A:HIS712 3.2 43.2 1.0
CB A:CYS703 3.7 55.8 1.0
N A:CYS703 4.0 56.5 1.0
CG A:HIS712 4.1 40.3 1.0
ND1 A:HIS712 4.2 54.9 1.0
CA A:CYS700 4.3 40.8 1.0
CA A:CYS703 4.4 48.3 1.0
CE1 A:PHE713 4.5 36.4 1.0
CA A:CYS730 4.5 43.7 1.0
CB A:LEU702 4.6 44.9 1.0
N A:CYS730 4.8 54.0 1.0
C A:CYS700 4.8 47.4 1.0
CD1 A:PHE713 4.9 28.8 1.0
O A:CYS700 5.0 48.5 1.0

Zinc binding site 5 out of 10 in 7m4m

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Zinc binding site 5 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with 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 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn805

b:59.0
occ:1.00
 ND1 A:HIS716 2.0 33.9 1.0
SG A:CYS714 2.3 57.5 1.0
SG A:CYS724 2.3 43.1 1.0
SG A:CYS727 2.3 55.7 1.0
CE1 A:HIS716 3.0 60.6 1.0
CG A:HIS716 3.1 50.3 1.0
CB A:CYS714 3.3 54.4 1.0
CB A:HIS716 3.4 55.4 1.0
CB A:CYS727 3.6 56.2 1.0
CB A:CYS724 3.6 57.9 1.0
CA A:CYS714 4.0 42.3 1.0
N A:HIS716 4.0 48.8 1.0
NE2 A:HIS716 4.1 65.0 1.0
N A:CYS727 4.2 50.7 1.0
CD2 A:HIS716 4.2 54.8 1.0
CA A:HIS716 4.4 47.0 1.0
CA A:CYS727 4.4 44.5 1.0
C A:CYS714 4.4 34.5 1.0
N A:GLN715 4.5 42.9 1.0
C A:GLU726 4.8 49.3 1.0
NH1 A:ARG718 4.8 48.2 1.0
NH2 A:ARG729 4.9 66.3 1.0
C A:CYS727 4.9 55.4 1.0
CA A:CYS724 4.9 54.7 1.0
CB A:GLU726 4.9 41.6 1.0

Zinc binding site 6 out of 10 in 7m4m

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Zinc binding site 6 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with 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 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:48.1
occ:1.00
 SG B:CYS623 2.2 57.8 1.0
SG B:CYS628 2.2 48.2 1.0
SG B:CYS605 2.3 37.5 1.0
SG B:CYS608 2.3 58.3 1.0
CB B:CYS628 2.8 54.0 1.0
CB B:CYS605 3.0 32.8 1.0
CB B:CYS623 3.1 38.7 1.0
CB B:CYS608 3.7 42.9 1.0
N B:CYS608 3.9 46.3 1.0
CB B:ASN625 4.2 50.1 1.0
CA B:CYS628 4.3 56.1 1.0
CA B:CYS608 4.3 43.3 1.0
CB B:PHE610 4.4 43.6 1.0
CA B:CYS605 4.5 28.5 1.0
CA B:CYS623 4.5 41.2 1.0
N B:ARG629 4.6 60.6 1.0
N B:PHE610 4.7 47.7 1.0
ND2 B:ASN625 4.7 52.0 1.0
C B:CYS628 4.7 51.9 1.0
CB B:SER607 4.8 51.9 1.0
C B:CYS608 4.8 51.9 1.0
N B:SER609 4.8 49.4 1.0

Zinc binding site 7 out of 10 in 7m4m

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Zinc binding site 7 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin


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 Rbr E3 Ligase RNF216 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:59.3
occ:1.00
 NE2 B:HIS643 2.1 58.2 1.0
SG B:CYS648 2.3 55.1 1.0
SG B:CYS636 2.3 70.9 1.0
SG B:CYS633 2.4 53.7 1.0
CD2 B:HIS643 3.0 55.4 1.0
CE1 B:HIS643 3.2 62.0 1.0
CB B:CYS633 3.3 36.2 1.0
CB B:CYS648 3.5 55.0 1.0
CB B:CYS636 3.7 55.5 1.0
CA B:CYS648 3.8 65.8 1.0
N B:CYS636 4.1 53.5 1.0
N B:CYS648 4.2 64.1 1.0
CG B:HIS643 4.2 62.5 1.0
ND1 B:HIS643 4.3 71.6 1.0
CA B:CYS636 4.4 46.5 1.0
CB B:LYS635 4.7 37.8 1.0
NZ B:LYS635 4.8 76.0 1.0
CA B:CYS633 4.8 41.0 1.0
C B:THR647 4.9 66.6 1.0
CE B:LYS635 5.0 82.5 1.0

Zinc binding site 8 out of 10 in 7m4m

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Zinc binding site 8 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin


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 Rbr E3 Ligase RNF216 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn803

b:57.5
occ:1.00
 SG B:CYS678 2.3 61.2 1.0
SG B:CYS695 2.3 58.6 1.0
SG B:CYS675 2.3 56.2 1.0
SG B:CYS693 2.3 64.1 1.0
CB B:CYS675 3.0 47.5 1.0
CB B:CYS693 3.1 60.9 1.0
CB B:CYS695 3.3 67.5 1.0
CB B:CYS678 3.4 52.6 1.0
N B:CYS678 3.8 50.3 1.0
N B:CYS695 4.1 59.7 1.0
CA B:CYS678 4.1 36.0 1.0
CA B:CYS695 4.3 60.9 1.0
CA B:CYS675 4.5 46.1 1.0
CA B:CYS693 4.5 41.8 1.0
C B:CYS678 4.7 47.8 1.0
CB B:ALA697 4.8 60.4 1.0
CB B:LYS677 4.8 56.0 1.0
N B:GLY679 4.8 46.4 1.0
C B:CYS693 4.8 50.2 1.0
N B:ARG694 4.8 50.2 1.0
OG1 B:THR680 4.9 73.5 1.0
C B:LYS677 4.9 42.3 1.0
CB B:THR680 4.9 54.3 1.0
N B:THR680 5.0 57.3 1.0
C B:CYS675 5.0 54.8 1.0

Zinc binding site 9 out of 10 in 7m4m

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Zinc binding site 9 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin


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 Rbr E3 Ligase RNF216 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn804

b:52.6
occ:1.00
 SG B:CYS700 2.1 48.4 1.0
NE2 B:HIS712 2.1 47.0 1.0
SG B:CYS703 2.2 47.6 1.0
SG B:CYS730 2.3 55.1 1.0
CD2 B:HIS712 2.9 54.3 1.0
CB B:CYS700 3.1 35.3 1.0
CB B:CYS730 3.1 48.6 1.0
CE1 B:HIS712 3.2 56.1 1.0
CB B:CYS703 3.6 46.6 1.0
N B:CYS703 3.9 49.8 1.0
CG B:HIS712 4.1 43.8 1.0
ND1 B:HIS712 4.2 58.8 1.0
CA B:CYS703 4.3 42.3 1.0
CA B:CYS700 4.5 40.4 1.0
CA B:CYS730 4.5 43.5 1.0
CB B:LEU702 4.6 48.2 1.0
CE1 B:PHE713 4.7 43.1 1.0
N B:CYS730 4.8 44.6 1.0
C B:CYS700 4.9 43.0 1.0
C B:LEU702 4.9 36.2 1.0

Zinc binding site 10 out of 10 in 7m4m

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Zinc binding site 10 out of 10 in the Crystal Structure of Rbr E3 Ligase RNF216 with Ubiquitin


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 Rbr E3 Ligase RNF216 with Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn805

b:51.6
occ:1.00
 ND1 B:HIS716 2.0 37.5 1.0
SG B:CYS724 2.2 46.1 1.0
SG B:CYS727 2.2 46.3 1.0
SG B:CYS714 2.3 39.5 1.0
CE1 B:HIS716 3.0 49.5 1.0
CG B:HIS716 3.0 46.4 1.0
CB B:CYS714 3.3 48.5 1.0
CB B:HIS716 3.4 53.5 1.0
CB B:CYS727 3.5 53.5 1.0
CB B:CYS724 3.6 54.8 1.0
N B:CYS727 4.0 41.1 1.0
N B:HIS716 4.1 46.0 1.0
NE2 B:HIS716 4.1 52.9 1.0
CA B:CYS714 4.1 46.6 1.0
CD2 B:HIS716 4.2 47.8 1.0
CA B:CYS727 4.2 47.5 1.0
CA B:HIS716 4.4 38.1 1.0
C B:CYS714 4.5 44.0 1.0
C B:GLU726 4.6 47.9 1.0
N B:GLN715 4.6 50.3 1.0
C B:CYS727 4.8 59.1 1.0
CB B:GLU726 4.8 47.6 1.0
CA B:CYS724 4.9 41.6 1.0
NH2 B:ARG729 5.0 59.4 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 23:08:31 2024

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