Zinc in PDB 8e0q: Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form

Enzymatic activity of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form

All present enzymatic activity of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form:
2.3.2.26;

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form (pdb code 8e0q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form, PDB code: 8e0q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8e0q

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Zinc binding site 1 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2801

b:74.3
occ:1.00
 SG A:CYS1232 2.3 84.4 1.0
SG A:CYS1179 2.3 64.4 1.0
SG A:CYS1208 2.3 63.4 1.0
SG A:CYS1211 2.3 77.0 1.0
CB A:CYS1211 3.3 55.4 1.0
CB A:CYS1232 3.4 70.9 1.0
CB A:CYS1208 3.6 58.4 1.0
CB A:CYS1179 3.7 57.9 1.0
N A:CYS1208 3.8 57.5 1.0
N A:SER1180 4.1 67.0 1.0
CA A:CYS1179 4.1 55.5 1.0
N A:CYS1211 4.2 69.0 1.0
CA A:CYS1208 4.3 54.6 1.0
ZN A:ZN2802 4.3 88.0 1.0
CB A:CYS1234 4.3 81.7 1.0
CA A:CYS1211 4.3 54.5 1.0
C A:CYS1179 4.6 67.3 1.0
CA A:CYS1232 4.8 67.8 1.0
N A:PHE1181 4.8 50.5 1.0
C A:CYS1207 4.8 65.0 1.0
O A:CYS1208 4.9 75.1 1.0
C A:CYS1208 4.9 64.8 1.0
CA A:CYS1207 4.9 63.1 1.0
SG A:CYS1240 5.0 54.7 1.0

Zinc binding site 2 out of 6 in 8e0q

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Zinc binding site 2 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2802

b:88.0
occ:1.00
 SG A:CYS1240 2.3 54.7 1.0
SG A:CYS1215 2.3 69.8 1.0
SG A:CYS1211 2.3 77.0 1.0
SG A:CYS1234 2.3 100.1 1.0
CB A:CYS1234 3.1 81.7 1.0
CB A:CYS1215 3.4 49.6 1.0
CB A:CYS1211 3.5 55.4 1.0
CB A:CYS1240 3.5 54.5 1.0
OG1 A:THR1242 3.8 57.5 1.0
CA A:CYS1240 3.9 55.1 1.0
CA A:CYS1211 4.3 54.5 1.0
ZN A:ZN2801 4.3 74.3 1.0
CB A:THR1242 4.5 49.6 1.0
CA A:CYS1234 4.6 72.6 1.0
N A:LYS1241 4.7 56.6 1.0
C A:CYS1240 4.7 53.1 1.0
CA A:CYS1215 4.8 39.1 1.0
N A:THR1242 4.8 46.5 1.0
C A:CYS1234 4.9 73.5 1.0
O A:CYS1211 5.0 62.8 1.0

Zinc binding site 3 out of 6 in 8e0q

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Zinc binding site 3 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2803

b:82.5
occ:1.00
 ND1 A:HIS1216 2.0 48.9 1.0
ND1 A:HIS1219 2.0 52.0 1.0
SG A:CYS1199 2.3 59.4 1.0
SG A:CYS1196 2.3 69.3 1.0
CE1 A:HIS1216 2.8 50.8 1.0
CE1 A:HIS1219 3.0 52.3 1.0
CG A:HIS1219 3.1 49.5 1.0
CG A:HIS1216 3.2 39.9 1.0
CB A:CYS1199 3.2 62.4 1.0
CB A:HIS1219 3.4 52.6 1.0
CB A:CYS1196 3.6 67.6 1.0
CB A:HIS1216 3.7 40.0 1.0
N A:CYS1199 3.7 63.5 1.0
NE2 A:HIS1216 4.0 38.9 1.0
CA A:CYS1199 4.1 64.3 1.0
NE2 A:HIS1219 4.1 58.2 1.0
CD2 A:HIS1219 4.2 52.1 1.0
CD2 A:HIS1216 4.2 46.9 1.0
CA A:HIS1216 4.3 36.6 1.0
CB A:THR1198 4.6 60.4 1.0
C A:THR1198 4.7 57.8 1.0
CG2 A:THR1198 4.9 63.6 1.0
CA A:CYS1196 4.9 66.0 1.0
CA A:HIS1219 4.9 47.4 1.0

Zinc binding site 4 out of 6 in 8e0q

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Zinc binding site 4 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2801

b:67.0
occ:1.00
 SG B:CYS1232 2.3 78.8 1.0
SG B:CYS1179 2.3 60.3 1.0
SG B:CYS1208 2.3 54.0 1.0
SG B:CYS1211 2.3 65.2 1.0
CB B:CYS1211 3.3 49.8 1.0
CB B:CYS1232 3.4 58.5 1.0
CB B:CYS1208 3.7 46.0 1.0
CB B:CYS1179 3.7 50.1 1.0
N B:CYS1208 3.8 42.5 1.0
N B:SER1180 4.0 54.5 1.0
CA B:CYS1179 4.2 44.8 1.0
N B:CYS1211 4.3 60.4 1.0
ZN B:ZN2802 4.3 96.6 1.0
CA B:CYS1208 4.3 38.0 1.0
CB B:CYS1234 4.3 71.1 1.0
CA B:CYS1211 4.4 49.7 1.0
OG1 B:THR1242 4.5 48.8 1.0
C B:CYS1179 4.6 55.6 1.0
N B:PHE1181 4.8 43.5 1.0
CA B:CYS1232 4.8 53.8 1.0
C B:CYS1207 4.9 46.0 1.0
CB B:SER1180 4.9 47.8 1.0
C B:CYS1208 5.0 51.9 1.0
CA B:CYS1207 5.0 40.3 1.0
CA B:SER1180 5.0 46.8 1.0

Zinc binding site 5 out of 6 in 8e0q

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Zinc binding site 5 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2802

b:96.6
occ:1.00
 SG B:CYS1240 2.3 63.9 1.0
SG B:CYS1215 2.3 70.0 1.0
SG B:CYS1211 2.3 65.2 1.0
SG B:CYS1234 2.3 94.8 1.0
CB B:CYS1234 3.2 71.1 1.0
CB B:CYS1215 3.4 51.6 1.0
CB B:CYS1240 3.4 59.6 1.0
CB B:CYS1211 3.4 49.8 1.0
OG1 B:THR1242 3.5 48.8 1.0
CA B:CYS1240 3.8 59.0 1.0
CA B:CYS1211 4.2 49.7 1.0
ZN B:ZN2801 4.3 67.0 1.0
CA B:CYS1234 4.6 65.0 1.0
N B:LYS1241 4.6 59.7 1.0
C B:CYS1240 4.7 60.9 1.0
CB B:THR1242 4.7 46.4 1.0
CA B:CYS1215 4.8 48.6 1.0
CG2 B:THR1242 4.8 49.2 1.0
C B:CYS1234 4.9 65.9 1.0
N B:THR1242 4.9 39.0 1.0
N B:CYS1240 5.0 56.6 1.0
O B:LYS1239 5.0 69.0 1.0

Zinc binding site 6 out of 6 in 8e0q

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Zinc binding site 6 out of 6 in the Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Human UBR5 Hect-Type E3 Ubiquitin Ligase in A C2 Symmetric Dimeric Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2803

b:87.9
occ:1.00
 ND1 B:HIS1216 2.0 50.5 1.0
ND1 B:HIS1219 2.0 58.7 1.0
SG B:CYS1199 2.3 60.5 1.0
SG B:CYS1196 2.3 65.5 1.0
CE1 B:HIS1216 2.8 55.1 1.0
CG B:HIS1219 3.0 52.5 1.0
CE1 B:HIS1219 3.1 62.8 1.0
CG B:HIS1216 3.2 42.9 1.0
CB B:HIS1219 3.2 53.1 1.0
CB B:CYS1199 3.3 60.2 1.0
N B:CYS1199 3.6 64.7 1.0
CB B:CYS1196 3.7 63.7 1.0
CB B:HIS1216 3.7 45.2 1.0
NE2 B:HIS1216 4.0 46.1 1.0
CA B:CYS1199 4.1 61.4 1.0
CD2 B:HIS1219 4.1 55.3 1.0
NE2 B:HIS1219 4.1 64.0 1.0
CD2 B:HIS1216 4.2 49.6 1.0
CB B:THR1198 4.3 61.5 1.0
CA B:HIS1216 4.4 45.8 1.0
C B:THR1198 4.6 60.0 1.0
CG2 B:THR1198 4.6 62.0 1.0
CA B:HIS1219 4.8 51.7 1.0
CA B:THR1198 4.8 58.0 1.0
N B:THR1198 4.9 57.7 1.0
CA B:CYS1196 5.0 61.2 1.0

Reference:

F.Wang, Q.He, W.Zhan, Z.Yu, E.Finkin-Groner, X.Ma, G.Lin, H.Li. Structure of the Human UBR5 E3 Ubiquitin Ligase Structure 2023.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2023.03.010
Page generated: Wed Oct 30 19:23:47 2024

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