Zinc in PDB 8p82: Cryo-Em Structure of Dimeric UBR5

Enzymatic activity of Cryo-Em Structure of Dimeric UBR5

All present enzymatic activity of Cryo-Em Structure of Dimeric UBR5:
2.3.2.26;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Dimeric UBR5 (pdb code 8p82). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Dimeric UBR5, PDB code: 8p82:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8p82

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of Dimeric UBR5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Dimeric UBR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3000

b:96.5
occ:1.00
 SG A:CYS1211 2.2 102.5 1.0
SG A:CYS1232 2.2 103.2 1.0
SG A:CYS1208 2.3 97.7 1.0
SG A:CYS1179 2.3 82.1 1.0
CB A:CYS1232 3.2 96.7 1.0
CB A:CYS1179 3.5 82.4 1.0
CB A:CYS1211 3.6 101.1 1.0
CB A:CYS1208 3.6 99.2 1.0
N A:CYS1208 3.9 104.7 1.0
CA A:CYS1179 4.1 77.4 1.0
CA A:CYS1208 4.3 98.1 1.0
N A:CYS1211 4.3 92.0 1.0
ZN A:ZN3001 4.4 102.9 1.0
CA A:CYS1211 4.5 95.5 1.0
N A:SER1180 4.5 88.7 1.0
CB A:CYS1234 4.6 109.0 1.0
O A:CYS1208 4.6 97.9 1.0
CA A:CYS1232 4.6 109.3 1.0
C A:CYS1179 4.7 85.8 1.0
OG1 A:THR1242 4.7 93.8 1.0
OG A:SER1180 4.8 100.8 1.0
C A:CYS1208 4.8 95.2 1.0
CB A:CYS1207 4.9 123.0 1.0
C A:CYS1207 4.9 118.2 1.0

Zinc binding site 2 out of 6 in 8p82

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of Dimeric UBR5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Dimeric UBR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3001

b:102.9
occ:1.00
 SG A:CYS1234 2.2 99.0 1.0
SG A:CYS1240 2.3 105.2 1.0
SG A:CYS1215 2.4 105.0 1.0
SG A:CYS1211 2.4 102.5 1.0
OG1 A:THR1242 3.1 93.8 1.0
CB A:CYS1211 3.1 101.1 1.0
CB A:CYS1215 3.3 103.9 1.0
CB A:CYS1234 3.4 109.0 1.0
CB A:CYS1240 3.4 107.8 1.0
CA A:CYS1211 3.8 95.5 1.0
CA A:CYS1240 3.9 105.5 1.0
ZN A:ZN3000 4.4 96.5 1.0
N A:LYS1241 4.4 92.9 1.0
CB A:THR1242 4.4 91.4 1.0
C A:CYS1240 4.4 96.6 1.0
CA A:CYS1234 4.6 115.7 1.0
C A:CYS1234 4.6 116.9 1.0
N A:THR1242 4.6 87.0 1.0
CG2 A:THR1242 4.7 97.7 1.0
CA A:CYS1215 4.8 97.5 1.0
N A:CYS1211 4.8 92.0 1.0
O A:CYS1234 4.8 120.0 1.0
C A:CYS1211 4.8 96.0 1.0
N A:TRP1235 4.9 121.1 1.0
O A:CYS1211 5.0 97.4 1.0

Zinc binding site 3 out of 6 in 8p82

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of Dimeric UBR5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Dimeric UBR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:115.3
occ:1.00
 ND1 A:HIS1216 2.0 107.6 1.0
ND1 A:HIS1219 2.0 109.5 1.0
SG A:CYS1199 2.0 148.7 1.0
SG A:CYS1196 2.1 129.8 1.0
CE1 A:HIS1219 2.7 108.6 1.0
CE1 A:HIS1216 2.9 115.4 1.0
CG A:HIS1216 2.9 105.3 1.0
CG A:HIS1219 3.0 109.6 1.0
CB A:HIS1216 3.3 102.8 1.0
CB A:CYS1199 3.3 154.4 1.0
CB A:HIS1219 3.5 112.6 1.0
CB A:CYS1196 3.6 136.4 1.0
NE2 A:HIS1219 3.8 110.8 1.0
NE2 A:HIS1216 3.9 114.1 1.0
CD2 A:HIS1216 3.9 112.5 1.0
CA A:HIS1216 3.9 99.5 1.0
CD2 A:HIS1219 4.0 109.4 1.0
N A:CYS1199 4.3 144.9 1.0
CA A:CYS1199 4.4 151.3 1.0
CB A:THR1198 4.5 130.7 1.0
O A:HIS1216 4.7 104.5 1.0
SG A:CYS1221 4.7 141.4 1.0
O A:CYS1196 4.8 149.9 1.0
CA A:CYS1196 4.8 141.8 1.0
C A:HIS1216 4.8 100.2 1.0
C A:THR1198 4.9 144.3 1.0
O A:CYS1215 5.0 104.6 1.0
CG2 A:THR1198 5.0 128.8 1.0
C A:CYS1196 5.0 146.1 1.0

Zinc binding site 4 out of 6 in 8p82

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of Dimeric UBR5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Dimeric UBR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3000

b:96.5
occ:1.00
 SG B:CYS1211 2.2 102.5 1.0
SG B:CYS1232 2.2 103.2 1.0
SG B:CYS1208 2.3 97.7 1.0
SG B:CYS1179 2.3 82.1 1.0
CB B:CYS1232 3.2 96.7 1.0
CB B:CYS1179 3.5 82.4 1.0
CB B:CYS1211 3.6 101.1 1.0
CB B:CYS1208 3.6 99.2 1.0
N B:CYS1208 3.9 104.7 1.0
CA B:CYS1179 4.1 77.4 1.0
CA B:CYS1208 4.3 98.1 1.0
N B:CYS1211 4.3 92.0 1.0
ZN B:ZN3001 4.4 102.9 1.0
CA B:CYS1211 4.5 95.5 1.0
N B:SER1180 4.5 88.7 1.0
CB B:CYS1234 4.6 109.0 1.0
O B:CYS1208 4.6 97.9 1.0
CA B:CYS1232 4.6 109.3 1.0
C B:CYS1179 4.7 85.8 1.0
OG1 B:THR1242 4.8 93.8 1.0
OG B:SER1180 4.8 100.8 1.0
C B:CYS1208 4.8 95.2 1.0
CB B:CYS1207 4.9 123.0 1.0
C B:CYS1207 4.9 118.2 1.0

Zinc binding site 5 out of 6 in 8p82

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of Dimeric UBR5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Dimeric UBR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:102.9
occ:1.00
 SG B:CYS1234 2.2 99.0 1.0
SG B:CYS1240 2.3 105.2 1.0
SG B:CYS1215 2.4 105.0 1.0
SG B:CYS1211 2.4 102.5 1.0
OG1 B:THR1242 3.1 93.8 1.0
CB B:CYS1211 3.1 101.1 1.0
CB B:CYS1215 3.3 103.9 1.0
CB B:CYS1234 3.4 109.0 1.0
CB B:CYS1240 3.4 107.8 1.0
CA B:CYS1211 3.8 95.5 1.0
CA B:CYS1240 3.9 105.5 1.0
ZN B:ZN3000 4.4 96.5 1.0
N B:LYS1241 4.4 92.9 1.0
CB B:THR1242 4.4 91.4 1.0
C B:CYS1240 4.4 96.6 1.0
CA B:CYS1234 4.6 115.7 1.0
C B:CYS1234 4.6 116.9 1.0
N B:THR1242 4.6 87.0 1.0
CG2 B:THR1242 4.7 97.7 1.0
CA B:CYS1215 4.8 97.5 1.0
N B:CYS1211 4.8 92.0 1.0
O B:CYS1234 4.8 120.0 1.0
C B:CYS1211 4.8 96.0 1.0
N B:TRP1235 4.9 121.1 1.0
O B:CYS1211 5.0 97.4 1.0

Zinc binding site 6 out of 6 in 8p82

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of Dimeric UBR5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Dimeric UBR5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:115.3
occ:1.00
 ND1 B:HIS1216 2.0 107.6 1.0
ND1 B:HIS1219 2.0 109.5 1.0
SG B:CYS1199 2.0 148.7 1.0
SG B:CYS1196 2.1 129.8 1.0
CE1 B:HIS1219 2.7 108.6 1.0
CE1 B:HIS1216 2.9 115.4 1.0
CG B:HIS1216 2.9 105.3 1.0
CG B:HIS1219 3.0 109.6 1.0
CB B:HIS1216 3.3 102.8 1.0
CB B:CYS1199 3.3 154.4 1.0
CB B:HIS1219 3.5 112.6 1.0
CB B:CYS1196 3.6 136.4 1.0
NE2 B:HIS1219 3.8 110.8 1.0
NE2 B:HIS1216 3.9 114.1 1.0
CD2 B:HIS1216 3.9 112.5 1.0
CA B:HIS1216 3.9 99.5 1.0
CD2 B:HIS1219 4.0 109.4 1.0
N B:CYS1199 4.3 144.9 1.0
CA B:CYS1199 4.4 151.3 1.0
CB B:THR1198 4.5 130.7 1.0
O B:HIS1216 4.7 104.5 1.0
SG B:CYS1221 4.7 141.4 1.0
O B:CYS1196 4.8 149.9 1.0
CA B:CYS1196 4.8 141.8 1.0
C B:HIS1216 4.8 100.2 1.0
C B:THR1198 4.9 144.3 1.0
O B:CYS1215 5.0 104.6 1.0
CG2 B:THR1198 5.0 128.8 1.0
C B:CYS1196 5.0 146.1 1.0

Reference:

N.A.Na, J.D.Aguirre, L.Kater, G.Kempf, S.Cavadini, N.H.Thoma. N/A N/A.
Page generated: Fri Jul 28 07:23:31 2023

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