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Zinc in PDB 7mey: Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron

Enzymatic activity of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron

All present enzymatic activity of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron:
2.3.2.23; 2.3.2.27;

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron (pdb code 7mey). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron, PDB code: 7mey:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7mey

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Zinc binding site 1 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:121.0
occ:1.00
 ND1 A:HIS160 2.1 82.8 1.0
ND1 A:HIS157 2.1 88.5 1.0
CE1 A:HIS157 2.2 88.5 1.0
CG A:HIS157 2.2 88.5 1.0
SG A:CYS136 2.3 78.0 1.0
SG A:CYS139 2.3 84.6 1.0
NE2 A:HIS157 2.3 88.5 1.0
CD2 A:HIS157 2.4 88.5 1.0
CE1 A:HIS160 2.7 82.8 1.0
CB A:CYS139 3.2 84.6 1.0
CB A:HIS157 3.3 88.5 1.0
CG A:HIS160 3.3 82.8 1.0
CB A:CYS136 3.5 78.0 1.0
N A:CYS139 3.7 84.6 1.0
CB A:HIS160 3.9 82.8 1.0
NE2 A:HIS160 4.0 82.8 1.0
CA A:CYS139 4.1 84.6 1.0
CD2 A:HIS160 4.3 82.8 1.0
CA A:HIS157 4.4 88.5 1.0
C A:GLU138 4.7 78.1 1.0
CA A:CYS136 4.8 78.0 1.0
CB A:GLU138 4.8 78.1 1.0
N A:GLU138 5.0 78.1 1.0

Zinc binding site 2 out of 7 in 7mey

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Zinc binding site 2 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:117.8
occ:1.00
 SG A:CYS148 2.2 80.7 1.0
SG A:CYS151 2.3 93.8 1.0
SG A:CYS175 2.3 76.6 1.0
SG A:CYS123 2.3 90.3 1.0
CB A:CYS123 2.9 90.3 1.0
CB A:CYS151 3.0 93.8 1.0
CB A:CYS175 3.0 76.6 1.0
CB A:CYS148 3.6 80.7 1.0
CB A:CYS177 4.1 88.7 1.0
CA A:CYS151 4.2 93.8 1.0
N A:CYS148 4.3 80.7 1.0
N A:CYS151 4.3 93.8 1.0
CE1 A:HIS118 4.3 117.2 1.0
ZN A:ZN2003 4.3 121.5 1.0
CA A:CYS123 4.4 90.3 1.0
CA A:CYS148 4.4 80.7 1.0
CA A:CYS175 4.5 76.6 1.0
NH2 A:ARG125 4.7 85.1 1.0
CZ A:ARG125 4.7 85.1 1.0
N A:CYS177 4.8 88.7 1.0
NE A:ARG125 4.8 85.1 1.0
CB A:ARG125 4.9 85.1 1.0
C A:CYS148 4.9 80.7 1.0
C A:CYS175 5.0 76.6 1.0

Zinc binding site 3 out of 7 in 7mey

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Zinc binding site 3 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:121.5
occ:1.00
 NE2 A:HIS118 2.0 117.2 1.0
SG A:CYS151 2.3 93.8 1.0
SG A:CYS177 2.3 88.7 1.0
SG A:CYS189 2.3 108.4 1.0
CE1 A:HIS118 2.6 117.2 1.0
CB A:CYS177 2.8 88.7 1.0
CB A:CYS189 3.2 108.4 1.0
CB A:CYS151 3.2 93.8 1.0
CD2 A:HIS118 3.3 117.2 1.0
CA A:CYS151 3.8 93.8 1.0
ND1 A:HIS118 3.9 117.2 1.0
CA A:CYS189 4.1 108.4 1.0
CG A:HIS118 4.2 117.2 1.0
CA A:CYS177 4.3 88.7 1.0
ZN A:ZN2002 4.3 117.8 1.0
C A:CYS177 4.7 88.7 1.0
O A:CYS151 4.7 93.8 1.0
N A:CYS151 4.8 93.8 1.0
CB A:CYS123 4.8 90.3 1.0
C A:CYS151 4.8 93.8 1.0

Zinc binding site 4 out of 7 in 7mey

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Zinc binding site 4 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:99.7
occ:1.00
 NE2 A:HIS1722 2.0 95.3 1.0
SG A:CYS1703 2.2 75.5 1.0
SG A:CYS1706 2.2 74.4 1.0
SG A:CYS1727 2.3 95.1 1.0
CD2 A:HIS1722 2.8 95.3 1.0
CB A:CYS1727 3.0 95.1 1.0
CB A:CYS1703 3.1 75.5 1.0
CE1 A:HIS1722 3.2 95.3 1.0
CB A:CYS1706 3.7 74.4 1.0
CG A:HIS1722 4.0 95.3 1.0
ND1 A:HIS1722 4.2 95.3 1.0
N A:CYS1706 4.2 74.4 1.0
CA A:CYS1727 4.3 95.1 1.0
O A:ASN1726 4.6 99.5 1.0
CA A:CYS1706 4.6 74.4 1.0
CA A:CYS1703 4.6 75.5 1.0
CE1 A:PHE1734 4.7 70.7 1.0
CB A:THR1705 4.8 67.2 1.0
CB A:VAL1708 4.8 84.3 1.0

Zinc binding site 5 out of 7 in 7mey

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Zinc binding site 5 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:146.3
occ:1.00
 ND1 A:HIS1297 2.0 113.9 1.0
SG A:CYS1323 2.2 112.9 1.0
SG A:CYS1320 2.3 122.0 1.0
SG A:CYS1295 2.3 107.7 1.0
CE1 A:HIS1297 2.7 113.9 1.0
CG A:HIS1297 3.1 113.9 1.0
CB A:CYS1320 3.1 122.0 1.0
CB A:CYS1295 3.1 107.7 1.0
CB A:HIS1297 3.7 113.9 1.0
CB A:CYS1323 3.7 112.9 1.0
NE2 A:HIS1297 3.8 113.9 1.0
N A:CYS1323 3.9 112.9 1.0
CD2 A:HIS1297 4.0 113.9 1.0
CB A:LEU1322 4.3 112.4 1.0
CA A:CYS1323 4.4 112.9 1.0
CA A:CYS1295 4.5 107.7 1.0
CA A:CYS1320 4.6 122.0 1.0
CG A:PRO1235 4.6 113.3 1.0
C A:LEU1322 4.8 112.4 1.0
C A:CYS1295 4.8 107.7 1.0
N A:LEU1322 4.8 112.4 1.0
CA A:LEU1322 4.9 112.4 1.0
CA A:HIS1297 4.9 113.9 1.0
N A:HIS1297 5.0 113.9 1.0

Zinc binding site 6 out of 7 in 7mey

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Zinc binding site 6 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2006

b:165.6
occ:1.00
 ND1 A:HIS1300 2.0 138.3 1.0
SG A:CYS1220 2.4 148.1 1.0
SG A:CYS1223 2.4 149.4 1.0
SG A:CYS1303 2.5 131.0 1.0
CE1 A:HIS1300 2.8 138.3 1.0
CG A:HIS1300 2.9 138.3 1.0
CB A:CYS1223 3.0 149.4 1.0
N A:CYS1223 3.2 149.4 1.0
CB A:HIS1300 3.4 138.3 1.0
CA A:CYS1223 3.7 149.4 1.0
NE2 A:HIS1300 3.8 138.3 1.0
CD2 A:HIS1300 3.9 138.3 1.0
CB A:CYS1220 3.9 148.1 1.0
CB A:CYS1303 4.1 131.0 1.0
N A:LEU1222 4.1 145.2 1.0
C A:LEU1222 4.2 145.2 1.0
CB A:LEU1222 4.2 145.2 1.0
CA A:LEU1222 4.4 145.2 1.0
C A:CYS1223 4.7 149.4 1.0
N A:ALA1221 4.8 147.0 1.0
CA A:HIS1300 4.8 138.3 1.0
O A:CYS1223 4.9 149.4 1.0
N A:HIS1300 5.0 138.3 1.0

Zinc binding site 7 out of 7 in 7mey

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Zinc binding site 7 out of 7 in the Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Yeast UBR1 in Complex with UBC2 and Monoubiquitinated N- Degron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2007

b:108.6
occ:1.00
 NE2 A:HIS1763 2.3 63.5 1.0
NE2 A:HIS161 2.3 74.5 1.0
OD2 A:ASP952 2.4 65.7 1.0
CD2 A:HIS1763 2.5 63.5 1.0
OD1 A:ASP1775 2.8 70.2 1.0
CE1 A:HIS161 3.0 74.5 1.0
OD2 A:ASP1775 3.2 70.2 1.0
CG A:ASP1775 3.3 70.2 1.0
CD2 A:HIS161 3.5 74.5 1.0
CG A:ASP952 3.5 65.7 1.0
CE1 A:HIS1763 3.6 63.5 1.0
CG A:HIS1763 3.8 63.5 1.0
OD1 A:ASP952 4.0 65.7 1.0
ND1 A:HIS161 4.2 74.5 1.0
ND1 A:HIS1763 4.3 63.5 1.0
CG A:HIS161 4.5 74.5 1.0
OH A:TYR933 4.6 51.8 1.0
CB A:ASP952 4.7 65.7 1.0
CB A:ASP1775 4.7 70.2 1.0

Reference:

M.Pan, Q.Zheng, T.Wang, L.Liang, Y.Yu, L.Liu, M.Zhao. Structural Insights Into the Initiation and Elongation of Ubiquitination By UBR1 Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-04097-8
Page generated: Tue Oct 29 23:16:06 2024

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