Zinc in PDB 8ieg: BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex
Enzymatic activity of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex
All present enzymatic activity of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex:
2.3.2.23;
2.3.2.27;
Zinc Binding Sites:
The binding sites of Zinc atom in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex
(pdb code 8ieg). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex, PDB code: 8ieg:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8ieg
Go back to
Zinc Binding Sites List in 8ieg
Zinc binding site 1 out
of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn801
b:169.9
occ:1.00
|
CE1
|
A:HIS665
|
1.9
|
124.1
|
1.0
|
ND1
|
A:HIS665
|
2.0
|
124.1
|
1.0
|
SG
|
A:CYS683
|
2.3
|
99.2
|
1.0
|
SG
|
A:CYS663
|
2.3
|
128.5
|
1.0
|
SG
|
A:CYS686
|
2.3
|
114.5
|
1.0
|
CB
|
A:CYS663
|
2.8
|
128.5
|
1.0
|
CB
|
A:CYS686
|
3.0
|
114.5
|
1.0
|
CB
|
A:CYS683
|
3.1
|
99.2
|
1.0
|
NE2
|
A:HIS665
|
3.2
|
124.1
|
1.0
|
N
|
A:CYS686
|
3.3
|
114.5
|
1.0
|
CG
|
A:HIS665
|
3.4
|
124.1
|
1.0
|
CA
|
A:CYS686
|
3.7
|
114.5
|
1.0
|
CD2
|
A:HIS665
|
3.9
|
124.1
|
1.0
|
CA
|
A:CYS663
|
4.2
|
128.5
|
1.0
|
CB
|
A:THR685
|
4.4
|
112.9
|
1.0
|
C
|
A:CYS686
|
4.4
|
114.5
|
1.0
|
CB
|
A:HIS665
|
4.4
|
124.1
|
1.0
|
O
|
A:CYS663
|
4.5
|
128.5
|
1.0
|
C
|
A:THR685
|
4.5
|
112.9
|
1.0
|
CA
|
A:CYS683
|
4.5
|
99.2
|
1.0
|
N
|
A:ASN687
|
4.6
|
106.5
|
1.0
|
C
|
A:CYS663
|
4.6
|
128.5
|
1.0
|
N
|
A:THR685
|
4.8
|
112.9
|
1.0
|
CA
|
A:THR685
|
4.8
|
112.9
|
1.0
|
CG2
|
A:THR685
|
4.9
|
112.9
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8ieg
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Zinc Binding Sites List in 8ieg
Zinc binding site 2 out
of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn802
b:174.1
occ:1.00
|
SG
|
A:CYS668
|
2.3
|
132.9
|
1.0
|
SG
|
A:CYS671
|
2.3
|
117.6
|
1.0
|
SG
|
A:CYS648
|
2.3
|
158.8
|
1.0
|
SG
|
A:CYS651
|
2.3
|
163.1
|
1.0
|
CB
|
A:CYS648
|
2.7
|
158.8
|
1.0
|
CB
|
A:CYS651
|
3.0
|
163.1
|
1.0
|
CB
|
A:CYS671
|
3.1
|
117.6
|
1.0
|
N
|
A:CYS651
|
3.4
|
163.1
|
1.0
|
CB
|
A:CYS668
|
3.7
|
132.9
|
1.0
|
CA
|
A:CYS651
|
3.8
|
163.1
|
1.0
|
CA
|
A:CYS648
|
4.2
|
158.8
|
1.0
|
CA
|
A:CYS671
|
4.3
|
117.6
|
1.0
|
N
|
A:CYS671
|
4.3
|
117.6
|
1.0
|
N
|
A:CYS668
|
4.3
|
132.9
|
1.0
|
CB
|
A:LEU650
|
4.4
|
163.6
|
1.0
|
O
|
A:CYS648
|
4.5
|
158.8
|
1.0
|
C
|
A:CYS648
|
4.5
|
158.8
|
1.0
|
C
|
A:LEU650
|
4.5
|
163.6
|
1.0
|
CA
|
A:CYS668
|
4.6
|
132.9
|
1.0
|
ND2
|
A:ASN654
|
4.7
|
172.5
|
1.0
|
N
|
A:SER652
|
4.8
|
165.0
|
1.0
|
C
|
A:CYS651
|
4.8
|
163.1
|
1.0
|
N
|
A:LEU650
|
4.8
|
163.6
|
1.0
|
CA
|
A:LEU650
|
4.8
|
163.6
|
1.0
|
O
|
A:CYS668
|
4.9
|
132.9
|
1.0
|
N
|
A:CYS648
|
5.0
|
158.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8ieg
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Zinc Binding Sites List in 8ieg
Zinc binding site 3 out
of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn801
b:271.5
occ:1.00
|
ND1
|
B:HIS665
|
2.1
|
173.6
|
1.0
|
SG
|
B:CYS683
|
2.3
|
180.9
|
1.0
|
SG
|
B:CYS663
|
2.3
|
165.2
|
1.0
|
SG
|
B:CYS686
|
2.3
|
190.7
|
1.0
|
CE1
|
B:HIS665
|
2.6
|
173.6
|
1.0
|
CB
|
B:CYS663
|
2.7
|
165.2
|
1.0
|
CB
|
B:CYS683
|
3.3
|
180.9
|
1.0
|
CG
|
B:HIS665
|
3.3
|
173.6
|
1.0
|
CB
|
B:CYS686
|
3.5
|
190.7
|
1.0
|
N
|
B:CYS686
|
3.6
|
190.7
|
1.0
|
NE2
|
B:HIS665
|
3.9
|
173.6
|
1.0
|
CB
|
B:HIS665
|
4.0
|
173.6
|
1.0
|
CA
|
B:CYS686
|
4.1
|
190.7
|
1.0
|
CA
|
B:CYS663
|
4.1
|
165.2
|
1.0
|
CD2
|
B:HIS665
|
4.2
|
173.6
|
1.0
|
C
|
B:CYS663
|
4.5
|
165.2
|
1.0
|
C
|
B:CYS686
|
4.6
|
190.7
|
1.0
|
CB
|
B:THR685
|
4.7
|
169.9
|
1.0
|
O
|
B:CYS663
|
4.7
|
165.2
|
1.0
|
N
|
B:HIS665
|
4.7
|
173.6
|
1.0
|
CA
|
B:CYS683
|
4.7
|
180.9
|
1.0
|
C
|
B:THR685
|
4.7
|
169.9
|
1.0
|
CB
|
B:LYS688
|
4.8
|
30.0
|
1.0
|
N
|
B:ASN687
|
4.8
|
189.5
|
1.0
|
N
|
B:THR685
|
4.8
|
169.9
|
1.0
|
N
|
B:LYS688
|
4.9
|
186.2
|
1.0
|
CA
|
B:THR685
|
5.0
|
169.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8ieg
Go back to
Zinc Binding Sites List in 8ieg
Zinc binding site 4 out
of 4 in the BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/ie/8ieg-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of BRE1(Mrbd-Ring)/RAD6-Ub/Nucleosome Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn802
b:248.4
occ:1.00
|
SG
|
B:CYS671
|
2.3
|
200.1
|
1.0
|
SG
|
B:CYS668
|
2.3
|
189.9
|
1.0
|
SG
|
B:CYS651
|
2.3
|
193.0
|
1.0
|
SG
|
B:CYS648
|
2.3
|
200.9
|
1.0
|
CB
|
B:CYS648
|
2.5
|
200.9
|
1.0
|
CB
|
B:CYS651
|
2.9
|
193.0
|
1.0
|
CB
|
B:CYS671
|
3.0
|
200.1
|
1.0
|
CB
|
B:CYS668
|
3.4
|
189.9
|
1.0
|
N
|
B:CYS651
|
3.5
|
193.0
|
1.0
|
CA
|
B:CYS651
|
3.8
|
193.0
|
1.0
|
CA
|
B:CYS648
|
4.0
|
200.9
|
1.0
|
N
|
B:CYS671
|
4.1
|
200.1
|
1.0
|
CA
|
B:CYS671
|
4.2
|
200.1
|
1.0
|
N
|
B:CYS668
|
4.2
|
189.9
|
1.0
|
CB
|
B:ASN654
|
4.3
|
187.7
|
1.0
|
CA
|
B:CYS668
|
4.3
|
189.9
|
1.0
|
O
|
B:ASN654
|
4.3
|
187.7
|
1.0
|
C
|
B:CYS648
|
4.4
|
200.9
|
1.0
|
CB
|
B:LEU650
|
4.5
|
196.4
|
1.0
|
C
|
B:LEU650
|
4.5
|
196.4
|
1.0
|
OD1
|
B:ASN654
|
4.7
|
187.7
|
1.0
|
O
|
B:CYS648
|
4.7
|
200.9
|
1.0
|
N
|
B:LEU650
|
4.7
|
196.4
|
1.0
|
N
|
B:CYS648
|
4.7
|
200.9
|
1.0
|
O
|
B:CYS668
|
4.8
|
189.9
|
1.0
|
CA
|
B:LEU650
|
4.8
|
196.4
|
1.0
|
C
|
B:CYS651
|
4.8
|
193.0
|
1.0
|
C
|
B:CYS668
|
4.8
|
189.9
|
1.0
|
N
|
B:SER652
|
4.9
|
187.1
|
1.0
|
N
|
B:ASN654
|
5.0
|
187.7
|
1.0
|
CG
|
B:ASN654
|
5.0
|
187.7
|
1.0
|
|
Reference:
Z.Deng,
H.Ai,
M.Sun,
Z.Tong,
Y.Du,
Q.Qu,
L.Zhang,
Z.Xu,
S.Tao,
Q.Shi,
J.B.Li,
M.Pan,
L.Liu.
Mechanistic Insights Into Nucleosomal H2B Monoubiquitylation Mediated By Yeast BRE1-RAD6 and Its Human Homolog RNF20/RNF40-HRAD6A. Mol.Cell 2023.
ISSN: ISSN 1097-2765
PubMed: 37633270
DOI: 10.1016/J.MOLCEL.2023.08.001
Page generated: Thu Dec 28 13:17:35 2023
|