Zinc in PDB 8tvw: Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
Enzymatic activity of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
All present enzymatic activity of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1):
2.7.7.6;
Other elements in 8tvw:
The structure of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
(pdb code 8tvw). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1), PDB code: 8tvw:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 1 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 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 Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1801
b:225.8
occ:1.00
|
O
|
A:CYS107
|
2.2
|
180.6
|
1.0
|
|
H
|
A:CYS110
|
2.3
|
183.6
|
1.0
|
|
SG
|
A:CYS167
|
2.3
|
193.3
|
1.0
|
|
O
|
A:MET108
|
2.4
|
175.4
|
1.0
|
|
N
|
A:CYS110
|
2.4
|
183.6
|
1.0
|
|
HB2
|
A:CYS110
|
2.5
|
183.6
|
1.0
|
|
C
|
A:MET108
|
2.7
|
175.4
|
1.0
|
|
C
|
A:HIS109
|
2.7
|
177.7
|
1.0
|
|
C
|
A:CYS107
|
2.9
|
180.6
|
1.0
|
|
N
|
A:HIS109
|
3.0
|
177.7
|
1.0
|
|
CB
|
A:CYS110
|
3.1
|
183.6
|
1.0
|
|
HB2
|
A:HIS109
|
3.1
|
177.7
|
1.0
|
|
CA
|
A:HIS109
|
3.2
|
177.7
|
1.0
|
|
HB3
|
A:CYS110
|
3.2
|
183.6
|
1.0
|
|
CA
|
A:CYS110
|
3.2
|
183.6
|
1.0
|
|
HB2
|
A:CYS167
|
3.3
|
193.3
|
1.0
|
|
O
|
A:HIS109
|
3.3
|
177.7
|
1.0
|
|
HB2
|
A:CYS107
|
3.3
|
180.6
|
1.0
|
|
HB3
|
A:CYS107
|
3.4
|
180.6
|
1.0
|
|
CB
|
A:CYS167
|
3.4
|
193.3
|
1.0
|
|
N
|
A:MET108
|
3.5
|
175.4
|
1.0
|
|
CA
|
A:MET108
|
3.6
|
175.4
|
1.0
|
|
H
|
A:HIS109
|
3.6
|
177.7
|
1.0
|
|
CB
|
A:HIS109
|
3.7
|
177.7
|
1.0
|
|
CB
|
A:CYS107
|
3.7
|
180.6
|
1.0
|
|
HA
|
A:CYS110
|
3.7
|
183.6
|
1.0
|
|
HB3
|
A:CYS167
|
3.8
|
193.3
|
1.0
|
|
CA
|
A:CYS107
|
3.9
|
180.6
|
1.0
|
|
HA
|
A:HIS109
|
4.1
|
177.7
|
1.0
|
|
H
|
A:MET108
|
4.2
|
175.4
|
1.0
|
|
HB3
|
A:HIS109
|
4.2
|
177.7
|
1.0
|
|
HB2
|
A:MET108
|
4.2
|
175.4
|
1.0
|
|
H
|
A:GLY111
|
4.2
|
172.4
|
1.0
|
|
CB
|
A:MET108
|
4.4
|
175.4
|
1.0
|
|
HA
|
A:MET108
|
4.4
|
175.4
|
1.0
|
|
H
|
A:CYS167
|
4.4
|
193.3
|
1.0
|
|
HB3
|
A:MET108
|
4.4
|
175.4
|
1.0
|
|
HE21
|
A:GLN171
|
4.5
|
180.0
|
1.0
|
|
C
|
A:CYS110
|
4.5
|
183.6
|
1.0
|
|
HA
|
A:CYS107
|
4.6
|
180.6
|
1.0
|
|
OD1
|
A:ASN169
|
4.7
|
185.0
|
1.0
|
|
N
|
A:GLY111
|
4.7
|
172.4
|
1.0
|
|
CA
|
A:CYS167
|
4.7
|
193.3
|
1.0
|
|
SG
|
A:CYS110
|
4.7
|
183.6
|
1.0
|
|
CG
|
A:HIS109
|
4.8
|
177.7
|
1.0
|
|
HD21
|
A:ASN169
|
4.8
|
185.0
|
1.0
|
|
SG
|
A:CYS148
|
4.8
|
187.0
|
1.0
|
|
N
|
A:CYS167
|
4.9
|
193.3
|
1.0
|
|
N
|
A:CYS107
|
4.9
|
180.6
|
1.0
|
|
Zinc binding site 2 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 2 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 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 Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1802
b:188.7
occ:1.00
|
HB3
|
A:CYS67
|
1.9
|
156.7
|
1.0
|
|
O
|
A:CYS67
|
2.1
|
156.7
|
1.0
|
|
NE2
|
A:HIS80
|
2.2
|
139.3
|
1.0
|
|
SG
|
A:CYS77
|
2.5
|
144.8
|
1.0
|
|
CB
|
A:CYS67
|
2.7
|
156.7
|
1.0
|
|
HB2
|
A:CYS70
|
2.7
|
156.9
|
1.0
|
|
C
|
A:CYS67
|
2.8
|
156.7
|
1.0
|
|
CD2
|
A:HIS80
|
3.0
|
139.3
|
1.0
|
|
HB2
|
A:CYS67
|
3.0
|
156.7
|
1.0
|
|
HD2
|
A:HIS80
|
3.1
|
139.3
|
1.0
|
|
O
|
A:PRO78
|
3.2
|
130.5
|
1.0
|
|
CA
|
A:CYS67
|
3.2
|
156.7
|
1.0
|
|
CE1
|
A:HIS80
|
3.2
|
139.3
|
1.0
|
|
HA
|
A:CYS67
|
3.4
|
156.7
|
1.0
|
|
SG
|
A:CYS70
|
3.4
|
156.9
|
1.0
|
|
CB
|
A:CYS70
|
3.4
|
156.9
|
1.0
|
|
HE1
|
A:HIS80
|
3.4
|
139.3
|
1.0
|
|
HB3
|
A:GLN68
|
3.6
|
151.8
|
1.0
|
|
HB3
|
A:CYS70
|
3.8
|
156.9
|
1.0
|
|
N
|
A:GLN68
|
4.0
|
151.8
|
1.0
|
|
SG
|
A:CYS67
|
4.1
|
156.7
|
1.0
|
|
HA2
|
A:GLY59
|
4.2
|
146.1
|
1.0
|
|
CG
|
A:HIS80
|
4.2
|
139.3
|
1.0
|
|
ND1
|
A:HIS80
|
4.2
|
139.3
|
1.0
|
|
CB
|
A:CYS77
|
4.3
|
144.8
|
1.0
|
|
H
|
A:CYS70
|
4.3
|
156.9
|
1.0
|
|
HA2
|
A:GLY79
|
4.3
|
135.7
|
1.0
|
|
CB
|
A:GLN68
|
4.3
|
151.8
|
1.0
|
|
HG
|
A:CYS67
|
4.4
|
156.7
|
1.0
|
|
C
|
A:PRO78
|
4.4
|
130.5
|
1.0
|
|
HB2
|
A:GLN68
|
4.4
|
151.8
|
1.0
|
|
HB3
|
A:CYS77
|
4.5
|
144.8
|
1.0
|
|
N
|
A:CYS67
|
4.6
|
156.7
|
1.0
|
|
H
|
A:GLN68
|
4.6
|
151.8
|
1.0
|
|
CA
|
A:GLN68
|
4.6
|
151.8
|
1.0
|
|
CA
|
A:CYS70
|
4.7
|
156.9
|
1.0
|
|
HB2
|
A:CYS77
|
4.8
|
144.8
|
1.0
|
|
HD2
|
A:PRO78
|
4.8
|
130.5
|
1.0
|
|
N
|
A:CYS70
|
4.9
|
156.9
|
1.0
|
|
O
|
A:LEU58
|
4.9
|
146.5
|
1.0
|
|
O
|
A:LYS66
|
4.9
|
155.9
|
1.0
|
|
H
|
A:SER60
|
5.0
|
155.0
|
1.0
|
|
CA
|
A:GLY79
|
5.0
|
135.7
|
1.0
|
|
C
|
A:CYS77
|
5.0
|
144.8
|
1.0
|
|
Zinc binding site 3 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 3 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 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 Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1301
b:211.8
occ:1.00
|
SG
|
B:CYS1182
|
2.3
|
144.0
|
1.0
|
|
SG
|
B:CYS1166
|
2.3
|
144.8
|
1.0
|
|
SG
|
B:CYS1163
|
2.3
|
139.2
|
1.0
|
|
SG
|
B:CYS1185
|
2.3
|
149.2
|
1.0
|
|
HB3
|
B:CYS1163
|
2.8
|
139.2
|
1.0
|
|
CB
|
B:CYS1163
|
2.9
|
139.2
|
1.0
|
|
HB2
|
B:CYS1163
|
3.0
|
139.2
|
1.0
|
|
H
|
B:CYS1166
|
3.0
|
144.8
|
1.0
|
|
HB2
|
B:CYS1185
|
3.1
|
149.2
|
1.0
|
|
CB
|
B:CYS1185
|
3.3
|
149.2
|
1.0
|
|
HB3
|
B:CYS1166
|
3.4
|
144.8
|
1.0
|
|
HB
|
B:ILE1165
|
3.4
|
141.3
|
1.0
|
|
HB3
|
B:CYS1182
|
3.4
|
144.0
|
1.0
|
|
CB
|
B:CYS1166
|
3.4
|
144.8
|
1.0
|
|
CB
|
B:CYS1182
|
3.5
|
144.0
|
1.0
|
|
N
|
B:CYS1166
|
3.6
|
144.8
|
1.0
|
|
HB3
|
B:CYS1185
|
3.8
|
149.2
|
1.0
|
|
HB2
|
B:CYS1182
|
3.8
|
144.0
|
1.0
|
|
O
|
B:CYS1166
|
4.0
|
144.8
|
1.0
|
|
CA
|
B:CYS1166
|
4.0
|
144.8
|
1.0
|
|
HG1
|
B:THR1170
|
4.1
|
134.6
|
1.0
|
|
HB2
|
B:CYS1166
|
4.2
|
144.8
|
1.0
|
|
CB
|
B:ILE1165
|
4.3
|
141.3
|
1.0
|
|
CA
|
B:CYS1163
|
4.4
|
139.2
|
1.0
|
|
C
|
B:CYS1166
|
4.4
|
144.8
|
1.0
|
|
H
|
B:ILE1165
|
4.5
|
141.3
|
1.0
|
|
OG1
|
B:THR1170
|
4.5
|
134.6
|
1.0
|
|
C
|
B:ILE1165
|
4.6
|
141.3
|
1.0
|
|
H
|
B:CYS1185
|
4.6
|
149.2
|
1.0
|
|
CA
|
B:CYS1185
|
4.6
|
149.2
|
1.0
|
|
O
|
B:CYS1182
|
4.6
|
144.0
|
1.0
|
|
N
|
B:CYS1185
|
4.7
|
149.2
|
1.0
|
|
HG22
|
B:ILE1165
|
4.7
|
141.3
|
1.0
|
|
CA
|
B:CYS1182
|
4.8
|
144.0
|
1.0
|
|
CA
|
B:ILE1165
|
4.8
|
141.3
|
1.0
|
|
HA
|
B:CYS1163
|
4.8
|
139.2
|
1.0
|
|
N
|
B:ILE1165
|
4.9
|
141.3
|
1.0
|
|
HA
|
B:CYS1166
|
4.9
|
144.8
|
1.0
|
|
HB3
|
B:ASN1187
|
4.9
|
141.7
|
1.0
|
|
C
|
B:CYS1163
|
4.9
|
139.2
|
1.0
|
|
Zinc binding site 4 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 4 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 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 Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:193.0
occ:1.00
|
H
|
C:CYS92
|
1.6
|
143.8
|
1.0
|
|
HG
|
C:CYS88
|
1.8
|
147.9
|
1.0
|
|
N
|
C:CYS92
|
2.1
|
143.8
|
1.0
|
|
SG
|
C:CYS92
|
2.3
|
143.8
|
1.0
|
|
SG
|
C:CYS95
|
2.4
|
135.3
|
1.0
|
|
O
|
C:CYS92
|
2.5
|
143.8
|
1.0
|
|
CA
|
C:CYS92
|
2.6
|
143.8
|
1.0
|
|
H
|
C:CYS95
|
2.6
|
135.3
|
1.0
|
|
C
|
C:CYS92
|
2.7
|
143.8
|
1.0
|
|
CB
|
C:CYS92
|
2.8
|
143.8
|
1.0
|
|
SG
|
C:CYS88
|
2.9
|
147.9
|
1.0
|
|
HB3
|
C:CYS92
|
3.0
|
143.8
|
1.0
|
|
C
|
C:HIS91
|
3.2
|
131.6
|
1.0
|
|
HA
|
C:HIS91
|
3.2
|
131.6
|
1.0
|
|
N
|
C:CYS95
|
3.2
|
135.3
|
1.0
|
|
HG
|
C:SER96
|
3.3
|
125.6
|
1.0
|
|
H
|
C:LYS94
|
3.4
|
138.2
|
1.0
|
|
HA
|
C:CYS92
|
3.5
|
143.8
|
1.0
|
|
CB
|
C:CYS95
|
3.5
|
135.3
|
1.0
|
|
HB2
|
C:CYS92
|
3.6
|
143.8
|
1.0
|
|
CA
|
C:HIS91
|
3.7
|
131.6
|
1.0
|
|
HB3
|
C:CYS95
|
3.7
|
135.3
|
1.0
|
|
CA
|
C:CYS95
|
3.7
|
135.3
|
1.0
|
|
HB3
|
C:CYS88
|
3.8
|
147.9
|
1.0
|
|
N
|
C:ASP93
|
3.8
|
135.4
|
1.0
|
|
SG
|
C:CYS86
|
3.9
|
138.1
|
1.0
|
|
N
|
C:LYS94
|
3.9
|
138.2
|
1.0
|
|
HB2
|
C:LYS94
|
3.9
|
138.2
|
1.0
|
|
CB
|
C:CYS88
|
3.9
|
147.9
|
1.0
|
|
C
|
C:CYS95
|
4.0
|
135.3
|
1.0
|
|
OG
|
C:SER96
|
4.0
|
125.6
|
1.0
|
|
H
|
C:SER96
|
4.0
|
125.6
|
1.0
|
|
HB2
|
C:HIS91
|
4.1
|
131.6
|
1.0
|
|
HB2
|
C:CYS88
|
4.1
|
147.9
|
1.0
|
|
O
|
C:HIS91
|
4.1
|
131.6
|
1.0
|
|
N
|
C:SER96
|
4.1
|
125.6
|
1.0
|
|
C
|
C:LYS94
|
4.2
|
138.2
|
1.0
|
|
HB3
|
C:SER96
|
4.3
|
125.6
|
1.0
|
|
H
|
C:ASP93
|
4.3
|
135.4
|
1.0
|
|
HB2
|
C:CYS95
|
4.3
|
135.3
|
1.0
|
|
CA
|
C:LYS94
|
4.4
|
138.2
|
1.0
|
|
HB3
|
C:CYS86
|
4.5
|
138.1
|
1.0
|
|
CB
|
C:HIS91
|
4.5
|
131.6
|
1.0
|
|
C
|
C:ASP93
|
4.6
|
135.4
|
1.0
|
|
CB
|
C:SER96
|
4.6
|
125.6
|
1.0
|
|
CB
|
C:LYS94
|
4.7
|
138.2
|
1.0
|
|
HA
|
C:CYS95
|
4.7
|
135.3
|
1.0
|
|
O
|
C:CYS95
|
4.7
|
135.3
|
1.0
|
|
CB
|
C:CYS86
|
4.7
|
138.1
|
1.0
|
|
CA
|
C:ASP93
|
4.7
|
135.4
|
1.0
|
|
HB2
|
C:CYS86
|
4.8
|
138.1
|
1.0
|
|
HE2
|
C:LYS94
|
4.9
|
138.2
|
1.0
|
|
N
|
C:HIS91
|
4.9
|
131.6
|
1.0
|
|
HA
|
C:ASP93
|
5.0
|
135.4
|
1.0
|
|
Zinc binding site 5 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 5 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 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 Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:291.6
occ:1.00
|
HB2
|
I:CYS10
|
1.4
|
257.2
|
1.0
|
|
CB
|
I:CYS10
|
2.1
|
257.2
|
1.0
|
|
SG
|
I:CYS7
|
2.3
|
253.4
|
1.0
|
|
SG
|
I:CYS10
|
2.3
|
257.2
|
1.0
|
|
HB3
|
I:CYS10
|
2.5
|
257.2
|
1.0
|
|
HB3
|
I:CYS7
|
2.6
|
253.4
|
1.0
|
|
CB
|
I:CYS7
|
2.8
|
253.4
|
1.0
|
|
HB2
|
I:CYS7
|
2.9
|
253.4
|
1.0
|
|
O
|
I:THR31
|
2.9
|
246.2
|
1.0
|
|
HD22
|
I:ASN12
|
3.1
|
245.5
|
1.0
|
|
HB2
|
I:ASN12
|
3.2
|
245.5
|
1.0
|
|
OG1
|
I:THR31
|
3.4
|
246.2
|
1.0
|
|
CA
|
I:CYS10
|
3.4
|
257.2
|
1.0
|
|
HB2
|
I:CYS32
|
3.4
|
252.1
|
1.0
|
|
HG1
|
I:THR31
|
3.5
|
246.2
|
1.0
|
|
H
|
I:CYS10
|
3.6
|
257.2
|
1.0
|
|
ND2
|
I:ASN12
|
3.6
|
245.5
|
1.0
|
|
C
|
I:THR31
|
3.7
|
246.2
|
1.0
|
|
N
|
I:CYS10
|
3.7
|
257.2
|
1.0
|
|
OD1
|
I:ASP9
|
3.7
|
257.4
|
1.0
|
|
HA
|
I:CYS32
|
3.8
|
252.1
|
1.0
|
|
H
|
I:ASN12
|
3.9
|
245.5
|
1.0
|
|
HB
|
I:THR31
|
3.9
|
246.2
|
1.0
|
|
CB
|
I:ASN12
|
4.0
|
245.5
|
1.0
|
|
HD21
|
I:ASN12
|
4.0
|
245.5
|
1.0
|
|
HA
|
I:CYS10
|
4.0
|
257.2
|
1.0
|
|
CG
|
I:ASN12
|
4.1
|
245.5
|
1.0
|
|
C
|
I:CYS10
|
4.1
|
257.2
|
1.0
|
|
CB
|
I:THR31
|
4.1
|
246.2
|
1.0
|
|
CB
|
I:CYS32
|
4.2
|
252.1
|
1.0
|
|
CA
|
I:CYS7
|
4.3
|
253.4
|
1.0
|
|
N
|
I:CYS32
|
4.3
|
252.1
|
1.0
|
|
CA
|
I:CYS32
|
4.3
|
252.1
|
1.0
|
|
HB3
|
I:CYS29
|
4.4
|
250.2
|
1.0
|
|
CA
|
I:THR31
|
4.5
|
246.2
|
1.0
|
|
C
|
I:ASP9
|
4.6
|
257.4
|
1.0
|
|
N
|
I:ASN12
|
4.6
|
245.5
|
1.0
|
|
HB3
|
I:ASN12
|
4.6
|
245.5
|
1.0
|
|
H
|
I:ASN11
|
4.6
|
242.7
|
1.0
|
|
N
|
I:ASN11
|
4.6
|
242.7
|
1.0
|
|
O
|
I:CYS10
|
4.6
|
257.2
|
1.0
|
|
HA
|
I:CYS7
|
4.7
|
253.4
|
1.0
|
|
HG
|
I:CYS32
|
4.8
|
252.1
|
1.0
|
|
C
|
I:CYS7
|
4.8
|
253.4
|
1.0
|
|
H
|
I:CYS7
|
4.8
|
253.4
|
1.0
|
|
H
|
I:ASP9
|
4.9
|
257.4
|
1.0
|
|
CA
|
I:ASN12
|
4.9
|
245.5
|
1.0
|
|
CG
|
I:ASP9
|
4.9
|
257.4
|
1.0
|
|
HB3
|
I:CYS32
|
4.9
|
252.1
|
1.0
|
|
H
|
I:CYS32
|
5.0
|
252.1
|
1.0
|
|
Zinc binding site 6 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 6 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 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 Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn202
b:269.0
occ:1.00
|
HG
|
I:CYS75
|
1.8
|
222.1
|
1.0
|
|
HB3
|
I:CYS103
|
1.8
|
223.2
|
1.0
|
|
SG
|
I:CYS106
|
2.3
|
229.0
|
1.0
|
|
CB
|
I:CYS103
|
2.4
|
223.2
|
1.0
|
|
SG
|
I:CYS103
|
2.4
|
223.2
|
1.0
|
|
HB2
|
I:CYS78
|
2.7
|
224.3
|
1.0
|
|
HB2
|
I:CYS103
|
2.8
|
223.2
|
1.0
|
|
SG
|
I:CYS78
|
2.8
|
224.3
|
1.0
|
|
SG
|
I:CYS75
|
2.9
|
222.1
|
1.0
|
|
HB3
|
I:HIS108
|
3.0
|
218.9
|
1.0
|
|
H
|
I:CYS106
|
3.1
|
229.0
|
1.0
|
|
H
|
I:HIS108
|
3.2
|
218.9
|
1.0
|
|
HB2
|
I:HIS108
|
3.3
|
218.9
|
1.0
|
|
CB
|
I:CYS78
|
3.3
|
224.3
|
1.0
|
|
OG
|
I:SER105
|
3.4
|
225.7
|
1.0
|
|
H
|
I:CYS78
|
3.4
|
224.3
|
1.0
|
|
HB2
|
I:CYS75
|
3.5
|
222.1
|
1.0
|
|
CB
|
I:HIS108
|
3.6
|
218.9
|
1.0
|
|
CB
|
I:CYS75
|
3.7
|
222.1
|
1.0
|
|
N
|
I:CYS106
|
3.7
|
229.0
|
1.0
|
|
CA
|
I:CYS103
|
3.7
|
223.2
|
1.0
|
|
CB
|
I:CYS106
|
3.8
|
229.0
|
1.0
|
|
HB3
|
I:CYS75
|
3.8
|
222.1
|
1.0
|
|
O
|
I:CYS103
|
3.9
|
223.2
|
1.0
|
|
HB3
|
I:CYS78
|
3.9
|
224.3
|
1.0
|
|
N
|
I:HIS108
|
4.0
|
218.9
|
1.0
|
|
C
|
I:CYS103
|
4.0
|
223.2
|
1.0
|
|
HB3
|
I:LYS77
|
4.1
|
221.7
|
1.0
|
|
HB3
|
I:CYS106
|
4.1
|
229.0
|
1.0
|
|
CA
|
I:CYS106
|
4.1
|
229.0
|
1.0
|
|
H
|
I:CYS103
|
4.1
|
223.2
|
1.0
|
|
N
|
I:CYS78
|
4.1
|
224.3
|
1.0
|
|
H
|
I:SER107
|
4.2
|
216.7
|
1.0
|
|
H
|
I:SER105
|
4.3
|
225.7
|
1.0
|
|
C
|
I:CYS106
|
4.3
|
229.0
|
1.0
|
|
CA
|
I:CYS78
|
4.3
|
224.3
|
1.0
|
|
HA
|
I:CYS103
|
4.3
|
223.2
|
1.0
|
|
CA
|
I:HIS108
|
4.4
|
218.9
|
1.0
|
|
N
|
I:SER107
|
4.4
|
216.7
|
1.0
|
|
N
|
I:CYS103
|
4.4
|
223.2
|
1.0
|
|
HB2
|
I:CYS106
|
4.5
|
229.0
|
1.0
|
|
C
|
I:SER105
|
4.7
|
225.7
|
1.0
|
|
CB
|
I:SER105
|
4.7
|
225.7
|
1.0
|
|
CG
|
I:HIS108
|
4.7
|
218.9
|
1.0
|
|
N
|
I:SER105
|
4.7
|
225.7
|
1.0
|
|
O
|
I:HIS108
|
4.8
|
218.9
|
1.0
|
|
HB3
|
I:SER80
|
4.8
|
218.9
|
1.0
|
|
HD3
|
I:LYS77
|
4.9
|
221.7
|
1.0
|
|
ND1
|
I:HIS108
|
4.9
|
218.9
|
1.0
|
|
H
|
I:LYS77
|
4.9
|
221.7
|
1.0
|
|
CA
|
I:SER105
|
4.9
|
225.7
|
1.0
|
|
HA
|
I:CYS78
|
5.0
|
224.3
|
1.0
|
|
O
|
I:CYS106
|
5.0
|
229.0
|
1.0
|
|
Zinc binding site 7 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 7 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:156.5
occ:1.00
|
N
|
J:CYS46
|
2.1
|
103.5
|
1.0
|
|
HA
|
J:CYS46
|
2.2
|
103.5
|
1.0
|
|
C
|
J:CYS45
|
2.3
|
100.2
|
1.0
|
|
SG
|
J:CYS46
|
2.3
|
103.5
|
1.0
|
|
SG
|
J:CYS45
|
2.4
|
100.2
|
1.0
|
|
SG
|
J:CYS7
|
2.4
|
96.9
|
1.0
|
|
CA
|
J:CYS46
|
2.5
|
103.5
|
1.0
|
|
O
|
J:CYS45
|
2.5
|
100.2
|
1.0
|
|
H
|
J:CYS46
|
2.6
|
103.5
|
1.0
|
|
CB
|
J:CYS46
|
2.8
|
103.5
|
1.0
|
|
CB
|
J:CYS45
|
3.2
|
100.2
|
1.0
|
|
HB2
|
J:CYS7
|
3.3
|
96.9
|
1.0
|
|
CA
|
J:CYS45
|
3.3
|
100.2
|
1.0
|
|
HB2
|
J:CYS46
|
3.4
|
103.5
|
1.0
|
|
HB2
|
J:CYS45
|
3.4
|
100.2
|
1.0
|
|
CB
|
J:CYS7
|
3.5
|
96.9
|
1.0
|
|
HB3
|
J:CYS46
|
3.6
|
103.5
|
1.0
|
|
HB2
|
J:CYS10
|
3.6
|
99.7
|
1.0
|
|
SG
|
J:CYS10
|
3.8
|
99.7
|
1.0
|
|
H
|
J:CYS10
|
3.8
|
99.7
|
1.0
|
|
HB3
|
J:CYS7
|
3.9
|
96.9
|
1.0
|
|
OG
|
J:SER9
|
3.9
|
93.5
|
1.0
|
|
HG
|
J:SER9
|
3.9
|
93.5
|
1.0
|
|
C
|
J:CYS46
|
3.9
|
103.5
|
1.0
|
|
HA
|
J:CYS45
|
4.0
|
100.2
|
1.0
|
|
HG2
|
J:MET49
|
4.1
|
96.9
|
1.0
|
|
HB3
|
J:CYS45
|
4.1
|
100.2
|
1.0
|
|
N
|
J:CYS45
|
4.2
|
100.2
|
1.0
|
|
CB
|
J:CYS10
|
4.2
|
99.7
|
1.0
|
|
HE
|
J:ARG43
|
4.3
|
100.1
|
1.0
|
|
H
|
J:CYS45
|
4.4
|
100.2
|
1.0
|
|
HB2
|
J:ARG43
|
4.4
|
100.1
|
1.0
|
|
N
|
J:CYS10
|
4.6
|
99.7
|
1.0
|
|
O
|
J:CYS46
|
4.6
|
103.5
|
1.0
|
|
H
|
J:ARG47
|
4.7
|
101.6
|
1.0
|
|
HH21
|
J:ARG43
|
4.7
|
100.1
|
1.0
|
|
O
|
J:ARG43
|
4.7
|
100.1
|
1.0
|
|
N
|
J:ARG47
|
4.7
|
101.6
|
1.0
|
|
CA
|
J:CYS7
|
4.8
|
96.9
|
1.0
|
|
H
|
J:SER9
|
4.8
|
93.5
|
1.0
|
|
HA
|
J:CYS7
|
4.8
|
96.9
|
1.0
|
|
HB3
|
J:CYS10
|
4.9
|
99.7
|
1.0
|
|
HB3
|
J:LYS12
|
4.9
|
97.8
|
1.0
|
|
HH21
|
J:ARG48
|
4.9
|
93.4
|
1.0
|
|
C
|
J:TYR44
|
5.0
|
95.4
|
1.0
|
|
CG
|
J:MET49
|
5.0
|
96.9
|
1.0
|
|
HB3
|
J:ARG43
|
5.0
|
100.1
|
1.0
|
|
Zinc binding site 8 out
of 8 in 8tvw
Go back to
Zinc Binding Sites List in 8tvw
Zinc binding site 8 out
of 8 in the Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1)
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Cryo-Em Structure of Cpd-Stalled Pol II (Conformation 1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:219.3
occ:1.00
|
HB2
|
L:ASP50
|
1.9
|
174.2
|
1.0
|
|
SG
|
L:CYS51
|
2.3
|
171.1
|
1.0
|
|
SG
|
L:CYS31
|
2.3
|
168.5
|
1.0
|
|
SG
|
L:CYS34
|
2.5
|
173.3
|
1.0
|
|
HB3
|
L:ASP50
|
2.6
|
174.2
|
1.0
|
|
CB
|
L:ASP50
|
2.6
|
174.2
|
1.0
|
|
HB2
|
L:CYS34
|
2.8
|
173.3
|
1.0
|
|
CB
|
L:CYS34
|
3.1
|
173.3
|
1.0
|
|
HG
|
L:SER36
|
3.2
|
170.0
|
1.0
|
|
C
|
L:ASP50
|
3.2
|
174.2
|
1.0
|
|
N
|
L:CYS51
|
3.3
|
171.1
|
1.0
|
|
HB3
|
L:CYS34
|
3.4
|
173.3
|
1.0
|
|
CA
|
L:ASP50
|
3.4
|
174.2
|
1.0
|
|
H
|
L:CYS51
|
3.5
|
171.1
|
1.0
|
|
CB
|
L:CYS51
|
3.6
|
171.1
|
1.0
|
|
OG
|
L:SER36
|
3.6
|
170.0
|
1.0
|
|
O
|
L:ASP50
|
3.7
|
174.2
|
1.0
|
|
H
|
L:ASP50
|
3.8
|
174.2
|
1.0
|
|
CA
|
L:CYS51
|
3.8
|
171.1
|
1.0
|
|
CG
|
L:ASP50
|
3.8
|
174.2
|
1.0
|
|
HA
|
L:CYS51
|
3.8
|
171.1
|
1.0
|
|
HB2
|
L:CYS51
|
3.9
|
171.1
|
1.0
|
|
CB
|
L:CYS31
|
3.9
|
168.5
|
1.0
|
|
HG
|
L:CYS48
|
4.0
|
164.4
|
1.0
|
|
OD2
|
L:ASP50
|
4.0
|
174.2
|
1.0
|
|
HB3
|
L:CYS31
|
4.0
|
168.5
|
1.0
|
|
SG
|
L:CYS48
|
4.1
|
164.4
|
1.0
|
|
N
|
L:ASP50
|
4.1
|
174.2
|
1.0
|
|
HA
|
L:ASP50
|
4.2
|
174.2
|
1.0
|
|
HB2
|
L:CYS31
|
4.3
|
168.5
|
1.0
|
|
HB3
|
L:CYS51
|
4.4
|
171.1
|
1.0
|
|
CA
|
L:CYS34
|
4.5
|
173.3
|
1.0
|
|
O
|
L:ALA32
|
4.7
|
157.1
|
1.0
|
|
HB3
|
L:SER36
|
4.8
|
170.0
|
1.0
|
|
CB
|
L:SER36
|
4.8
|
170.0
|
1.0
|
|
N
|
L:CYS34
|
4.9
|
173.3
|
1.0
|
|
H
|
L:SER36
|
4.9
|
170.0
|
1.0
|
|
OD1
|
L:ASP50
|
4.9
|
174.2
|
1.0
|
|
Reference:
R.D.Sarsam,
J.Xu,
I.Lahiri,
W.Gong,
Q.Li,
J.Oh,
Z.Zhou,
P.Hou,
J.Chong,
N.Hao,
S.Li,
D.Wang,
A.E.Leschziner.
ELF1 Promotes RAD26'S Interaction with Lesion-Arrested Pol II For Transcription-Coupled Repair. Proc.Natl.Acad.Sci.Usa V. 121 45121 2024.
ISSN: ESSN 1091-6490
PubMed: 38194460
DOI: 10.1073/PNAS.2314245121
Page generated: Thu Oct 31 11:49:38 2024
|
