Zinc in PDB 7opd: Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Enzymatic activity of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Other elements in 7opd:
The structure of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
(pdb code 7opd). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5), PDB code: 7opd:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7opd
Go back to
Zinc Binding Sites List in 7opd
Zinc binding site 1 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2001
b:73.6
occ:1.00
|
NE2
|
A:HIS84
|
2.0
|
37.7
|
1.0
|
SG
|
A:CYS74
|
2.2
|
43.6
|
1.0
|
SG
|
A:CYS81
|
2.2
|
38.4
|
1.0
|
SG
|
A:CYS71
|
2.3
|
49.4
|
1.0
|
CD2
|
A:HIS84
|
2.5
|
37.7
|
1.0
|
CB
|
A:CYS71
|
2.9
|
49.4
|
1.0
|
CE1
|
A:HIS84
|
3.3
|
37.7
|
1.0
|
O
|
A:PRO82
|
3.7
|
32.1
|
1.0
|
CB
|
A:CYS81
|
3.8
|
38.4
|
1.0
|
CB
|
A:CYS74
|
3.8
|
43.6
|
1.0
|
CG
|
A:HIS84
|
3.8
|
37.7
|
1.0
|
CA
|
A:GLY63
|
3.9
|
44.7
|
1.0
|
N
|
A:CYS74
|
4.0
|
43.6
|
1.0
|
ND1
|
A:HIS84
|
4.1
|
37.7
|
1.0
|
N
|
A:GLY63
|
4.4
|
44.7
|
1.0
|
CA
|
A:CYS71
|
4.4
|
49.4
|
1.0
|
CA
|
A:CYS74
|
4.5
|
43.6
|
1.0
|
CA
|
A:CYS81
|
4.5
|
38.4
|
1.0
|
CB
|
A:THR73
|
4.5
|
42.6
|
1.0
|
C
|
A:GLY63
|
4.6
|
44.7
|
1.0
|
C
|
A:PRO82
|
4.8
|
32.1
|
1.0
|
C
|
A:CYS81
|
4.8
|
38.4
|
1.0
|
OG1
|
A:THR73
|
5.0
|
42.6
|
1.0
|
N
|
A:THR73
|
5.0
|
42.6
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7opd
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Zinc Binding Sites List in 7opd
Zinc binding site 2 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2002
b:139.6
occ:1.00
|
SG
|
A:CYS184
|
2.1
|
113.8
|
1.0
|
SG
|
A:CYS111
|
2.3
|
97.2
|
1.0
|
SG
|
A:CYS154
|
2.3
|
111.9
|
1.0
|
CB
|
A:CYS154
|
2.7
|
111.9
|
1.0
|
SG
|
A:CYS114
|
3.0
|
102.0
|
1.0
|
CB
|
A:CYS184
|
3.1
|
113.8
|
1.0
|
CB
|
A:CYS114
|
3.3
|
102.0
|
1.0
|
N
|
A:CYS184
|
3.5
|
113.8
|
1.0
|
N
|
A:CYS114
|
3.6
|
102.0
|
1.0
|
CB
|
A:CYS111
|
3.7
|
97.2
|
1.0
|
CA
|
A:CYS184
|
3.8
|
113.8
|
1.0
|
CA
|
A:CYS114
|
4.0
|
102.0
|
1.0
|
CA
|
A:CYS154
|
4.2
|
111.9
|
1.0
|
NE2
|
A:GLN188
|
4.2
|
102.2
|
1.0
|
C
|
A:CYS184
|
4.3
|
113.8
|
1.0
|
N
|
A:GLY185
|
4.4
|
112.1
|
1.0
|
CB
|
A:PHE113
|
4.4
|
99.0
|
1.0
|
C
|
A:GLY183
|
4.6
|
108.0
|
1.0
|
C
|
A:PHE113
|
4.7
|
99.0
|
1.0
|
CD2
|
A:PHE113
|
4.8
|
99.0
|
1.0
|
N
|
A:ARG186
|
4.9
|
106.7
|
1.0
|
N
|
A:PHE113
|
4.9
|
99.0
|
1.0
|
CA
|
A:GLY183
|
4.9
|
108.0
|
1.0
|
CA
|
A:PHE113
|
4.9
|
99.0
|
1.0
|
N
|
A:CYS154
|
4.9
|
111.9
|
1.0
|
C
|
A:CYS154
|
5.0
|
111.9
|
1.0
|
CA
|
A:CYS111
|
5.0
|
97.2
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7opd
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Zinc Binding Sites List in 7opd
Zinc binding site 3 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1201
b:83.3
occ:1.00
|
SG
|
B:CYS1122
|
2.3
|
39.9
|
1.0
|
SG
|
B:CYS1119
|
2.3
|
41.8
|
1.0
|
SG
|
B:CYS1137
|
2.3
|
53.6
|
1.0
|
SG
|
B:CYS1140
|
2.3
|
51.7
|
1.0
|
CB
|
B:CYS1119
|
2.8
|
41.8
|
1.0
|
CB
|
B:CYS1137
|
3.1
|
53.6
|
1.0
|
CB
|
B:CYS1140
|
3.1
|
51.7
|
1.0
|
CB
|
B:CYS1122
|
3.6
|
39.9
|
1.0
|
N
|
B:CYS1140
|
3.6
|
51.7
|
1.0
|
CA
|
B:CYS1140
|
4.0
|
51.7
|
1.0
|
N
|
B:CYS1122
|
4.0
|
39.9
|
1.0
|
OD1
|
B:ASN1142
|
4.1
|
54.8
|
1.0
|
CA
|
B:CYS1119
|
4.3
|
41.8
|
1.0
|
CA
|
B:CYS1122
|
4.4
|
39.9
|
1.0
|
CA
|
B:CYS1137
|
4.5
|
53.6
|
1.0
|
C
|
B:GLY1139
|
4.6
|
52.1
|
1.0
|
CB
|
B:LEU1121
|
4.7
|
40.5
|
1.0
|
CG
|
B:ASN1142
|
4.9
|
54.8
|
1.0
|
CA
|
B:GLY1139
|
4.9
|
52.1
|
1.0
|
C
|
B:CYS1137
|
5.0
|
53.6
|
1.0
|
C
|
B:CYS1119
|
5.0
|
41.8
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7opd
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Zinc Binding Sites List in 7opd
Zinc binding site 4 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:123.5
occ:1.00
|
SG
|
C:CYS97
|
2.2
|
41.5
|
1.0
|
SG
|
C:CYS90
|
2.2
|
65.4
|
1.0
|
SG
|
C:CYS88
|
2.2
|
57.8
|
1.0
|
SG
|
C:CYS94
|
2.3
|
49.6
|
1.0
|
CB
|
C:CYS88
|
3.0
|
57.8
|
1.0
|
CB
|
C:CYS97
|
3.1
|
41.5
|
1.0
|
CB
|
C:CYS94
|
3.5
|
49.6
|
1.0
|
CB
|
C:CYS90
|
3.6
|
65.4
|
1.0
|
N
|
C:CYS94
|
3.6
|
49.6
|
1.0
|
N
|
C:CYS97
|
4.0
|
41.5
|
1.0
|
CA
|
C:CYS94
|
4.0
|
49.6
|
1.0
|
C
|
C:PHE93
|
4.0
|
40.0
|
1.0
|
CA
|
C:CYS97
|
4.1
|
41.5
|
1.0
|
O
|
C:CYS94
|
4.2
|
49.6
|
1.0
|
CA
|
C:CYS88
|
4.4
|
57.8
|
1.0
|
C
|
C:CYS94
|
4.4
|
49.6
|
1.0
|
CA
|
C:PHE93
|
4.5
|
40.0
|
1.0
|
O
|
C:PHE93
|
4.6
|
40.0
|
1.0
|
O
|
C:GLU91
|
4.6
|
69.3
|
1.0
|
N
|
C:CYS90
|
4.6
|
65.4
|
1.0
|
CA
|
C:CYS90
|
4.6
|
65.4
|
1.0
|
C
|
C:GLU96
|
4.8
|
44.7
|
1.0
|
C
|
C:CYS97
|
4.9
|
41.5
|
1.0
|
C
|
C:CYS88
|
4.9
|
57.8
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7opd
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Zinc Binding Sites List in 7opd
Zinc binding site 5 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:132.6
occ:1.00
|
SG
|
I:CYS20
|
2.3
|
97.6
|
1.0
|
SG
|
I:CYS42
|
2.3
|
104.2
|
1.0
|
SG
|
I:CYS17
|
2.3
|
100.9
|
1.0
|
SG
|
I:CYS39
|
2.3
|
103.8
|
1.0
|
CB
|
I:CYS17
|
2.4
|
100.9
|
1.0
|
CB
|
I:CYS39
|
2.5
|
103.8
|
1.0
|
CB
|
I:CYS42
|
3.5
|
104.2
|
1.0
|
CA
|
I:CYS17
|
3.8
|
100.9
|
1.0
|
CB
|
I:CYS20
|
3.9
|
97.6
|
1.0
|
N
|
I:CYS42
|
4.0
|
104.2
|
1.0
|
CA
|
I:CYS39
|
4.0
|
103.8
|
1.0
|
N
|
I:CYS20
|
4.2
|
97.6
|
1.0
|
CB
|
I:TYR44
|
4.2
|
106.3
|
1.0
|
CA
|
I:CYS42
|
4.3
|
104.2
|
1.0
|
CA
|
I:CYS20
|
4.6
|
97.6
|
1.0
|
N
|
I:CYS17
|
4.6
|
100.9
|
1.0
|
CD2
|
I:LEU24
|
4.6
|
102.0
|
1.0
|
C
|
I:CYS42
|
4.7
|
104.2
|
1.0
|
O
|
I:ASN22
|
4.7
|
92.5
|
1.0
|
C
|
I:CYS17
|
4.7
|
100.9
|
1.0
|
N
|
I:CYS39
|
4.8
|
103.8
|
1.0
|
C
|
I:CYS39
|
4.8
|
103.8
|
1.0
|
N
|
I:ASN22
|
4.8
|
92.5
|
1.0
|
N
|
I:TYR44
|
4.9
|
106.3
|
1.0
|
CB
|
I:ASN22
|
4.9
|
92.5
|
1.0
|
N
|
I:ASN21
|
5.0
|
92.8
|
1.0
|
O
|
I:CYS42
|
5.0
|
104.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7opd
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Zinc Binding Sites List in 7opd
Zinc binding site 6 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn202
b:94.4
occ:1.00
|
SG
|
I:CYS89
|
2.2
|
68.1
|
1.0
|
SG
|
I:CYS86
|
2.3
|
61.9
|
1.0
|
SG
|
I:CYS119
|
2.3
|
64.3
|
1.0
|
SG
|
I:CYS114
|
2.3
|
53.6
|
1.0
|
CB
|
I:CYS114
|
2.6
|
53.6
|
1.0
|
CB
|
I:CYS86
|
3.1
|
61.9
|
1.0
|
CB
|
I:CYS89
|
3.5
|
68.1
|
1.0
|
CB
|
I:CYS119
|
3.5
|
64.3
|
1.0
|
CB
|
I:HIS121
|
3.8
|
57.0
|
1.0
|
N
|
I:CYS89
|
4.1
|
68.1
|
1.0
|
CA
|
I:CYS114
|
4.1
|
53.6
|
1.0
|
N
|
I:HIS121
|
4.2
|
57.0
|
1.0
|
CA
|
I:CYS89
|
4.4
|
68.1
|
1.0
|
CA
|
I:CYS86
|
4.5
|
61.9
|
1.0
|
CA
|
I:HIS121
|
4.6
|
57.0
|
1.0
|
CB
|
I:ALA116
|
4.7
|
64.0
|
1.0
|
N
|
I:GLY120
|
4.7
|
59.6
|
1.0
|
CB
|
I:LYS88
|
4.7
|
66.2
|
1.0
|
CB
|
I:HIS91
|
4.8
|
63.0
|
1.0
|
CA
|
I:CYS119
|
4.8
|
64.3
|
1.0
|
C
|
I:CYS119
|
4.8
|
64.3
|
1.0
|
C
|
I:CYS114
|
4.9
|
53.6
|
1.0
|
CG
|
I:HIS121
|
4.9
|
57.0
|
1.0
|
C
|
I:LYS88
|
4.9
|
66.2
|
1.0
|
N
|
I:CYS114
|
4.9
|
53.6
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7opd
Go back to
Zinc Binding Sites List in 7opd
Zinc binding site 7 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:36.2
occ:1.00
|
SG
|
J:CYS10
|
2.2
|
9.7
|
1.0
|
SG
|
J:CYS44
|
2.2
|
9.7
|
1.0
|
SG
|
J:CYS7
|
2.3
|
41.6
|
1.0
|
SG
|
J:CYS45
|
2.3
|
14.2
|
1.0
|
CB
|
J:CYS7
|
3.0
|
41.6
|
1.0
|
N
|
J:CYS45
|
3.4
|
14.2
|
1.0
|
CB
|
J:CYS44
|
3.4
|
9.7
|
1.0
|
CB
|
J:CYS10
|
3.4
|
9.7
|
1.0
|
CB
|
J:CYS45
|
3.7
|
14.2
|
1.0
|
N
|
J:CYS10
|
3.8
|
9.7
|
1.0
|
CA
|
J:CYS45
|
3.8
|
14.2
|
1.0
|
C
|
J:CYS44
|
3.9
|
9.7
|
1.0
|
CA
|
J:CYS10
|
4.2
|
9.7
|
1.0
|
CA
|
J:CYS44
|
4.2
|
9.7
|
1.0
|
NE
|
J:ARG42
|
4.2
|
8.2
|
1.0
|
CA
|
J:CYS7
|
4.5
|
41.6
|
1.0
|
CB
|
J:THR9
|
4.6
|
13.4
|
1.0
|
O
|
J:CYS44
|
4.6
|
9.7
|
1.0
|
CB
|
J:LYS12
|
4.6
|
14.3
|
1.0
|
CB
|
J:ARG42
|
4.7
|
8.2
|
1.0
|
N
|
J:GLY11
|
4.8
|
15.1
|
1.0
|
NH2
|
J:ARG42
|
4.9
|
8.2
|
1.0
|
C
|
J:THR9
|
4.9
|
13.4
|
1.0
|
N
|
J:CYS44
|
4.9
|
9.7
|
1.0
|
N
|
J:LYS12
|
4.9
|
14.3
|
1.0
|
N
|
J:THR9
|
5.0
|
13.4
|
1.0
|
C
|
J:CYS7
|
5.0
|
41.6
|
1.0
|
C
|
J:CYS10
|
5.0
|
9.7
|
1.0
|
CD
|
J:ARG42
|
5.0
|
8.2
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7opd
Go back to
Zinc Binding Sites List in 7opd
Zinc binding site 8 out
of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:96.7
occ:1.00
|
SG
|
L:CYS36
|
2.2
|
56.7
|
1.0
|
SG
|
L:CYS22
|
2.2
|
51.3
|
1.0
|
SG
|
L:CYS39
|
2.3
|
58.5
|
1.0
|
SG
|
L:CYS19
|
2.3
|
46.0
|
1.0
|
CB
|
L:CYS36
|
2.8
|
56.7
|
1.0
|
CB
|
L:CYS19
|
3.1
|
46.0
|
1.0
|
CB
|
L:CYS22
|
3.3
|
51.3
|
1.0
|
CB
|
L:CYS39
|
3.6
|
58.5
|
1.0
|
N
|
L:CYS39
|
3.7
|
58.5
|
1.0
|
N
|
L:CYS22
|
4.0
|
51.3
|
1.0
|
CB
|
L:TYR41
|
4.1
|
45.1
|
1.0
|
CA
|
L:CYS39
|
4.1
|
58.5
|
1.0
|
OE1
|
L:GLU38
|
4.1
|
66.6
|
1.0
|
CA
|
L:CYS22
|
4.2
|
51.3
|
1.0
|
CA
|
L:CYS36
|
4.3
|
56.7
|
1.0
|
N
|
L:TYR41
|
4.3
|
45.1
|
1.0
|
N
|
L:GLY40
|
4.4
|
57.1
|
1.0
|
C
|
L:CYS39
|
4.5
|
58.5
|
1.0
|
CA
|
L:CYS19
|
4.5
|
46.0
|
1.0
|
CB
|
L:GLU38
|
4.5
|
66.6
|
1.0
|
C
|
L:GLU38
|
4.6
|
66.6
|
1.0
|
OG1
|
L:THR24
|
4.7
|
56.1
|
1.0
|
N
|
L:GLU38
|
4.7
|
66.6
|
1.0
|
C
|
L:CYS36
|
4.8
|
56.7
|
1.0
|
CA
|
L:TYR41
|
4.8
|
45.1
|
1.0
|
CA
|
L:GLU38
|
4.9
|
66.6
|
1.0
|
C
|
L:CYS22
|
4.9
|
51.3
|
1.0
|
CB
|
L:THR24
|
5.0
|
56.1
|
1.0
|
|
Reference:
G.Kokic,
F.R.Wagner,
A.Chernev,
H.Urlaub,
P.Cramer.
Structural Basis of Human Transcription-Dna Repair Coupling. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 34526721
DOI: 10.1038/S41586-021-03906-4
Page generated: Wed Oct 30 08:40:45 2024
|