Zinc in PDB 7ol0: Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Enzymatic activity of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
All present enzymatic activity of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5):
2.7.7.6;
Other elements in 7ol0:
The structure of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
(pdb code 7ol0). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5), PDB code: 7ol0:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7ol0
Go back to
Zinc Binding Sites List in 7ol0
Zinc binding site 1 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2002
b:70.0
occ:1.00
|
NE2
|
A:HIS84
|
2.1
|
41.4
|
1.0
|
SG
|
A:CYS74
|
2.3
|
51.6
|
1.0
|
SG
|
A:CYS71
|
2.3
|
53.9
|
1.0
|
SG
|
A:CYS81
|
2.3
|
47.3
|
1.0
|
CD2
|
A:HIS84
|
2.7
|
41.4
|
1.0
|
CB
|
A:CYS71
|
2.9
|
53.9
|
1.0
|
CE1
|
A:HIS84
|
3.2
|
41.4
|
1.0
|
CB
|
A:CYS81
|
3.5
|
47.3
|
1.0
|
N
|
A:CYS74
|
3.8
|
51.6
|
1.0
|
CB
|
A:CYS74
|
3.9
|
51.6
|
1.0
|
CG
|
A:HIS84
|
4.0
|
41.4
|
1.0
|
ND1
|
A:HIS84
|
4.2
|
41.4
|
1.0
|
CA
|
A:CYS81
|
4.2
|
47.3
|
1.0
|
CA
|
A:CYS74
|
4.3
|
51.6
|
1.0
|
O
|
A:CYS74
|
4.3
|
51.6
|
1.0
|
CA
|
A:CYS71
|
4.4
|
53.9
|
1.0
|
CB
|
A:THR73
|
4.5
|
46.5
|
1.0
|
CA
|
A:GLY63
|
4.5
|
47.4
|
1.0
|
C
|
A:CYS74
|
4.6
|
51.6
|
1.0
|
N
|
A:GLY83
|
4.7
|
41.1
|
1.0
|
CD
|
A:PRO82
|
4.7
|
42.9
|
1.0
|
N
|
A:THR73
|
4.8
|
46.5
|
1.0
|
C
|
A:THR73
|
4.8
|
46.5
|
1.0
|
C
|
A:CYS81
|
4.9
|
47.3
|
1.0
|
N
|
A:GLY63
|
4.9
|
47.4
|
1.0
|
CA
|
A:THR73
|
4.9
|
46.5
|
1.0
|
CA
|
A:GLY83
|
5.0
|
41.1
|
1.0
|
N
|
A:PRO82
|
5.0
|
42.9
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7ol0
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Zinc Binding Sites List in 7ol0
Zinc binding site 2 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2003
b:116.6
occ:1.00
|
SG
|
A:CYS111
|
2.3
|
72.6
|
1.0
|
SG
|
A:CYS184
|
2.3
|
78.9
|
1.0
|
SG
|
A:CYS114
|
2.3
|
75.6
|
1.0
|
SG
|
A:CYS154
|
2.3
|
81.2
|
1.0
|
CB
|
A:CYS154
|
3.1
|
81.2
|
1.0
|
CB
|
A:CYS111
|
3.2
|
72.6
|
1.0
|
CB
|
A:CYS114
|
3.7
|
75.6
|
1.0
|
CB
|
A:CYS184
|
3.8
|
78.9
|
1.0
|
N
|
A:CYS184
|
3.9
|
78.9
|
1.0
|
CA
|
A:CYS184
|
4.2
|
78.9
|
1.0
|
O
|
A:CYS184
|
4.2
|
78.9
|
1.0
|
N
|
A:CYS114
|
4.2
|
75.6
|
1.0
|
C
|
A:CYS184
|
4.3
|
78.9
|
1.0
|
NE2
|
A:GLN188
|
4.4
|
75.7
|
1.0
|
CA
|
A:CYS114
|
4.6
|
75.6
|
1.0
|
CA
|
A:CYS154
|
4.6
|
81.2
|
1.0
|
CA
|
A:CYS111
|
4.6
|
72.6
|
1.0
|
C
|
A:GLY183
|
4.9
|
68.1
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7ol0
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Zinc Binding Sites List in 7ol0
Zinc binding site 3 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2000
b:100.5
occ:1.00
|
SG
|
B:CYS1199
|
2.3
|
49.1
|
1.0
|
SG
|
B:CYS1214
|
2.3
|
64.8
|
1.0
|
SG
|
B:CYS1196
|
2.3
|
50.7
|
1.0
|
SG
|
B:CYS1217
|
2.3
|
65.7
|
1.0
|
CB
|
B:CYS1196
|
2.9
|
50.7
|
1.0
|
CB
|
B:CYS1199
|
3.1
|
49.1
|
1.0
|
CB
|
B:CYS1217
|
3.2
|
65.7
|
1.0
|
CB
|
B:CYS1214
|
3.5
|
64.8
|
1.0
|
N
|
B:CYS1199
|
3.6
|
49.1
|
1.0
|
CA
|
B:CYS1199
|
4.0
|
49.1
|
1.0
|
N
|
B:CYS1217
|
4.3
|
65.7
|
1.0
|
CA
|
B:CYS1196
|
4.4
|
50.7
|
1.0
|
CA
|
B:CYS1217
|
4.4
|
65.7
|
1.0
|
OD1
|
B:ASN1219
|
4.5
|
64.1
|
1.0
|
CB
|
B:LEU1198
|
4.7
|
48.8
|
1.0
|
N
|
B:GLY1200
|
4.8
|
42.8
|
1.0
|
C
|
B:CYS1199
|
4.8
|
49.1
|
1.0
|
C
|
B:LEU1198
|
4.8
|
48.8
|
1.0
|
CA
|
B:CYS1214
|
4.9
|
64.8
|
1.0
|
C
|
B:CYS1196
|
4.9
|
50.7
|
1.0
|
O
|
B:ARG1215
|
5.0
|
65.2
|
1.0
|
ND2
|
B:ASN1219
|
5.0
|
64.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7ol0
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Zinc Binding Sites List in 7ol0
Zinc binding site 4 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:88.7
occ:1.00
|
SG
|
C:CYS94
|
2.3
|
35.5
|
1.0
|
SG
|
C:CYS90
|
2.3
|
49.6
|
1.0
|
SG
|
C:CYS88
|
2.3
|
45.6
|
1.0
|
SG
|
C:CYS97
|
2.3
|
32.8
|
1.0
|
CB
|
C:CYS88
|
3.1
|
45.6
|
1.0
|
CB
|
C:CYS97
|
3.2
|
32.8
|
1.0
|
CB
|
C:CYS90
|
3.4
|
49.6
|
1.0
|
CB
|
C:CYS94
|
3.4
|
35.5
|
1.0
|
N
|
C:CYS94
|
3.6
|
35.5
|
1.0
|
N
|
C:CYS97
|
4.0
|
32.8
|
1.0
|
CA
|
C:CYS94
|
4.0
|
35.5
|
1.0
|
O
|
C:CYS94
|
4.2
|
35.5
|
1.0
|
CA
|
C:CYS97
|
4.2
|
32.8
|
1.0
|
N
|
C:CYS90
|
4.3
|
49.6
|
1.0
|
C
|
C:CYS94
|
4.4
|
35.5
|
1.0
|
CA
|
C:CYS90
|
4.4
|
49.6
|
1.0
|
CA
|
C:CYS88
|
4.4
|
45.6
|
1.0
|
C
|
C:PHE93
|
4.5
|
37.1
|
1.0
|
C
|
C:GLU96
|
4.6
|
37.8
|
1.0
|
NZ
|
Z:LYS718
|
4.7
|
54.4
|
1.0
|
C
|
C:CYS88
|
4.7
|
45.6
|
1.0
|
CA
|
C:PHE93
|
4.7
|
37.1
|
1.0
|
CB
|
C:GLU96
|
4.8
|
37.8
|
1.0
|
N
|
C:GLU96
|
4.9
|
37.8
|
1.0
|
N
|
C:THR89
|
5.0
|
45.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7ol0
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Zinc Binding Sites List in 7ol0
Zinc binding site 5 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:85.2
occ:1.00
|
SG
|
I:CYS119
|
2.3
|
54.6
|
1.0
|
SG
|
I:CYS114
|
2.3
|
40.7
|
1.0
|
SG
|
I:CYS89
|
2.3
|
57.6
|
1.0
|
SG
|
I:CYS86
|
2.3
|
54.1
|
1.0
|
CB
|
I:CYS114
|
3.1
|
40.7
|
1.0
|
CB
|
I:CYS86
|
3.1
|
54.1
|
1.0
|
CB
|
I:CYS119
|
3.4
|
54.6
|
1.0
|
CB
|
I:CYS89
|
3.5
|
57.6
|
1.0
|
N
|
I:CYS89
|
3.9
|
57.6
|
1.0
|
CA
|
I:CYS89
|
4.2
|
57.6
|
1.0
|
CB
|
I:HIS91
|
4.2
|
49.0
|
1.0
|
CB
|
I:HIS121
|
4.4
|
43.7
|
1.0
|
CB
|
I:ALA116
|
4.5
|
48.6
|
1.0
|
CA
|
I:CYS114
|
4.5
|
40.7
|
1.0
|
CA
|
I:CYS86
|
4.6
|
54.1
|
1.0
|
N
|
I:HIS91
|
4.7
|
49.0
|
1.0
|
C
|
I:CYS89
|
4.7
|
57.6
|
1.0
|
CB
|
I:LYS88
|
4.7
|
54.7
|
1.0
|
CA
|
I:CYS119
|
4.8
|
54.6
|
1.0
|
N
|
I:GLY90
|
4.9
|
54.0
|
1.0
|
N
|
I:HIS121
|
4.9
|
43.7
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7ol0
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Zinc Binding Sites List in 7ol0
Zinc binding site 6 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn202
b:95.8
occ:1.00
|
SG
|
I:CYS20
|
2.3
|
61.5
|
1.0
|
SG
|
I:CYS39
|
2.3
|
55.9
|
1.0
|
SG
|
I:CYS17
|
2.3
|
57.5
|
1.0
|
SG
|
I:CYS42
|
2.3
|
67.4
|
1.0
|
CB
|
I:CYS42
|
2.9
|
67.4
|
1.0
|
CB
|
I:CYS20
|
3.1
|
61.5
|
1.0
|
CB
|
I:CYS17
|
3.3
|
57.5
|
1.0
|
CB
|
I:CYS39
|
3.4
|
55.9
|
1.0
|
N
|
I:CYS20
|
3.5
|
61.5
|
1.0
|
N
|
I:CYS42
|
3.8
|
67.4
|
1.0
|
CA
|
I:CYS20
|
3.8
|
61.5
|
1.0
|
CA
|
I:CYS42
|
3.9
|
67.4
|
1.0
|
C
|
I:CYS20
|
4.4
|
61.5
|
1.0
|
N
|
I:ASN21
|
4.5
|
53.5
|
1.0
|
C
|
I:ASN41
|
4.5
|
61.6
|
1.0
|
CA
|
I:CYS17
|
4.7
|
57.5
|
1.0
|
C
|
I:GLU19
|
4.7
|
63.4
|
1.0
|
CA
|
I:CYS39
|
4.8
|
55.9
|
1.0
|
CB
|
I:TYR44
|
4.8
|
57.6
|
1.0
|
N
|
I:ASN22
|
4.9
|
51.4
|
1.0
|
CB
|
I:ASN41
|
4.9
|
61.6
|
1.0
|
N
|
I:GLU19
|
4.9
|
63.4
|
1.0
|
CB
|
I:GLU19
|
4.9
|
63.4
|
1.0
|
OE1
|
I:GLU19
|
4.9
|
63.4
|
1.0
|
N
|
I:ASN41
|
5.0
|
61.6
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7ol0
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Zinc Binding Sites List in 7ol0
Zinc binding site 7 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:43.0
occ:1.00
|
SG
|
J:CYS45
|
2.3
|
20.5
|
1.0
|
SG
|
J:CYS10
|
2.3
|
19.2
|
1.0
|
SG
|
J:CYS44
|
2.3
|
22.2
|
1.0
|
SG
|
J:CYS7
|
2.3
|
30.8
|
1.0
|
CB
|
J:CYS7
|
3.1
|
30.8
|
1.0
|
N
|
J:CYS45
|
3.3
|
20.5
|
1.0
|
CB
|
J:CYS10
|
3.4
|
19.2
|
1.0
|
CB
|
J:CYS44
|
3.5
|
22.2
|
1.0
|
CB
|
J:CYS45
|
3.5
|
20.5
|
1.0
|
CA
|
J:CYS45
|
3.7
|
20.5
|
1.0
|
C
|
J:CYS44
|
3.7
|
22.2
|
1.0
|
N
|
J:CYS10
|
3.8
|
19.2
|
1.0
|
CA
|
J:CYS10
|
4.1
|
19.2
|
1.0
|
CA
|
J:CYS44
|
4.2
|
22.2
|
1.0
|
O
|
J:CYS44
|
4.2
|
22.2
|
1.0
|
NE
|
J:ARG42
|
4.2
|
18.4
|
1.0
|
CA
|
J:CYS7
|
4.6
|
30.8
|
1.0
|
CB
|
J:THR9
|
4.6
|
23.9
|
1.0
|
CB
|
J:LYS12
|
4.6
|
17.5
|
1.0
|
N
|
J:GLY11
|
4.6
|
18.8
|
1.0
|
NH2
|
J:ARG42
|
4.7
|
18.4
|
1.0
|
C
|
J:CYS10
|
4.8
|
19.2
|
1.0
|
N
|
J:LYS12
|
4.8
|
17.5
|
1.0
|
N
|
J:CYS44
|
4.8
|
22.2
|
1.0
|
C
|
J:THR9
|
4.8
|
23.9
|
1.0
|
CB
|
J:ARG42
|
4.9
|
18.4
|
1.0
|
CG2
|
J:THR9
|
4.9
|
23.9
|
1.0
|
N
|
J:THR9
|
5.0
|
23.9
|
1.0
|
CZ
|
J:ARG42
|
5.0
|
18.4
|
1.0
|
C
|
J:CYS7
|
5.0
|
30.8
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7ol0
Go back to
Zinc Binding Sites List in 7ol0
Zinc binding site 8 out
of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:86.5
occ:1.00
|
SG
|
L:CYS22
|
2.3
|
46.4
|
1.0
|
SG
|
L:CYS19
|
2.3
|
40.8
|
1.0
|
SG
|
L:CYS36
|
2.3
|
49.3
|
1.0
|
SG
|
L:CYS39
|
2.3
|
52.0
|
1.0
|
CB
|
L:CYS19
|
3.0
|
40.8
|
1.0
|
CB
|
L:CYS36
|
3.1
|
49.3
|
1.0
|
CB
|
L:CYS22
|
3.4
|
46.4
|
1.0
|
CB
|
L:CYS39
|
3.8
|
52.0
|
1.0
|
N
|
L:CYS39
|
3.9
|
52.0
|
1.0
|
N
|
L:CYS22
|
4.1
|
46.4
|
1.0
|
OG1
|
L:THR24
|
4.2
|
45.0
|
1.0
|
CA
|
L:CYS22
|
4.3
|
46.4
|
1.0
|
CA
|
L:CYS39
|
4.3
|
52.0
|
1.0
|
CA
|
L:CYS19
|
4.5
|
40.8
|
1.0
|
CB
|
L:TYR41
|
4.5
|
39.4
|
1.0
|
CA
|
L:CYS36
|
4.5
|
49.3
|
1.0
|
CB
|
L:GLU38
|
4.6
|
58.4
|
1.0
|
CG
|
L:GLU21
|
4.7
|
48.6
|
1.0
|
N
|
L:TYR41
|
4.7
|
39.4
|
1.0
|
N
|
L:GLY40
|
4.7
|
46.6
|
1.0
|
C
|
L:CYS39
|
4.8
|
52.0
|
1.0
|
C
|
L:CYS22
|
4.9
|
46.4
|
1.0
|
C
|
L:GLU38
|
5.0
|
58.4
|
1.0
|
N
|
L:HIS23
|
5.0
|
43.8
|
1.0
|
|
Reference:
Y.Chen,
S.M.Vos,
C.Dienemann,
M.Ninov,
H.Urlaub,
P.Cramer.
Allosteric Transcription Stimulation By Rna Polymerase II Super Elongation Complex To Be Published.
Page generated: Wed Oct 30 08:34:30 2024
|