Zinc in PDB 6gmh: Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Enzymatic activity of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
All present enzymatic activity of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6:
2.7.7.6;
Other elements in 6gmh:
The structure of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
(pdb code 6gmh). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the
Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6, PDB code: 6gmh:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Zinc binding site 1 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 1 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2001
b:0.6
occ:1.00
|
NE2
|
A:HIS84
|
2.2
|
0.3
|
1.0
|
SG
|
A:CYS74
|
2.5
|
0.8
|
1.0
|
CD2
|
A:HIS84
|
2.6
|
0.3
|
1.0
|
SG
|
A:CYS71
|
2.6
|
0.2
|
1.0
|
CB
|
A:CYS71
|
3.2
|
0.2
|
1.0
|
O
|
A:PRO82
|
3.4
|
0.1
|
1.0
|
CE1
|
A:HIS84
|
3.5
|
0.3
|
1.0
|
CB
|
A:CYS81
|
3.7
|
0.4
|
1.0
|
SG
|
A:CYS81
|
3.7
|
0.4
|
1.0
|
OG1
|
A:THR73
|
3.7
|
0.6
|
1.0
|
CG
|
A:HIS84
|
3.9
|
0.3
|
1.0
|
CB
|
A:CYS74
|
4.1
|
0.8
|
1.0
|
CA
|
A:GLY63
|
4.2
|
0.2
|
1.0
|
ND1
|
A:HIS84
|
4.3
|
0.3
|
1.0
|
N
|
A:CYS74
|
4.3
|
0.8
|
1.0
|
O
|
A:CYS74
|
4.6
|
0.8
|
1.0
|
N
|
A:GLY63
|
4.6
|
0.2
|
1.0
|
C
|
A:PRO82
|
4.6
|
0.1
|
1.0
|
CA
|
A:CYS71
|
4.7
|
0.2
|
1.0
|
CA
|
A:CYS74
|
4.7
|
0.8
|
1.0
|
C
|
A:GLY63
|
4.9
|
0.2
|
1.0
|
CA
|
A:CYS81
|
5.0
|
0.4
|
1.0
|
|
Zinc binding site 2 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 2 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2002
b:0.0
occ:1.00
|
SG
|
A:CYS114
|
2.6
|
0.5
|
1.0
|
SG
|
A:CYS111
|
2.7
|
0.9
|
1.0
|
CE1
|
A:TYR187
|
3.1
|
0.0
|
1.0
|
CZ
|
A:TYR187
|
3.4
|
0.0
|
1.0
|
CD1
|
A:TYR187
|
3.5
|
0.0
|
1.0
|
CD
|
A:LYS116
|
3.6
|
0.2
|
1.0
|
CB
|
A:CYS111
|
3.7
|
0.9
|
1.0
|
OH
|
A:TYR187
|
3.8
|
0.0
|
1.0
|
SG
|
A:CYS184
|
3.9
|
0.2
|
1.0
|
CE2
|
A:TYR187
|
4.0
|
0.0
|
1.0
|
CG
|
A:TYR187
|
4.1
|
0.0
|
1.0
|
N
|
A:CYS184
|
4.2
|
0.2
|
1.0
|
CB
|
A:LYS116
|
4.2
|
0.2
|
1.0
|
CG
|
A:LYS116
|
4.3
|
0.2
|
1.0
|
CB
|
A:CYS114
|
4.3
|
0.5
|
1.0
|
CD2
|
A:TYR187
|
4.3
|
0.0
|
1.0
|
CE
|
A:LYS116
|
4.4
|
0.2
|
1.0
|
NZ
|
A:LYS116
|
4.4
|
0.2
|
1.0
|
O
|
A:GLY182
|
4.5
|
0.7
|
1.0
|
CA
|
A:GLY183
|
4.6
|
0.6
|
1.0
|
CB
|
A:CYS184
|
4.8
|
0.2
|
1.0
|
O
|
A:PHE112
|
4.8
|
0.2
|
1.0
|
C
|
A:GLY183
|
5.0
|
0.6
|
1.0
|
|
Zinc binding site 3 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 3 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1201
b:0.7
occ:1.00
|
SG
|
B:CYS1122
|
2.5
|
0.5
|
1.0
|
SG
|
B:CYS1137
|
2.5
|
0.2
|
1.0
|
SG
|
B:CYS1119
|
2.5
|
0.1
|
1.0
|
CB
|
B:CYS1140
|
2.5
|
0.2
|
1.0
|
CB
|
B:CYS1119
|
2.9
|
0.1
|
1.0
|
SG
|
B:CYS1140
|
3.2
|
0.2
|
1.0
|
CB
|
B:CYS1137
|
3.4
|
0.2
|
1.0
|
CA
|
B:CYS1140
|
3.9
|
0.2
|
1.0
|
CB
|
B:CYS1122
|
4.0
|
0.5
|
1.0
|
O
|
B:CYS1122
|
4.0
|
0.5
|
1.0
|
N
|
B:CYS1122
|
4.0
|
0.5
|
1.0
|
N
|
B:CYS1140
|
4.3
|
0.2
|
1.0
|
CA
|
B:CYS1119
|
4.4
|
0.1
|
1.0
|
CA
|
B:CYS1122
|
4.4
|
0.5
|
1.0
|
C
|
B:CYS1122
|
4.6
|
0.5
|
1.0
|
CA
|
B:CYS1137
|
4.8
|
0.2
|
1.0
|
ND2
|
B:ASN1142
|
4.8
|
0.3
|
1.0
|
C
|
B:CYS1140
|
4.9
|
0.2
|
1.0
|
OD1
|
B:ASN1142
|
4.9
|
0.3
|
1.0
|
O
|
B:CYS1137
|
4.9
|
0.2
|
1.0
|
O
|
B:ARG1138
|
4.9
|
0.6
|
1.0
|
C
|
B:CYS1137
|
5.0
|
0.2
|
1.0
|
CB
|
B:LEU1121
|
5.0
|
0.8
|
1.0
|
|
Zinc binding site 4 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 4 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:0.4
occ:1.00
|
SG
|
C:CYS90
|
2.4
|
0.0
|
1.0
|
SG
|
C:CYS88
|
2.4
|
0.1
|
1.0
|
SG
|
C:CYS94
|
2.4
|
91.8
|
1.0
|
SG
|
C:CYS97
|
2.5
|
92.7
|
1.0
|
CB
|
C:CYS97
|
2.5
|
92.7
|
1.0
|
CB
|
C:CYS88
|
2.9
|
0.1
|
1.0
|
N
|
C:CYS97
|
3.6
|
92.7
|
1.0
|
CA
|
C:CYS97
|
3.6
|
92.7
|
1.0
|
CB
|
C:CYS90
|
3.7
|
0.0
|
1.0
|
CB
|
C:CYS94
|
3.8
|
91.8
|
1.0
|
N
|
C:CYS94
|
4.1
|
91.8
|
1.0
|
C
|
C:GLU96
|
4.3
|
92.2
|
1.0
|
CA
|
C:CYS88
|
4.3
|
0.1
|
1.0
|
CA
|
C:CYS94
|
4.4
|
91.8
|
1.0
|
O
|
C:CYS94
|
4.5
|
91.8
|
1.0
|
N
|
C:CYS90
|
4.6
|
0.0
|
1.0
|
CA
|
C:CYS90
|
4.7
|
0.0
|
1.0
|
C
|
C:CYS94
|
4.7
|
91.8
|
1.0
|
C
|
C:CYS97
|
4.7
|
92.7
|
1.0
|
C
|
C:CYS88
|
4.8
|
0.1
|
1.0
|
CB
|
C:GLU96
|
4.9
|
92.2
|
1.0
|
O
|
C:GLU96
|
4.9
|
92.2
|
1.0
|
CA
|
C:GLU96
|
5.0
|
92.2
|
1.0
|
|
Zinc binding site 5 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 5 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:0.5
occ:1.00
|
SG
|
I:CYS17
|
2.4
|
0.9
|
1.0
|
SG
|
I:CYS39
|
2.4
|
0.9
|
1.0
|
SG
|
I:CYS20
|
2.4
|
0.9
|
1.0
|
SG
|
I:CYS42
|
2.5
|
0.1
|
1.0
|
CB
|
I:CYS39
|
2.6
|
0.9
|
1.0
|
CB
|
I:CYS17
|
3.1
|
0.9
|
1.0
|
CB
|
I:CYS42
|
3.8
|
0.1
|
1.0
|
N
|
I:CYS42
|
3.8
|
0.1
|
1.0
|
CB
|
I:CYS20
|
4.0
|
0.9
|
1.0
|
CA
|
I:CYS39
|
4.1
|
0.9
|
1.0
|
N
|
I:CYS20
|
4.2
|
0.9
|
1.0
|
O
|
I:CYS42
|
4.2
|
0.1
|
1.0
|
CA
|
I:CYS42
|
4.2
|
0.1
|
1.0
|
C
|
I:CYS42
|
4.5
|
0.1
|
1.0
|
CA
|
I:CYS17
|
4.5
|
0.9
|
1.0
|
CA
|
I:CYS20
|
4.6
|
0.9
|
1.0
|
CB
|
I:ASN41
|
4.8
|
0.8
|
1.0
|
CB
|
I:TYR44
|
4.8
|
0.5
|
1.0
|
C
|
I:CYS39
|
4.9
|
0.9
|
1.0
|
N
|
I:CYS39
|
4.9
|
0.9
|
1.0
|
CB
|
I:GLU19
|
4.9
|
0.6
|
1.0
|
C
|
I:ASN41
|
4.9
|
0.8
|
1.0
|
CB
|
I:ASN22
|
4.9
|
0.4
|
1.0
|
N
|
I:ASN41
|
4.9
|
0.8
|
1.0
|
OD1
|
I:ASN22
|
5.0
|
0.4
|
1.0
|
|
Zinc binding site 6 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 6 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn202
b:0.7
occ:1.00
|
SG
|
I:CYS114
|
2.4
|
0.0
|
1.0
|
SG
|
I:CYS89
|
2.4
|
0.4
|
1.0
|
SG
|
I:CYS119
|
2.4
|
0.7
|
1.0
|
SG
|
I:CYS86
|
2.4
|
0.2
|
1.0
|
CB
|
I:CYS86
|
2.8
|
0.2
|
1.0
|
CB
|
I:CYS119
|
3.4
|
0.7
|
1.0
|
CB
|
I:CYS114
|
3.4
|
0.0
|
1.0
|
CB
|
I:CYS89
|
3.8
|
0.4
|
1.0
|
CB
|
I:HIS91
|
4.0
|
0.7
|
1.0
|
N
|
I:CYS89
|
4.0
|
0.4
|
1.0
|
N
|
I:HIS91
|
4.2
|
0.7
|
1.0
|
CA
|
I:CYS86
|
4.3
|
0.2
|
1.0
|
CA
|
I:CYS89
|
4.4
|
0.4
|
1.0
|
N
|
I:GLY90
|
4.6
|
0.3
|
1.0
|
O
|
I:THR115
|
4.6
|
0.1
|
1.0
|
C
|
I:CYS89
|
4.7
|
0.4
|
1.0
|
CA
|
I:HIS91
|
4.7
|
0.7
|
1.0
|
CA
|
I:CYS119
|
4.8
|
0.7
|
1.0
|
CA
|
I:CYS114
|
4.9
|
0.0
|
1.0
|
CB
|
I:HIS121
|
5.0
|
0.3
|
1.0
|
O
|
I:HIS91
|
5.0
|
0.7
|
1.0
|
|
Zinc binding site 7 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 7 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:96.0
occ:1.00
|
SG
|
J:CYS45
|
2.4
|
71.3
|
1.0
|
SG
|
J:CYS44
|
2.4
|
71.2
|
1.0
|
SG
|
J:CYS7
|
2.4
|
66.2
|
1.0
|
CB
|
J:CYS10
|
2.5
|
70.5
|
1.0
|
N
|
J:CYS45
|
3.0
|
71.3
|
1.0
|
CB
|
J:CYS7
|
3.1
|
66.2
|
1.0
|
C
|
J:CYS44
|
3.2
|
71.2
|
1.0
|
CA
|
J:CYS45
|
3.3
|
71.3
|
1.0
|
CB
|
J:CYS44
|
3.3
|
71.2
|
1.0
|
CB
|
J:CYS45
|
3.4
|
71.3
|
1.0
|
N
|
J:CYS10
|
3.4
|
70.5
|
1.0
|
CA
|
J:CYS10
|
3.6
|
70.5
|
1.0
|
O
|
J:CYS44
|
3.7
|
71.2
|
1.0
|
SG
|
J:CYS10
|
3.7
|
70.5
|
1.0
|
CA
|
J:CYS44
|
3.9
|
71.2
|
1.0
|
CA
|
J:CYS7
|
4.6
|
66.2
|
1.0
|
C
|
J:CYS10
|
4.6
|
70.5
|
1.0
|
C
|
J:THR9
|
4.6
|
66.8
|
1.0
|
N
|
J:GLY11
|
4.7
|
68.9
|
1.0
|
N
|
J:CYS44
|
4.7
|
71.2
|
1.0
|
CB
|
J:THR9
|
4.7
|
66.8
|
1.0
|
NE
|
J:ARG42
|
4.8
|
70.3
|
1.0
|
C
|
J:CYS45
|
4.8
|
71.3
|
1.0
|
CB
|
J:LYS12
|
4.9
|
67.0
|
1.0
|
|
Zinc binding site 8 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 8 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:0.3
occ:1.00
|
O
|
L:GLU38
|
2.5
|
0.3
|
1.0
|
SG
|
L:CYS22
|
2.5
|
0.5
|
1.0
|
SG
|
L:CYS39
|
2.5
|
0.6
|
1.0
|
SG
|
L:CYS19
|
2.6
|
0.5
|
1.0
|
SG
|
L:CYS36
|
2.6
|
0.9
|
1.0
|
CB
|
L:CYS36
|
2.9
|
0.9
|
1.0
|
CB
|
L:CYS19
|
3.5
|
0.5
|
1.0
|
C
|
L:GLU38
|
3.6
|
0.3
|
1.0
|
CB
|
L:CYS22
|
3.7
|
0.5
|
1.0
|
CB
|
L:CYS39
|
3.9
|
0.6
|
1.0
|
CB
|
L:TYR41
|
4.0
|
0.9
|
1.0
|
N
|
L:CYS22
|
4.2
|
0.5
|
1.0
|
N
|
L:TYR41
|
4.3
|
0.9
|
1.0
|
CA
|
L:CYS36
|
4.3
|
0.9
|
1.0
|
CG
|
L:GLU38
|
4.3
|
0.3
|
1.0
|
N
|
L:CYS39
|
4.4
|
0.6
|
1.0
|
CA
|
L:CYS39
|
4.5
|
0.6
|
1.0
|
CA
|
L:CYS22
|
4.5
|
0.5
|
1.0
|
N
|
L:GLY40
|
4.6
|
0.9
|
1.0
|
C
|
L:CYS39
|
4.6
|
0.6
|
1.0
|
CA
|
L:GLU38
|
4.7
|
0.3
|
1.0
|
C
|
L:CYS36
|
4.7
|
0.9
|
1.0
|
N
|
L:GLU38
|
4.7
|
0.3
|
1.0
|
CA
|
L:TYR41
|
4.8
|
0.9
|
1.0
|
O
|
L:CYS36
|
4.9
|
0.9
|
1.0
|
CA
|
L:CYS19
|
4.9
|
0.5
|
1.0
|
CB
|
L:GLU21
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 9 out
of 9 in 6gmh
Go back to
Zinc Binding Sites List in 6gmh
Zinc binding site 9 out
of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Zn201
b:0.6
occ:1.00
|
SG
|
Y:CYS33
|
2.6
|
0.7
|
1.0
|
SG
|
Y:CYS19
|
2.6
|
0.8
|
1.0
|
SG
|
Y:CYS36
|
2.7
|
0.2
|
1.0
|
SG
|
Y:CYS16
|
2.7
|
0.0
|
1.0
|
CB
|
Y:CYS36
|
2.7
|
0.2
|
1.0
|
CB
|
Y:CYS19
|
3.4
|
0.8
|
1.0
|
CB
|
Y:CYS16
|
3.7
|
0.0
|
1.0
|
CB
|
Y:CYS33
|
3.8
|
0.7
|
1.0
|
N
|
Y:CYS19
|
3.8
|
0.8
|
1.0
|
N
|
Y:CYS36
|
3.9
|
0.2
|
1.0
|
CA
|
Y:CYS36
|
3.9
|
0.2
|
1.0
|
CD1
|
Y:LEU40
|
4.1
|
0.2
|
1.0
|
CA
|
Y:CYS19
|
4.2
|
0.8
|
1.0
|
CB
|
Y:LEU18
|
4.2
|
0.8
|
1.0
|
CB
|
Y:ASN35
|
4.4
|
0.3
|
1.0
|
C
|
Y:LEU18
|
4.6
|
0.8
|
1.0
|
C
|
Y:ASN35
|
4.7
|
0.3
|
1.0
|
CG
|
Y:LEU18
|
4.7
|
0.8
|
1.0
|
C
|
Y:CYS36
|
4.7
|
0.2
|
1.0
|
CD2
|
Y:LEU18
|
4.8
|
0.8
|
1.0
|
CA
|
Y:LEU18
|
4.8
|
0.8
|
1.0
|
N
|
Y:LEU18
|
4.9
|
0.8
|
1.0
|
CA
|
Y:ASN35
|
5.0
|
0.3
|
1.0
|
|
Reference:
S.M.Vos,
L.Farnung,
M.Boehning,
C.Wigge,
A.Linden,
H.Urlaub,
P.Cramer.
Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6. Nature V. 560 607 2018.
ISSN: ISSN 0028-0836
PubMed: 30135578
DOI: 10.1038/S41586-018-0440-4
Page generated: Mon Oct 28 21:54:40 2024
|