Zinc in PDB 6rid: Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex
Enzymatic activity of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex
All present enzymatic activity of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex:
2.7.7.6;
Other elements in 6rid:
The structure of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex
(pdb code 6rid). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex, PDB code: 6rid:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6rid
Go back to
Zinc Binding Sites List in 6rid
Zinc binding site 1 out
of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1302
b:75.7
occ:1.00
|
NE2
|
A:HIS62
|
2.1
|
48.9
|
1.0
|
SG
|
A:CYS52
|
2.2
|
60.1
|
1.0
|
SG
|
A:CYS59
|
2.2
|
52.6
|
1.0
|
SG
|
A:CYS49
|
2.3
|
59.7
|
1.0
|
CD2
|
A:HIS62
|
2.8
|
48.9
|
1.0
|
CB
|
A:CYS49
|
3.0
|
59.7
|
1.0
|
CE1
|
A:HIS62
|
3.2
|
48.9
|
1.0
|
CB
|
A:CYS59
|
3.4
|
52.6
|
1.0
|
CB
|
A:CYS52
|
3.5
|
60.1
|
1.0
|
CG
|
A:HIS62
|
4.0
|
48.9
|
1.0
|
N
|
A:CYS52
|
4.1
|
60.1
|
1.0
|
ND1
|
A:HIS62
|
4.1
|
48.9
|
1.0
|
CA
|
A:CYS59
|
4.3
|
52.6
|
1.0
|
CA
|
A:CYS52
|
4.4
|
60.1
|
1.0
|
CA
|
A:GLY42
|
4.5
|
55.5
|
1.0
|
CA
|
A:CYS49
|
4.5
|
59.7
|
1.0
|
N
|
A:GLY61
|
4.5
|
49.0
|
1.0
|
CB
|
A:THR51
|
4.5
|
55.7
|
1.0
|
N
|
A:ALA43
|
4.8
|
60.6
|
1.0
|
CA
|
A:GLY61
|
4.8
|
49.0
|
1.0
|
C
|
A:CYS59
|
4.9
|
52.6
|
1.0
|
N
|
A:PHE60
|
4.9
|
45.6
|
1.0
|
N
|
A:GLY42
|
5.0
|
55.5
|
1.0
|
C
|
A:THR51
|
5.0
|
55.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6rid
Go back to
Zinc Binding Sites List in 6rid
Zinc binding site 2 out
of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1303
b:0.2
occ:1.00
|
SG
|
A:CYS93
|
2.3
|
0.5
|
1.0
|
CB
|
A:CYS135
|
2.3
|
0.6
|
1.0
|
SG
|
A:CYS90
|
2.6
|
0.3
|
1.0
|
SG
|
A:CYS130
|
2.6
|
0.0
|
1.0
|
SG
|
A:CYS135
|
2.7
|
0.6
|
1.0
|
CB
|
A:CYS130
|
3.5
|
0.0
|
1.0
|
N
|
A:CYS93
|
3.5
|
0.5
|
1.0
|
CB
|
A:CYS93
|
3.6
|
0.5
|
1.0
|
CA
|
A:CYS135
|
3.6
|
0.6
|
1.0
|
CB
|
A:CYS90
|
3.8
|
0.3
|
1.0
|
O
|
A:CYS135
|
3.9
|
0.6
|
1.0
|
C
|
A:CYS135
|
3.9
|
0.6
|
1.0
|
OE1
|
A:GLN137
|
4.0
|
0.6
|
1.0
|
CB
|
A:HIS92
|
4.1
|
0.6
|
1.0
|
CA
|
A:CYS93
|
4.2
|
0.5
|
1.0
|
C
|
A:HIS92
|
4.4
|
0.6
|
1.0
|
CA
|
A:HIS92
|
4.6
|
0.6
|
1.0
|
N
|
A:HIS92
|
4.6
|
0.6
|
1.0
|
N
|
A:CYS135
|
4.7
|
0.6
|
1.0
|
N
|
A:MET136
|
4.9
|
0.1
|
1.0
|
CG
|
A:HIS92
|
4.9
|
0.6
|
1.0
|
CA
|
A:CYS130
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6rid
Go back to
Zinc Binding Sites List in 6rid
Zinc binding site 3 out
of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1201
b:77.2
occ:1.00
|
SG
|
B:CYS1090
|
2.2
|
42.0
|
1.0
|
SG
|
B:CYS1103
|
2.3
|
51.8
|
1.0
|
SG
|
B:CYS1087
|
2.3
|
44.9
|
1.0
|
SG
|
B:CYS1106
|
2.4
|
53.9
|
1.0
|
CB
|
B:CYS1106
|
3.0
|
53.9
|
1.0
|
CB
|
B:CYS1103
|
3.2
|
51.8
|
1.0
|
CB
|
B:CYS1087
|
3.4
|
44.9
|
1.0
|
CB
|
B:CYS1090
|
3.8
|
42.0
|
1.0
|
CG
|
B:PRO1113
|
3.8
|
55.5
|
1.0
|
N
|
B:CYS1106
|
3.9
|
53.9
|
1.0
|
CA
|
B:CYS1106
|
4.0
|
53.9
|
1.0
|
N
|
B:CYS1090
|
4.2
|
42.0
|
1.0
|
OD1
|
B:ASN1089
|
4.5
|
47.2
|
1.0
|
OD1
|
B:ASP1092
|
4.5
|
41.9
|
1.0
|
CD
|
B:PRO1113
|
4.6
|
55.5
|
1.0
|
CA
|
B:CYS1090
|
4.7
|
42.0
|
1.0
|
CA
|
B:CYS1103
|
4.7
|
51.8
|
1.0
|
CB
|
B:ASN1089
|
4.7
|
47.2
|
1.0
|
C
|
B:ARG1105
|
4.8
|
48.1
|
1.0
|
CA
|
B:CYS1087
|
4.8
|
44.9
|
1.0
|
CB
|
B:ARG1105
|
4.9
|
48.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6rid
Go back to
Zinc Binding Sites List in 6rid
Zinc binding site 4 out
of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:28.3
occ:1.00
|
SG
|
J:CYS10
|
2.2
|
13.1
|
1.0
|
SG
|
J:CYS7
|
2.3
|
11.7
|
1.0
|
SG
|
J:CYS40
|
2.3
|
14.4
|
1.0
|
SG
|
J:CYS39
|
2.3
|
15.3
|
1.0
|
CB
|
J:CYS7
|
3.2
|
11.7
|
1.0
|
N
|
J:CYS40
|
3.2
|
14.4
|
1.0
|
CB
|
J:CYS10
|
3.3
|
13.1
|
1.0
|
CB
|
J:CYS39
|
3.4
|
15.3
|
1.0
|
N
|
J:CYS10
|
3.5
|
13.1
|
1.0
|
CB
|
J:CYS40
|
3.6
|
14.4
|
1.0
|
CA
|
J:CYS40
|
3.7
|
14.4
|
1.0
|
C
|
J:CYS39
|
3.8
|
15.3
|
1.0
|
CA
|
J:CYS10
|
4.0
|
13.1
|
1.0
|
CA
|
J:CYS39
|
4.1
|
15.3
|
1.0
|
CB
|
J:THR9
|
4.3
|
10.9
|
1.0
|
CB
|
J:ASN37
|
4.5
|
19.9
|
1.0
|
O
|
J:CYS39
|
4.5
|
15.3
|
1.0
|
C
|
J:THR9
|
4.6
|
10.9
|
1.0
|
CA
|
J:CYS7
|
4.6
|
11.7
|
1.0
|
N
|
J:CYS39
|
4.6
|
15.3
|
1.0
|
N
|
J:THR9
|
4.7
|
10.9
|
1.0
|
N
|
J:GLY11
|
4.8
|
13.7
|
1.0
|
CA
|
J:THR9
|
4.8
|
10.9
|
1.0
|
C
|
J:CYS10
|
4.8
|
13.1
|
1.0
|
CG2
|
J:THR9
|
4.8
|
10.9
|
1.0
|
OD1
|
J:ASN37
|
5.0
|
19.9
|
1.0
|
C
|
J:CYS7
|
5.0
|
11.7
|
1.0
|
|
Reference:
H.S.Hillen,
J.Bartuli,
C.Grimm,
C.Dienemann,
K.Bedenk,
A.A.Szalay,
U.Fischer,
P.Cramer.
Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes. Cell V. 179 1525 2019.
ISSN: ISSN 1097-4172
PubMed: 31835031
DOI: 10.1016/J.CELL.2019.11.023
Page generated: Tue Oct 29 06:34:08 2024
|