Zinc in PDB 8dy9: Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors
Enzymatic activity of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors
All present enzymatic activity of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors:
2.7.7.6;
Other elements in 8dy9:
The structure of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors
(pdb code 8dy9). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors, PDB code: 8dy9:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 8dy9
Go back to
Zinc Binding Sites List in 8dy9
Zinc binding site 1 out
of 3 in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn2000
b:85.8
occ:1.00
|
SG
|
D:CYS972
|
2.3
|
57.0
|
1.0
|
SG
|
D:CYS886
|
2.3
|
63.8
|
1.0
|
SG
|
D:CYS969
|
2.3
|
57.3
|
1.0
|
SG
|
D:CYS962
|
2.3
|
62.7
|
1.0
|
HB2
|
D:CYS972
|
3.1
|
57.0
|
1.0
|
HB3
|
D:CYS886
|
3.1
|
63.8
|
1.0
|
HH21
|
D:ARG957
|
3.2
|
62.4
|
1.0
|
CB
|
D:CYS886
|
3.4
|
63.8
|
1.0
|
CB
|
D:CYS972
|
3.4
|
57.0
|
1.0
|
HA
|
D:CYS962
|
3.4
|
62.7
|
1.0
|
H
|
D:CYS886
|
3.4
|
63.8
|
1.0
|
HB3
|
D:CYS969
|
3.5
|
57.3
|
1.0
|
CB
|
D:CYS962
|
3.6
|
62.7
|
1.0
|
CB
|
D:CYS969
|
3.6
|
57.3
|
1.0
|
HB2
|
D:SER964
|
3.7
|
64.3
|
1.0
|
HB2
|
D:CYS962
|
3.7
|
62.7
|
1.0
|
H
|
D:CYS969
|
3.8
|
57.3
|
1.0
|
HG21
|
D:THR888
|
3.8
|
67.6
|
1.0
|
H
|
D:CYS972
|
3.8
|
57.0
|
1.0
|
H
|
D:GLU963
|
3.9
|
67.5
|
1.0
|
NH2
|
D:ARG957
|
3.9
|
62.4
|
1.0
|
H
|
D:SER964
|
3.9
|
64.3
|
1.0
|
CA
|
D:CYS962
|
4.0
|
62.7
|
1.0
|
HB3
|
D:CYS972
|
4.0
|
57.0
|
1.0
|
HG22
|
D:THR888
|
4.0
|
67.6
|
1.0
|
HB2
|
D:CYS886
|
4.1
|
63.8
|
1.0
|
HH22
|
D:ARG957
|
4.1
|
62.4
|
1.0
|
N
|
D:CYS886
|
4.1
|
63.8
|
1.0
|
N
|
D:CYS969
|
4.3
|
57.3
|
1.0
|
HB2
|
D:CYS969
|
4.3
|
57.3
|
1.0
|
CG2
|
D:THR888
|
4.4
|
67.6
|
1.0
|
N
|
D:CYS972
|
4.4
|
57.0
|
1.0
|
CA
|
D:CYS886
|
4.4
|
63.8
|
1.0
|
HB3
|
D:CYS962
|
4.4
|
62.7
|
1.0
|
N
|
D:GLU963
|
4.4
|
67.5
|
1.0
|
CA
|
D:CYS969
|
4.4
|
57.3
|
1.0
|
CA
|
D:CYS972
|
4.5
|
57.0
|
1.0
|
CB
|
D:SER964
|
4.6
|
64.3
|
1.0
|
C
|
D:CYS962
|
4.6
|
62.7
|
1.0
|
O
|
D:CYS969
|
4.6
|
57.3
|
1.0
|
N
|
D:SER964
|
4.6
|
64.3
|
1.0
|
HE
|
D:ARG957
|
4.7
|
62.4
|
1.0
|
HB
|
D:THR888
|
4.8
|
67.6
|
1.0
|
H
|
D:THR888
|
4.8
|
67.6
|
1.0
|
C
|
D:CYS969
|
4.8
|
57.3
|
1.0
|
HB3
|
D:SER964
|
4.8
|
64.3
|
1.0
|
HA
|
D:ASP885
|
4.9
|
61.9
|
1.0
|
HA
|
D:CYS972
|
4.9
|
57.0
|
1.0
|
HA
|
D:THR968
|
5.0
|
55.5
|
1.0
|
|
Zinc binding site 2 out
of 3 in 8dy9
Go back to
Zinc Binding Sites List in 8dy9
Zinc binding site 2 out
of 3 in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn2001
b:100.2
occ:1.00
|
SG
|
D:CYS62
|
2.3
|
89.2
|
1.0
|
SG
|
D:CYS75
|
2.3
|
98.0
|
1.0
|
SG
|
D:CYS78
|
2.3
|
91.5
|
1.0
|
SG
|
D:CYS60
|
2.3
|
87.5
|
1.0
|
H
|
D:CYS62
|
2.9
|
89.2
|
1.0
|
HB2
|
D:CYS60
|
2.9
|
87.5
|
1.0
|
HB3
|
D:CYS75
|
3.0
|
98.0
|
1.0
|
CB
|
D:CYS75
|
3.2
|
98.0
|
1.0
|
CB
|
D:CYS60
|
3.2
|
87.5
|
1.0
|
HB3
|
D:ARG77
|
3.4
|
98.2
|
1.0
|
H
|
D:CYS78
|
3.4
|
91.5
|
1.0
|
HB2
|
D:CYS75
|
3.4
|
98.0
|
1.0
|
H
|
D:GLY63
|
3.4
|
92.2
|
1.0
|
H
|
D:LYS64
|
3.5
|
99.6
|
1.0
|
N
|
D:CYS62
|
3.6
|
89.2
|
1.0
|
CB
|
D:CYS62
|
3.7
|
89.2
|
1.0
|
CB
|
D:CYS78
|
3.7
|
91.5
|
1.0
|
HB3
|
D:CYS78
|
3.8
|
91.5
|
1.0
|
HB3
|
D:CYS60
|
3.8
|
87.5
|
1.0
|
HB3
|
D:LYS64
|
3.8
|
99.6
|
1.0
|
H
|
D:TYR61
|
3.8
|
84.0
|
1.0
|
HB3
|
D:CYS62
|
3.9
|
89.2
|
1.0
|
HD1
|
D:TYR65
|
3.9
|
99.4
|
1.0
|
N
|
D:CYS78
|
4.0
|
91.5
|
1.0
|
N
|
D:GLY63
|
4.1
|
92.2
|
1.0
|
CA
|
D:CYS62
|
4.1
|
89.2
|
1.0
|
N
|
D:TYR61
|
4.2
|
84.0
|
1.0
|
N
|
D:LYS64
|
4.3
|
99.6
|
1.0
|
CB
|
D:ARG77
|
4.3
|
98.2
|
1.0
|
H
|
D:TYR65
|
4.4
|
99.4
|
1.0
|
CA
|
D:CYS60
|
4.5
|
87.5
|
1.0
|
HB2
|
D:CYS78
|
4.5
|
91.5
|
1.0
|
HB2
|
D:CYS62
|
4.5
|
89.2
|
1.0
|
C
|
D:CYS60
|
4.5
|
87.5
|
1.0
|
HB2
|
D:LYS64
|
4.5
|
99.6
|
1.0
|
CA
|
D:CYS78
|
4.5
|
91.5
|
1.0
|
CB
|
D:LYS64
|
4.5
|
99.6
|
1.0
|
H
|
D:ARG77
|
4.5
|
98.2
|
1.0
|
HB
|
D:VAL80
|
4.6
|
82.9
|
1.0
|
C
|
D:CYS62
|
4.6
|
89.2
|
1.0
|
HB3
|
D:TYR61
|
4.6
|
84.0
|
1.0
|
CA
|
D:CYS75
|
4.6
|
98.0
|
1.0
|
HE1
|
D:TYR65
|
4.6
|
99.4
|
1.0
|
HB2
|
D:ARG77
|
4.7
|
98.2
|
1.0
|
C
|
D:TYR61
|
4.7
|
84.0
|
1.0
|
CD1
|
D:TYR65
|
4.8
|
99.4
|
1.0
|
HG2
|
D:ARG77
|
4.8
|
98.2
|
1.0
|
O
|
D:CYS75
|
4.9
|
98.0
|
1.0
|
H
|
D:VAL80
|
4.9
|
82.9
|
1.0
|
H
|
D:GLY79
|
4.9
|
91.2
|
1.0
|
CA
|
D:TYR61
|
4.9
|
84.0
|
1.0
|
C
|
D:CYS75
|
4.9
|
98.0
|
1.0
|
C
|
D:ARG77
|
4.9
|
98.2
|
1.0
|
|
Zinc binding site 3 out
of 3 in 8dy9
Go back to
Zinc Binding Sites List in 8dy9
Zinc binding site 3 out
of 3 in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn2000
b:88.9
occ:1.00
|
SG
|
I:CYS122
|
2.3
|
47.4
|
1.0
|
SG
|
I:CYS18
|
2.3
|
53.8
|
1.0
|
SG
|
I:CYS19
|
2.3
|
49.1
|
1.0
|
HD2
|
I:ARG16
|
2.6
|
59.5
|
1.0
|
H
|
I:CYS19
|
3.2
|
49.1
|
1.0
|
HB2
|
I:CYS122
|
3.4
|
47.4
|
1.0
|
HH11
|
I:ARG16
|
3.4
|
59.5
|
1.0
|
CD
|
I:ARG16
|
3.5
|
59.5
|
1.0
|
N
|
I:CYS19
|
3.5
|
49.1
|
1.0
|
CB
|
I:CYS122
|
3.5
|
47.4
|
1.0
|
HB3
|
I:ARG16
|
3.6
|
59.5
|
1.0
|
CB
|
I:CYS19
|
3.6
|
49.1
|
1.0
|
HA
|
I:ASP123
|
3.6
|
44.2
|
1.0
|
HD3
|
I:ARG16
|
3.7
|
59.5
|
1.0
|
HA
|
I:CYS19
|
3.7
|
49.1
|
1.0
|
N
|
I:ASP123
|
3.7
|
44.2
|
1.0
|
H
|
I:ASP123
|
3.8
|
44.2
|
1.0
|
CA
|
I:CYS19
|
3.8
|
49.1
|
1.0
|
C
|
I:CYS122
|
3.8
|
47.4
|
1.0
|
HB2
|
I:ASP123
|
3.9
|
44.2
|
1.0
|
CB
|
I:CYS18
|
4.0
|
53.8
|
1.0
|
HB2
|
I:CYS19
|
4.0
|
49.1
|
1.0
|
CA
|
I:ASP123
|
4.1
|
44.2
|
1.0
|
NH1
|
I:ARG16
|
4.1
|
59.5
|
1.0
|
HG2
|
I:ARG16
|
4.2
|
59.5
|
1.0
|
C
|
I:CYS18
|
4.2
|
53.8
|
1.0
|
HB2
|
I:CYS18
|
4.2
|
53.8
|
1.0
|
O
|
I:CYS122
|
4.2
|
47.4
|
1.0
|
CG
|
I:ARG16
|
4.2
|
59.5
|
1.0
|
HB3
|
I:CYS122
|
4.2
|
47.4
|
1.0
|
CA
|
I:CYS122
|
4.3
|
47.4
|
1.0
|
CB
|
I:ARG16
|
4.3
|
59.5
|
1.0
|
HB3
|
I:CYS19
|
4.4
|
49.1
|
1.0
|
HB3
|
I:ALA120
|
4.4
|
46.2
|
1.0
|
NE
|
I:ARG16
|
4.5
|
59.5
|
1.0
|
CB
|
I:ASP123
|
4.5
|
44.2
|
1.0
|
HB3
|
I:CYS18
|
4.6
|
53.8
|
1.0
|
CA
|
I:CYS18
|
4.6
|
53.8
|
1.0
|
HB2
|
I:ARG16
|
4.6
|
59.5
|
1.0
|
HH12
|
I:ARG16
|
4.7
|
59.5
|
1.0
|
CZ
|
I:ARG16
|
4.7
|
59.5
|
1.0
|
H
|
I:CYS18
|
4.8
|
53.8
|
1.0
|
O
|
I:CYS18
|
5.0
|
53.8
|
1.0
|
|
Reference:
M.Lilic,
E.A.Campbell.
Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors To Be Published.
Page generated: Wed Oct 30 19:21:12 2024
|