Zinc in PDB 7x76: Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
Enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
All present enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers:
2.7.7.6;
Other elements in 7x76:
The structure of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers also contains other interesting chemical elements:
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Zinc atom in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
(pdb code 7x76). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the
Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers, PDB code: 7x76:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 1 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1402
b:92.4
occ:1.00
|
SG
|
D:CYS78
|
2.3
|
75.3
|
1.0
|
|
SG
|
D:CYS75
|
2.3
|
84.8
|
1.0
|
|
SG
|
D:CYS62
|
2.3
|
83.3
|
1.0
|
|
SG
|
D:CYS60
|
2.3
|
79.3
|
1.0
|
|
H
|
D:CYS62
|
2.5
|
83.3
|
1.0
|
|
HB2
|
D:CYS60
|
3.1
|
79.3
|
1.0
|
|
H
|
D:CYS78
|
3.1
|
75.3
|
1.0
|
|
H
|
D:TYR61
|
3.2
|
76.6
|
1.0
|
|
N
|
D:CYS62
|
3.3
|
83.3
|
1.0
|
|
HB3
|
D:LYS64
|
3.3
|
89.4
|
1.0
|
|
HB3
|
D:CYS62
|
3.3
|
83.3
|
1.0
|
|
CB
|
D:CYS60
|
3.3
|
79.3
|
1.0
|
|
CB
|
D:CYS62
|
3.4
|
83.3
|
1.0
|
|
HB2
|
D:ARG77
|
3.6
|
85.6
|
1.0
|
|
H
|
D:LYS64
|
3.7
|
89.4
|
1.0
|
|
CB
|
D:CYS75
|
3.8
|
84.8
|
1.0
|
|
CB
|
D:CYS78
|
3.8
|
75.3
|
1.0
|
|
N
|
D:TYR61
|
3.8
|
76.6
|
1.0
|
|
CA
|
D:CYS62
|
3.9
|
83.3
|
1.0
|
|
HB3
|
D:CYS78
|
3.9
|
75.3
|
1.0
|
|
HB3
|
D:CYS60
|
3.9
|
79.3
|
1.0
|
|
N
|
D:CYS78
|
3.9
|
75.3
|
1.0
|
|
HB3
|
D:CYS75
|
3.9
|
84.8
|
1.0
|
|
HB2
|
D:CYS75
|
3.9
|
84.8
|
1.0
|
|
HB3
|
D:ARG77
|
4.2
|
85.6
|
1.0
|
|
HB2
|
D:CYS62
|
4.2
|
83.3
|
1.0
|
|
CB
|
D:LYS64
|
4.3
|
89.4
|
1.0
|
|
CB
|
D:ARG77
|
4.3
|
85.6
|
1.0
|
|
HB3
|
D:TYR61
|
4.3
|
76.6
|
1.0
|
|
HB
|
D:VAL80
|
4.3
|
68.8
|
1.0
|
|
C
|
D:TYR61
|
4.4
|
76.6
|
1.0
|
|
CA
|
D:CYS78
|
4.4
|
75.3
|
1.0
|
|
H
|
D:GLY63
|
4.4
|
90.7
|
1.0
|
|
CA
|
D:CYS60
|
4.5
|
79.3
|
1.0
|
|
C
|
D:CYS60
|
4.5
|
79.3
|
1.0
|
|
HB2
|
D:CYS78
|
4.5
|
75.3
|
1.0
|
|
N
|
D:LYS64
|
4.5
|
89.4
|
1.0
|
|
H
|
D:GLY79
|
4.5
|
70.2
|
1.0
|
|
C
|
D:CYS62
|
4.5
|
83.3
|
1.0
|
|
H
|
D:VAL80
|
4.5
|
68.8
|
1.0
|
|
H
|
D:ARG77
|
4.6
|
85.6
|
1.0
|
|
CA
|
D:TYR61
|
4.6
|
76.6
|
1.0
|
|
HB2
|
D:LYS64
|
4.6
|
89.4
|
1.0
|
|
N
|
D:GLY63
|
4.7
|
90.7
|
1.0
|
|
HA
|
D:CYS62
|
4.7
|
83.3
|
1.0
|
|
HG2
|
D:LYS64
|
4.7
|
89.4
|
1.0
|
|
CA
|
D:LYS64
|
4.8
|
89.4
|
1.0
|
|
HG23
|
D:VAL80
|
4.9
|
68.8
|
1.0
|
|
HD1
|
D:TYR65
|
4.9
|
90.2
|
1.0
|
|
C
|
D:ARG77
|
4.9
|
85.6
|
1.0
|
|
HA
|
D:CYS60
|
4.9
|
79.3
|
1.0
|
|
C
|
D:LYS64
|
5.0
|
89.4
|
1.0
|
|
CB
|
D:TYR61
|
5.0
|
76.6
|
1.0
|
|
N
|
D:GLY79
|
5.0
|
70.2
|
1.0
|
|
Zinc binding site 2 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 2 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1403
b:101.7
occ:1.00
|
SG
|
D:CYS972
|
2.3
|
62.8
|
1.0
|
|
SG
|
D:CYS969
|
2.3
|
63.1
|
1.0
|
|
SG
|
D:CYS962
|
2.3
|
69.3
|
1.0
|
|
SG
|
D:CYS886
|
2.3
|
74.8
|
1.0
|
|
HB2
|
D:CYS886
|
2.6
|
74.8
|
1.0
|
|
HB2
|
D:CYS972
|
2.7
|
62.8
|
1.0
|
|
HA
|
D:CYS962
|
3.0
|
69.3
|
1.0
|
|
CB
|
D:CYS886
|
3.0
|
74.8
|
1.0
|
|
CB
|
D:CYS972
|
3.0
|
62.8
|
1.0
|
|
HB2
|
D:CYS962
|
3.2
|
69.3
|
1.0
|
|
CB
|
D:CYS962
|
3.2
|
69.3
|
1.0
|
|
H
|
D:CYS969
|
3.3
|
63.1
|
1.0
|
|
HB3
|
D:CYS969
|
3.5
|
63.1
|
1.0
|
|
H
|
D:GLU963
|
3.5
|
79.3
|
1.0
|
|
CA
|
D:CYS962
|
3.5
|
69.3
|
1.0
|
|
CB
|
D:CYS969
|
3.5
|
63.1
|
1.0
|
|
HB3
|
D:CYS972
|
3.6
|
62.8
|
1.0
|
|
H
|
D:CYS972
|
3.7
|
62.8
|
1.0
|
|
HA
|
D:CYS886
|
3.7
|
74.8
|
1.0
|
|
HB3
|
D:CYS886
|
3.7
|
74.8
|
1.0
|
|
CA
|
D:CYS886
|
3.9
|
74.8
|
1.0
|
|
N
|
D:GLU963
|
4.0
|
79.3
|
1.0
|
|
N
|
D:CYS969
|
4.0
|
63.1
|
1.0
|
|
HB3
|
D:CYS962
|
4.1
|
69.3
|
1.0
|
|
HB2
|
D:SER964
|
4.2
|
67.2
|
1.0
|
|
CA
|
D:CYS972
|
4.2
|
62.8
|
1.0
|
|
C
|
D:CYS962
|
4.2
|
69.3
|
1.0
|
|
N
|
D:CYS972
|
4.3
|
62.8
|
1.0
|
|
HB2
|
D:CYS969
|
4.3
|
63.1
|
1.0
|
|
H
|
D:CYS886
|
4.3
|
74.8
|
1.0
|
|
CA
|
D:CYS969
|
4.3
|
63.1
|
1.0
|
|
HD3
|
D:ARG957
|
4.4
|
79.5
|
1.0
|
|
N
|
D:CYS886
|
4.4
|
74.8
|
1.0
|
|
HA
|
D:CYS972
|
4.5
|
62.8
|
1.0
|
|
O
|
D:CYS969
|
4.8
|
63.1
|
1.0
|
|
N
|
D:CYS962
|
4.8
|
69.3
|
1.0
|
|
HG22
|
D:THR888
|
4.8
|
83.2
|
1.0
|
|
C
|
D:CYS969
|
4.8
|
63.1
|
1.0
|
|
HA
|
D:THR968
|
4.9
|
57.4
|
1.0
|
|
HB3
|
D:SER964
|
4.9
|
67.2
|
1.0
|
|
CB
|
D:SER964
|
4.9
|
67.2
|
1.0
|
|
C
|
D:GLU963
|
5.0
|
79.3
|
1.0
|
|
HB
|
D:THR968
|
5.0
|
57.4
|
1.0
|
|
Zinc binding site 3 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 3 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn201
b:292.2
occ:1.00
|
SG
|
G:CYS130
|
2.3
|
224.8
|
1.0
|
|
SG
|
G:CYS93
|
2.3
|
222.8
|
1.0
|
|
SG
|
G:CYS133
|
2.3
|
221.3
|
1.0
|
|
SG
|
G:CYS90
|
2.3
|
220.7
|
1.0
|
|
HB2
|
G:CYS93
|
2.8
|
222.8
|
1.0
|
|
H
|
G:CYS130
|
3.0
|
224.8
|
1.0
|
|
HB2
|
G:CYS130
|
3.1
|
224.8
|
1.0
|
|
CB
|
G:CYS93
|
3.1
|
222.8
|
1.0
|
|
HB2
|
G:CYS90
|
3.3
|
220.7
|
1.0
|
|
H
|
G:CYS93
|
3.3
|
222.8
|
1.0
|
|
CB
|
G:CYS130
|
3.3
|
224.8
|
1.0
|
|
CB
|
G:CYS90
|
3.4
|
220.7
|
1.0
|
|
HB3
|
G:CYS90
|
3.7
|
220.7
|
1.0
|
|
N
|
G:CYS130
|
3.7
|
224.8
|
1.0
|
|
HZ1
|
G:LYS95
|
3.8
|
222.6
|
1.0
|
|
HB3
|
G:CYS93
|
3.9
|
222.8
|
1.0
|
|
N
|
G:CYS93
|
3.9
|
222.8
|
1.0
|
|
HB3
|
G:ALA92
|
3.9
|
215.4
|
1.0
|
|
HZ3
|
G:LYS95
|
3.9
|
222.6
|
1.0
|
|
HB3
|
G:CYS130
|
4.1
|
224.8
|
1.0
|
|
CB
|
G:CYS133
|
4.1
|
221.3
|
1.0
|
|
CA
|
G:CYS130
|
4.1
|
224.8
|
1.0
|
|
CA
|
G:CYS93
|
4.1
|
222.8
|
1.0
|
|
OD1
|
G:ASP132
|
4.2
|
219.9
|
1.0
|
|
HB2
|
G:CYS133
|
4.3
|
221.3
|
1.0
|
|
NZ
|
G:LYS95
|
4.3
|
222.6
|
1.0
|
|
HA
|
G:THR129
|
4.4
|
221.1
|
1.0
|
|
H
|
G:CYS133
|
4.5
|
221.3
|
1.0
|
|
HB3
|
G:CYS133
|
4.6
|
221.3
|
1.0
|
|
HA
|
G:CYS130
|
4.6
|
224.8
|
1.0
|
|
HA
|
G:CYS93
|
4.6
|
222.8
|
1.0
|
|
HE2
|
G:LYS95
|
4.7
|
222.6
|
1.0
|
|
HH
|
H:TYR117
|
4.8
|
222.4
|
1.0
|
|
CA
|
G:CYS90
|
4.8
|
220.7
|
1.0
|
|
HB2
|
G:LYS95
|
4.8
|
222.6
|
1.0
|
|
C
|
G:THR129
|
4.8
|
221.1
|
1.0
|
|
CB
|
G:ALA92
|
4.8
|
215.4
|
1.0
|
|
H
|
G:ALA92
|
4.9
|
215.4
|
1.0
|
|
HA
|
G:CYS133
|
4.9
|
221.3
|
1.0
|
|
H
|
G:GLY94
|
4.9
|
221.4
|
1.0
|
|
C
|
G:ALA92
|
4.9
|
215.4
|
1.0
|
|
CA
|
G:CYS133
|
4.9
|
221.3
|
1.0
|
|
OD2
|
G:ASP132
|
5.0
|
219.9
|
1.0
|
|
CG
|
G:ASP132
|
5.0
|
219.9
|
1.0
|
|
N
|
G:CYS133
|
5.0
|
221.3
|
1.0
|
|
Zinc binding site 4 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 4 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn202
b:277.9
occ:1.00
|
SG
|
G:CYS79
|
1.7
|
222.5
|
1.0
|
|
HE1
|
G:HIS87
|
1.9
|
223.0
|
1.0
|
|
HE2
|
G:HIS85
|
2.0
|
223.7
|
1.0
|
|
OD2
|
G:ASP65
|
2.0
|
217.4
|
1.0
|
|
HB3
|
G:CYS79
|
2.1
|
222.5
|
1.0
|
|
CB
|
G:CYS79
|
2.2
|
222.5
|
1.0
|
|
HE1
|
G:HIS85
|
2.3
|
223.7
|
1.0
|
|
NE2
|
G:HIS87
|
2.3
|
223.0
|
1.0
|
|
NE2
|
G:HIS85
|
2.3
|
223.7
|
1.0
|
|
HB2
|
G:CYS79
|
2.3
|
222.5
|
1.0
|
|
CE1
|
G:HIS87
|
2.3
|
223.0
|
1.0
|
|
CE1
|
G:HIS85
|
2.5
|
223.7
|
1.0
|
|
CG
|
G:ASP65
|
3.2
|
217.4
|
1.0
|
|
CD2
|
G:HIS85
|
3.5
|
223.7
|
1.0
|
|
ND1
|
G:HIS85
|
3.6
|
223.7
|
1.0
|
|
ND1
|
G:HIS87
|
3.6
|
223.0
|
1.0
|
|
CA
|
G:CYS79
|
3.7
|
222.5
|
1.0
|
|
CD2
|
G:HIS87
|
3.7
|
223.0
|
1.0
|
|
H
|
G:CYS79
|
3.8
|
222.5
|
1.0
|
|
HB2
|
G:ASP65
|
3.8
|
217.4
|
1.0
|
|
HD2
|
G:HIS85
|
4.0
|
223.7
|
1.0
|
|
CB
|
G:ASP65
|
4.1
|
217.4
|
1.0
|
|
HG3
|
G:GLU98
|
4.1
|
220.1
|
1.0
|
|
CG
|
G:HIS85
|
4.1
|
223.7
|
1.0
|
|
OD1
|
G:ASP65
|
4.1
|
217.4
|
1.0
|
|
HG2
|
G:GLU98
|
4.2
|
220.1
|
1.0
|
|
O
|
G:THR81
|
4.2
|
215.3
|
1.0
|
|
HD1
|
G:HIS87
|
4.2
|
223.0
|
1.0
|
|
HA
|
G:CYS79
|
4.2
|
222.5
|
1.0
|
|
N
|
G:CYS79
|
4.2
|
222.5
|
1.0
|
|
HD2
|
G:HIS87
|
4.3
|
223.0
|
1.0
|
|
HB3
|
G:ASP65
|
4.3
|
217.4
|
1.0
|
|
CG
|
G:HIS87
|
4.3
|
223.0
|
1.0
|
|
C
|
G:CYS79
|
4.4
|
222.5
|
1.0
|
|
CG
|
G:GLU98
|
4.6
|
220.1
|
1.0
|
|
O
|
G:CYS79
|
4.8
|
222.5
|
1.0
|
|
Zinc binding site 5 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 5 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn203
b:267.8
occ:1.00
|
HD2
|
G:HIS122
|
2.0
|
220.8
|
1.0
|
|
HE1
|
G:HIS86
|
2.1
|
221.1
|
1.0
|
|
NE2
|
G:HIS84
|
2.3
|
218.9
|
1.0
|
|
NE2
|
G:HIS86
|
2.3
|
221.1
|
1.0
|
|
NE2
|
G:HIS122
|
2.3
|
220.8
|
1.0
|
|
CD2
|
G:HIS122
|
2.3
|
220.8
|
1.0
|
|
CE1
|
G:HIS86
|
2.4
|
221.1
|
1.0
|
|
HE1
|
G:HIS84
|
2.4
|
218.9
|
1.0
|
|
CE1
|
G:HIS84
|
2.6
|
218.9
|
1.0
|
|
OE2
|
G:GLU105
|
2.7
|
211.9
|
1.0
|
|
OE1
|
G:GLU105
|
2.9
|
211.9
|
1.0
|
|
CD
|
G:GLU105
|
3.1
|
211.9
|
1.0
|
|
CD2
|
G:HIS86
|
3.6
|
221.1
|
1.0
|
|
CE1
|
G:HIS122
|
3.6
|
220.8
|
1.0
|
|
ND1
|
G:HIS86
|
3.6
|
221.1
|
1.0
|
|
CD2
|
G:HIS84
|
3.6
|
218.9
|
1.0
|
|
CG
|
G:HIS122
|
3.6
|
220.8
|
1.0
|
|
ND1
|
G:HIS84
|
3.9
|
218.9
|
1.0
|
|
HD2
|
G:HIS84
|
4.1
|
218.9
|
1.0
|
|
HD2
|
G:HIS86
|
4.1
|
221.1
|
1.0
|
|
HD1
|
G:HIS86
|
4.1
|
221.1
|
1.0
|
|
HE1
|
G:HIS122
|
4.2
|
220.8
|
1.0
|
|
CG
|
G:HIS86
|
4.2
|
221.1
|
1.0
|
|
ND1
|
G:HIS122
|
4.2
|
220.8
|
1.0
|
|
CG
|
G:HIS84
|
4.4
|
218.9
|
1.0
|
|
HB
|
G:VAL124
|
4.4
|
218.1
|
1.0
|
|
CG
|
G:GLU105
|
4.4
|
211.9
|
1.0
|
|
HD1
|
G:HIS84
|
4.5
|
218.9
|
1.0
|
|
HB2
|
G:HIS122
|
4.6
|
220.8
|
1.0
|
|
HG2
|
G:GLU105
|
4.7
|
211.9
|
1.0
|
|
HG3
|
G:GLU105
|
4.7
|
211.9
|
1.0
|
|
CB
|
G:HIS122
|
4.8
|
220.8
|
1.0
|
|
HA
|
G:HIS85
|
4.8
|
223.7
|
1.0
|
|
O
|
G:HIS122
|
4.8
|
220.8
|
1.0
|
|
HG23
|
G:VAL104
|
4.9
|
209.9
|
1.0
|
|
Zinc binding site 6 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 6 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn201
b:296.0
occ:1.00
|
SG
|
H:CYS130
|
2.3
|
233.9
|
1.0
|
|
SG
|
H:CYS93
|
2.3
|
234.1
|
1.0
|
|
SG
|
H:CYS90
|
2.3
|
233.6
|
1.0
|
|
SG
|
H:CYS133
|
2.3
|
234.0
|
1.0
|
|
HB2
|
H:CYS130
|
2.6
|
233.9
|
1.0
|
|
CB
|
H:CYS130
|
2.7
|
233.9
|
1.0
|
|
HB3
|
H:CYS130
|
2.7
|
233.9
|
1.0
|
|
HZ3
|
H:LYS95
|
2.9
|
227.3
|
1.0
|
|
HB2
|
H:CYS93
|
2.9
|
234.1
|
1.0
|
|
HZ1
|
H:LYS95
|
2.9
|
227.3
|
1.0
|
|
CB
|
H:CYS93
|
3.2
|
234.1
|
1.0
|
|
NZ
|
H:LYS95
|
3.3
|
227.3
|
1.0
|
|
OD1
|
H:ASP132
|
3.4
|
231.8
|
1.0
|
|
HB3
|
H:ALA92
|
3.5
|
233.3
|
1.0
|
|
H
|
H:CYS93
|
3.5
|
234.1
|
1.0
|
|
CB
|
H:CYS90
|
3.6
|
233.6
|
1.0
|
|
HB2
|
H:CYS90
|
3.6
|
233.6
|
1.0
|
|
HZ2
|
H:LYS95
|
3.6
|
227.3
|
1.0
|
|
HB3
|
H:CYS90
|
3.8
|
233.6
|
1.0
|
|
HB3
|
H:CYS93
|
3.9
|
234.1
|
1.0
|
|
N
|
H:CYS93
|
4.0
|
234.1
|
1.0
|
|
CB
|
H:CYS133
|
4.0
|
234.0
|
1.0
|
|
HB2
|
H:CYS133
|
4.1
|
234.0
|
1.0
|
|
H
|
H:CYS133
|
4.1
|
234.0
|
1.0
|
|
CA
|
H:CYS130
|
4.2
|
233.9
|
1.0
|
|
CA
|
H:CYS93
|
4.2
|
234.1
|
1.0
|
|
H
|
H:CYS130
|
4.4
|
233.9
|
1.0
|
|
CB
|
H:ALA92
|
4.5
|
233.3
|
1.0
|
|
CG
|
H:ASP132
|
4.5
|
231.8
|
1.0
|
|
HB3
|
H:CYS133
|
4.5
|
234.0
|
1.0
|
|
HE2
|
H:LYS95
|
4.6
|
227.3
|
1.0
|
|
CE
|
H:LYS95
|
4.6
|
227.3
|
1.0
|
|
N
|
H:CYS133
|
4.6
|
234.0
|
1.0
|
|
H
|
H:ALA92
|
4.7
|
233.3
|
1.0
|
|
HA
|
H:CYS130
|
4.7
|
233.9
|
1.0
|
|
HG3
|
H:LYS95
|
4.7
|
227.3
|
1.0
|
|
HB1
|
H:ALA92
|
4.8
|
233.3
|
1.0
|
|
OD2
|
H:ASP132
|
4.8
|
231.8
|
1.0
|
|
HA
|
H:CYS93
|
4.8
|
234.1
|
1.0
|
|
C
|
H:ALA92
|
4.8
|
233.3
|
1.0
|
|
N
|
H:CYS130
|
4.8
|
233.9
|
1.0
|
|
CA
|
H:CYS133
|
4.9
|
234.0
|
1.0
|
|
C
|
H:CYS130
|
4.9
|
233.9
|
1.0
|
|
H
|
H:GLY94
|
4.9
|
227.6
|
1.0
|
|
H
|
H:ASP132
|
5.0
|
231.8
|
1.0
|
|
CA
|
H:CYS90
|
5.0
|
233.6
|
1.0
|
|
Zinc binding site 7 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 7 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn202
b:266.9
occ:1.00
|
SG
|
H:CYS79
|
2.3
|
220.9
|
1.0
|
|
NE2
|
H:HIS87
|
2.3
|
219.7
|
1.0
|
|
NE2
|
H:HIS85
|
2.3
|
219.8
|
1.0
|
|
HB3
|
H:ASP65
|
2.3
|
218.6
|
1.0
|
|
HE1
|
H:HIS87
|
2.9
|
219.7
|
1.0
|
|
CE1
|
H:HIS87
|
3.0
|
219.7
|
1.0
|
|
CD2
|
H:HIS85
|
3.1
|
219.8
|
1.0
|
|
CE1
|
H:HIS85
|
3.2
|
219.8
|
1.0
|
|
OD2
|
H:ASP65
|
3.2
|
218.6
|
1.0
|
|
CB
|
H:ASP65
|
3.2
|
218.6
|
1.0
|
|
HD2
|
H:HIS85
|
3.2
|
219.8
|
1.0
|
|
HB2
|
H:CYS79
|
3.3
|
220.9
|
1.0
|
|
CB
|
H:CYS79
|
3.4
|
220.9
|
1.0
|
|
HE1
|
H:HIS85
|
3.4
|
219.8
|
1.0
|
|
HB2
|
H:ASP65
|
3.5
|
218.6
|
1.0
|
|
CD2
|
H:HIS87
|
3.5
|
219.7
|
1.0
|
|
CG
|
H:ASP65
|
3.6
|
218.6
|
1.0
|
|
HH12
|
H:ARG77
|
3.8
|
218.9
|
1.0
|
|
HD2
|
H:HIS87
|
3.8
|
219.7
|
1.0
|
|
HB3
|
H:CYS79
|
3.8
|
220.9
|
1.0
|
|
HG2
|
H:GLU98
|
4.1
|
219.9
|
1.0
|
|
CG
|
H:HIS85
|
4.1
|
219.8
|
1.0
|
|
ND1
|
H:HIS85
|
4.2
|
219.8
|
1.0
|
|
ND1
|
H:HIS87
|
4.2
|
219.7
|
1.0
|
|
H
|
H:ASP65
|
4.2
|
218.6
|
1.0
|
|
CA
|
H:ASP65
|
4.4
|
218.6
|
1.0
|
|
NH1
|
H:ARG77
|
4.5
|
218.9
|
1.0
|
|
CG
|
H:HIS87
|
4.5
|
219.7
|
1.0
|
|
HA
|
H:ASP65
|
4.5
|
218.6
|
1.0
|
|
HH11
|
H:ARG77
|
4.6
|
218.9
|
1.0
|
|
N
|
H:ASP65
|
4.6
|
218.6
|
1.0
|
|
CA
|
H:CYS79
|
4.7
|
220.9
|
1.0
|
|
H
|
H:CYS79
|
4.7
|
220.9
|
1.0
|
|
H
|
H:HIS85
|
4.8
|
219.8
|
1.0
|
|
OD1
|
H:ASP65
|
4.8
|
218.6
|
1.0
|
|
HD1
|
H:HIS85
|
4.9
|
219.8
|
1.0
|
|
HD1
|
H:HIS87
|
4.9
|
219.7
|
1.0
|
|
N
|
H:CYS79
|
4.9
|
220.9
|
1.0
|
|
CG
|
H:GLU98
|
5.0
|
219.9
|
1.0
|
|
HA
|
H:CYS79
|
5.0
|
220.9
|
1.0
|
|
Zinc binding site 8 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 8 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn203
b:287.4
occ:1.00
|
HD2
|
H:HIS122
|
2.0
|
223.6
|
1.0
|
|
OE2
|
H:GLU105
|
2.2
|
216.9
|
1.0
|
|
NE2
|
H:HIS84
|
2.3
|
220.5
|
1.0
|
|
NE2
|
H:HIS86
|
2.3
|
220.3
|
1.0
|
|
CD2
|
H:HIS122
|
2.4
|
223.6
|
1.0
|
|
NE2
|
H:HIS122
|
2.6
|
223.6
|
1.0
|
|
CD
|
H:GLU105
|
2.8
|
216.9
|
1.0
|
|
OE1
|
H:GLU105
|
3.0
|
216.9
|
1.0
|
|
CE1
|
H:HIS84
|
3.1
|
220.5
|
1.0
|
|
CD2
|
H:HIS86
|
3.1
|
220.3
|
1.0
|
|
HE1
|
H:HIS84
|
3.2
|
220.5
|
1.0
|
|
HD2
|
H:HIS86
|
3.2
|
220.3
|
1.0
|
|
CE1
|
H:HIS86
|
3.3
|
220.3
|
1.0
|
|
CD2
|
H:HIS84
|
3.4
|
220.5
|
1.0
|
|
OE2
|
H:GLU100
|
3.5
|
216.7
|
1.0
|
|
HE1
|
H:HIS86
|
3.6
|
220.3
|
1.0
|
|
HD2
|
H:HIS84
|
3.6
|
220.5
|
1.0
|
|
CG
|
H:HIS122
|
3.7
|
223.6
|
1.0
|
|
OE1
|
H:GLU100
|
3.8
|
216.7
|
1.0
|
|
CE1
|
H:HIS122
|
3.8
|
223.6
|
1.0
|
|
CD
|
H:GLU100
|
4.1
|
216.7
|
1.0
|
|
HG2
|
H:GLU105
|
4.1
|
216.9
|
1.0
|
|
CG
|
H:GLU105
|
4.1
|
216.9
|
1.0
|
|
HG21
|
H:VAL104
|
4.2
|
210.9
|
1.0
|
|
HG23
|
H:VAL104
|
4.3
|
210.9
|
1.0
|
|
ND1
|
H:HIS84
|
4.3
|
220.5
|
1.0
|
|
CG
|
H:HIS86
|
4.3
|
220.3
|
1.0
|
|
ND1
|
H:HIS122
|
4.3
|
223.6
|
1.0
|
|
ND1
|
H:HIS86
|
4.4
|
220.3
|
1.0
|
|
HB2
|
H:HIS122
|
4.4
|
223.6
|
1.0
|
|
CG
|
H:HIS84
|
4.4
|
220.5
|
1.0
|
|
HE1
|
H:HIS122
|
4.5
|
223.6
|
1.0
|
|
HG3
|
H:GLU105
|
4.5
|
216.9
|
1.0
|
|
CB
|
H:HIS122
|
4.7
|
223.6
|
1.0
|
|
CG2
|
H:VAL104
|
4.7
|
210.9
|
1.0
|
|
Zinc binding site 9 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 9 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn201
b:300.9
occ:1.00
|
SG
|
M:CYS133
|
2.3
|
215.7
|
1.0
|
|
SG
|
M:CYS90
|
2.3
|
227.1
|
1.0
|
|
SG
|
M:CYS130
|
2.3
|
223.1
|
1.0
|
|
SG
|
M:CYS93
|
2.3
|
225.1
|
1.0
|
|
HB2
|
M:CYS93
|
2.8
|
225.1
|
1.0
|
|
H
|
M:CYS130
|
2.8
|
223.1
|
1.0
|
|
HB2
|
M:CYS130
|
3.0
|
223.1
|
1.0
|
|
CB
|
M:CYS93
|
3.1
|
225.1
|
1.0
|
|
CB
|
M:CYS130
|
3.3
|
223.1
|
1.0
|
|
HB3
|
M:ALA92
|
3.4
|
225.9
|
1.0
|
|
H
|
M:CYS93
|
3.4
|
225.1
|
1.0
|
|
CB
|
M:CYS90
|
3.5
|
227.1
|
1.0
|
|
HB3
|
M:CYS90
|
3.5
|
227.1
|
1.0
|
|
HB2
|
M:CYS90
|
3.6
|
227.1
|
1.0
|
|
N
|
M:CYS130
|
3.6
|
223.1
|
1.0
|
|
HZ2
|
M:LYS95
|
3.7
|
220.2
|
1.0
|
|
N
|
M:CYS93
|
3.8
|
225.1
|
1.0
|
|
HB3
|
M:CYS93
|
3.9
|
225.1
|
1.0
|
|
HB3
|
M:CYS130
|
4.0
|
223.1
|
1.0
|
|
CA
|
M:CYS93
|
4.0
|
225.1
|
1.0
|
|
CA
|
M:CYS130
|
4.1
|
223.1
|
1.0
|
|
CB
|
M:CYS133
|
4.1
|
215.7
|
1.0
|
|
HA
|
M:THR129
|
4.2
|
222.9
|
1.0
|
|
HD2
|
M:LYS95
|
4.2
|
220.2
|
1.0
|
|
OD1
|
M:ASP132
|
4.2
|
213.0
|
1.0
|
|
HB2
|
M:CYS133
|
4.3
|
215.7
|
1.0
|
|
CB
|
M:ALA92
|
4.3
|
225.9
|
1.0
|
|
HA
|
M:CYS93
|
4.5
|
225.1
|
1.0
|
|
H
|
M:CYS133
|
4.5
|
215.7
|
1.0
|
|
HB3
|
M:CYS133
|
4.5
|
215.7
|
1.0
|
|
C
|
M:ALA92
|
4.5
|
225.9
|
1.0
|
|
NZ
|
M:LYS95
|
4.6
|
220.2
|
1.0
|
|
HB1
|
M:ALA92
|
4.6
|
225.9
|
1.0
|
|
H
|
M:ALA92
|
4.7
|
225.9
|
1.0
|
|
HA
|
M:CYS130
|
4.7
|
223.1
|
1.0
|
|
C
|
M:THR129
|
4.7
|
222.9
|
1.0
|
|
HZ3
|
M:LYS95
|
4.8
|
220.2
|
1.0
|
|
OD2
|
M:ASP132
|
4.8
|
213.0
|
1.0
|
|
CA
|
M:ALA92
|
4.9
|
225.9
|
1.0
|
|
CA
|
M:CYS90
|
4.9
|
227.1
|
1.0
|
|
CG
|
M:ASP132
|
4.9
|
213.0
|
1.0
|
|
CA
|
M:THR129
|
4.9
|
222.9
|
1.0
|
|
HB2
|
M:ALA92
|
4.9
|
225.9
|
1.0
|
|
HZ1
|
M:LYS95
|
5.0
|
220.2
|
1.0
|
|
Zinc binding site 10 out
of 14 in 7x76
Go back to
Zinc Binding Sites List in 7x76
Zinc binding site 10 out
of 14 in the Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Cryo-Em Structure of Streptomyces Coelicolor Rnap-Promoter Open Complex with Two Zur Dimers within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn202
b:269.2
occ:1.00
|
HB3
|
M:CYS79
|
1.7
|
219.2
|
1.0
|
|
CB
|
M:CYS79
|
2.2
|
219.2
|
1.0
|
|
SG
|
M:CYS79
|
2.3
|
219.2
|
1.0
|
|
NE2
|
M:HIS85
|
2.3
|
220.7
|
1.0
|
|
NE2
|
M:HIS87
|
2.3
|
222.6
|
1.0
|
|
HD2
|
M:HIS85
|
2.5
|
220.7
|
1.0
|
|
HB2
|
M:CYS79
|
2.6
|
219.2
|
1.0
|
|
CD2
|
M:HIS85
|
2.7
|
220.7
|
1.0
|
|
HG3
|
M:GLU98
|
3.1
|
221.4
|
1.0
|
|
OD2
|
M:ASP65
|
3.2
|
218.1
|
1.0
|
|
CD2
|
M:HIS87
|
3.2
|
222.6
|
1.0
|
|
CE1
|
M:HIS87
|
3.3
|
222.6
|
1.0
|
|
HD2
|
M:HIS87
|
3.4
|
222.6
|
1.0
|
|
HG2
|
M:GLU98
|
3.4
|
221.4
|
1.0
|
|
HE1
|
M:HIS87
|
3.5
|
222.6
|
1.0
|
|
CE1
|
M:HIS85
|
3.5
|
220.7
|
1.0
|
|
HH11
|
M:ARG77
|
3.6
|
217.7
|
1.0
|
|
CA
|
M:CYS79
|
3.6
|
219.2
|
1.0
|
|
CG
|
M:GLU98
|
3.7
|
221.4
|
1.0
|
|
HH12
|
M:ARG77
|
3.8
|
217.7
|
1.0
|
|
OG1
|
M:THR81
|
3.8
|
211.6
|
1.0
|
|
HA
|
M:CYS79
|
3.8
|
219.2
|
1.0
|
|
CG
|
M:HIS85
|
3.9
|
220.7
|
1.0
|
|
NH1
|
M:ARG77
|
3.9
|
217.7
|
1.0
|
|
HG1
|
M:THR81
|
4.0
|
211.6
|
1.0
|
|
HE1
|
M:HIS85
|
4.0
|
220.7
|
1.0
|
|
OE2
|
M:GLU98
|
4.0
|
221.4
|
1.0
|
|
H
|
M:THR81
|
4.1
|
211.6
|
1.0
|
|
O
|
M:THR81
|
4.1
|
211.6
|
1.0
|
|
CG
|
M:ASP65
|
4.3
|
218.1
|
1.0
|
|
C
|
M:CYS79
|
4.3
|
219.2
|
1.0
|
|
ND1
|
M:HIS85
|
4.3
|
220.7
|
1.0
|
|
CD
|
M:GLU98
|
4.4
|
221.4
|
1.0
|
|
ND1
|
M:HIS87
|
4.4
|
222.6
|
1.0
|
|
CG
|
M:HIS87
|
4.4
|
222.6
|
1.0
|
|
H
|
M:SER80
|
4.5
|
211.2
|
1.0
|
|
H
|
M:CYS79
|
4.6
|
219.2
|
1.0
|
|
N
|
M:SER80
|
4.6
|
211.2
|
1.0
|
|
N
|
M:CYS79
|
4.7
|
219.2
|
1.0
|
|
HD3
|
M:ARG77
|
4.7
|
217.7
|
1.0
|
|
N
|
M:THR81
|
4.7
|
211.6
|
1.0
|
|
HB3
|
M:GLU98
|
4.9
|
221.4
|
1.0
|
|
CB
|
M:GLU98
|
4.9
|
221.4
|
1.0
|
|
HB2
|
M:ASP65
|
4.9
|
218.1
|
1.0
|
|
O
|
M:CYS79
|
5.0
|
219.2
|
1.0
|
|
OD1
|
M:ASP65
|
5.0
|
218.1
|
1.0
|
|
CB
|
M:THR81
|
5.0
|
211.6
|
1.0
|
|
Reference:
X.Yang,
Y.Wang,
G.Liu,
Z.Deng,
S.Lin,
J.Zheng.
Structural Basis of Streptomyces Transcription Activation By Zinc Uptake Regulator. Nucleic Acids Res. V. 50 8363 2022.
ISSN: ESSN 1362-4962
PubMed: 35871291
DOI: 10.1093/NAR/GKAC627
Page generated: Wed Oct 30 14:51:55 2024
|
