Zinc in PDB 7vpz: Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
Enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
All present enzymatic activity of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer:
2.7.7.6;
Other elements in 7vpz:
The structure of Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
(pdb code 7vpz). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer, PDB code: 7vpz:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 7vpz
Go back to
Zinc Binding Sites List in 7vpz
Zinc binding site 1 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1402
b:167.6
occ:1.00
|
SG
|
D:CYS78
|
2.3
|
149.9
|
1.0
|
SG
|
D:CYS62
|
2.3
|
153.6
|
1.0
|
SG
|
D:CYS75
|
2.3
|
158.5
|
1.0
|
SG
|
D:CYS60
|
2.3
|
157.2
|
1.0
|
CB
|
D:CYS60
|
3.0
|
157.2
|
1.0
|
CB
|
D:CYS62
|
3.6
|
153.6
|
1.0
|
N
|
D:CYS62
|
3.6
|
153.6
|
1.0
|
CB
|
D:CYS78
|
3.8
|
149.9
|
1.0
|
CB
|
D:CYS75
|
3.9
|
158.5
|
1.0
|
N
|
D:TYR61
|
3.9
|
141.7
|
1.0
|
N
|
D:CYS78
|
4.0
|
149.9
|
1.0
|
CA
|
D:CYS62
|
4.1
|
153.6
|
1.0
|
CB
|
D:LYS64
|
4.2
|
155.8
|
1.0
|
CA
|
D:CYS60
|
4.2
|
157.2
|
1.0
|
C
|
D:CYS60
|
4.3
|
157.2
|
1.0
|
CB
|
D:ARG77
|
4.4
|
163.1
|
1.0
|
CA
|
D:CYS78
|
4.5
|
149.9
|
1.0
|
N
|
D:LYS64
|
4.5
|
155.8
|
1.0
|
C
|
D:TYR61
|
4.6
|
141.7
|
1.0
|
C
|
D:CYS62
|
4.7
|
153.6
|
1.0
|
CA
|
D:TYR61
|
4.8
|
141.7
|
1.0
|
N
|
D:TYR65
|
4.8
|
161.0
|
1.0
|
N
|
D:GLY63
|
4.8
|
159.8
|
1.0
|
CA
|
D:LYS64
|
4.9
|
155.8
|
1.0
|
O
|
D:CYS75
|
4.9
|
158.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 7vpz
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Zinc Binding Sites List in 7vpz
Zinc binding site 2 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1403
b:180.9
occ:1.00
|
SG
|
D:CYS972
|
2.3
|
129.4
|
1.0
|
SG
|
D:CYS962
|
2.3
|
126.4
|
1.0
|
SG
|
D:CYS969
|
2.3
|
130.3
|
1.0
|
SG
|
D:CYS886
|
2.3
|
143.1
|
1.0
|
CB
|
D:CYS886
|
2.6
|
143.1
|
1.0
|
CB
|
D:CYS962
|
3.2
|
126.4
|
1.0
|
CB
|
D:CYS972
|
3.3
|
129.4
|
1.0
|
CA
|
D:CYS886
|
3.5
|
143.1
|
1.0
|
CA
|
D:CYS962
|
3.6
|
126.4
|
1.0
|
CB
|
D:CYS969
|
3.7
|
130.3
|
1.0
|
N
|
D:GLU963
|
4.0
|
138.6
|
1.0
|
N
|
D:CYS886
|
4.2
|
143.1
|
1.0
|
N
|
D:CYS969
|
4.3
|
130.3
|
1.0
|
C
|
D:CYS962
|
4.3
|
126.4
|
1.0
|
N
|
D:CYS972
|
4.4
|
129.4
|
1.0
|
CA
|
D:CYS972
|
4.4
|
129.4
|
1.0
|
CA
|
D:CYS969
|
4.5
|
130.3
|
1.0
|
C
|
D:CYS886
|
4.7
|
143.1
|
1.0
|
C
|
D:GLU963
|
4.9
|
138.6
|
1.0
|
O
|
D:CYS969
|
4.9
|
130.3
|
1.0
|
N
|
D:GLY887
|
4.9
|
143.5
|
1.0
|
N
|
D:CYS962
|
4.9
|
126.4
|
1.0
|
O
|
D:GLU963
|
4.9
|
138.6
|
1.0
|
C
|
D:CYS969
|
5.0
|
130.3
|
1.0
|
NE
|
D:ARG957
|
5.0
|
139.7
|
1.0
|
|
Zinc binding site 3 out
of 8 in 7vpz
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Zinc Binding Sites List in 7vpz
Zinc binding site 3 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn201
b:425.3
occ:1.00
|
SG
|
M:CYS93
|
2.3
|
382.8
|
1.0
|
SG
|
M:CYS90
|
2.3
|
387.0
|
1.0
|
SG
|
M:CYS133
|
2.3
|
371.7
|
1.0
|
SG
|
M:CYS130
|
2.3
|
381.9
|
1.0
|
CB
|
M:CYS130
|
3.2
|
381.9
|
1.0
|
CB
|
M:CYS93
|
3.3
|
382.8
|
1.0
|
N
|
M:CYS130
|
3.5
|
381.9
|
1.0
|
CB
|
M:CYS90
|
3.5
|
387.0
|
1.0
|
CA
|
M:CYS130
|
4.0
|
381.9
|
1.0
|
N
|
M:CYS93
|
4.0
|
382.8
|
1.0
|
CB
|
M:CYS133
|
4.1
|
371.7
|
1.0
|
CA
|
M:CYS93
|
4.2
|
382.8
|
1.0
|
OD1
|
M:ASP132
|
4.3
|
369.4
|
1.0
|
CB
|
M:ALA92
|
4.5
|
378.6
|
1.0
|
C
|
M:THR129
|
4.6
|
377.2
|
1.0
|
C
|
M:ALA92
|
4.7
|
378.6
|
1.0
|
CA
|
M:THR129
|
4.7
|
377.2
|
1.0
|
OD2
|
M:ASP132
|
4.8
|
369.4
|
1.0
|
CA
|
M:CYS90
|
4.9
|
387.0
|
1.0
|
CG
|
M:ASP132
|
4.9
|
369.4
|
1.0
|
C
|
M:CYS130
|
5.0
|
381.9
|
1.0
|
|
Zinc binding site 4 out
of 8 in 7vpz
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Zinc Binding Sites List in 7vpz
Zinc binding site 4 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn202
b:389.8
occ:1.00
|
SG
|
M:CYS79
|
2.3
|
382.8
|
1.0
|
NE2
|
M:HIS85
|
2.3
|
379.9
|
1.0
|
NE2
|
M:HIS87
|
2.3
|
380.7
|
1.0
|
CB
|
M:CYS79
|
2.3
|
382.8
|
1.0
|
CD2
|
M:HIS85
|
2.7
|
379.9
|
1.0
|
OD2
|
M:ASP65
|
2.8
|
385.1
|
1.0
|
CD2
|
M:HIS87
|
3.1
|
380.7
|
1.0
|
CE1
|
M:HIS87
|
3.4
|
380.7
|
1.0
|
CE1
|
M:HIS85
|
3.5
|
379.9
|
1.0
|
CA
|
M:CYS79
|
3.8
|
382.8
|
1.0
|
CG
|
M:GLU98
|
3.9
|
377.4
|
1.0
|
CG
|
M:ASP65
|
4.0
|
385.1
|
1.0
|
CG
|
M:HIS85
|
4.0
|
379.9
|
1.0
|
NH1
|
M:ARG77
|
4.0
|
389.5
|
1.0
|
O
|
M:THR81
|
4.2
|
371.2
|
1.0
|
OE2
|
M:GLU98
|
4.3
|
377.4
|
1.0
|
CG
|
M:HIS87
|
4.3
|
380.7
|
1.0
|
ND1
|
M:HIS85
|
4.4
|
379.9
|
1.0
|
ND1
|
M:HIS87
|
4.4
|
380.7
|
1.0
|
C
|
M:CYS79
|
4.5
|
382.8
|
1.0
|
CD
|
M:GLU98
|
4.6
|
377.4
|
1.0
|
N
|
M:CYS79
|
4.7
|
382.8
|
1.0
|
CB
|
M:ASP65
|
4.8
|
385.1
|
1.0
|
OD1
|
M:ASP65
|
4.9
|
385.1
|
1.0
|
N
|
M:SER80
|
4.9
|
369.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 7vpz
Go back to
Zinc Binding Sites List in 7vpz
Zinc binding site 5 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn203
b:432.2
occ:1.00
|
OE2
|
M:GLU105
|
2.1
|
402.8
|
1.0
|
NE2
|
M:HIS86
|
2.3
|
386.1
|
1.0
|
NE2
|
M:HIS84
|
2.3
|
379.0
|
1.0
|
NE2
|
M:HIS122
|
2.3
|
389.1
|
1.0
|
CE1
|
M:HIS86
|
2.6
|
386.1
|
1.0
|
CD
|
M:GLU105
|
2.7
|
402.8
|
1.0
|
CD2
|
M:HIS84
|
2.8
|
379.0
|
1.0
|
OE1
|
M:GLU105
|
2.9
|
402.8
|
1.0
|
CE1
|
M:HIS122
|
3.1
|
389.1
|
1.0
|
CD2
|
M:HIS122
|
3.2
|
389.1
|
1.0
|
CD2
|
M:HIS86
|
3.4
|
386.1
|
1.0
|
CE1
|
M:HIS84
|
3.5
|
379.0
|
1.0
|
ND1
|
M:HIS86
|
3.7
|
386.1
|
1.0
|
CG
|
M:HIS84
|
4.0
|
379.0
|
1.0
|
CG
|
M:GLU105
|
4.1
|
402.8
|
1.0
|
CG
|
M:HIS86
|
4.1
|
386.1
|
1.0
|
ND1
|
M:HIS122
|
4.1
|
389.1
|
1.0
|
CG
|
M:HIS122
|
4.2
|
389.1
|
1.0
|
ND1
|
M:HIS84
|
4.3
|
379.0
|
1.0
|
CG2
|
M:VAL104
|
4.9
|
396.7
|
1.0
|
|
Zinc binding site 6 out
of 8 in 7vpz
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Zinc Binding Sites List in 7vpz
Zinc binding site 6 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn201
b:442.1
occ:1.00
|
SG
|
N:CYS133
|
2.3
|
395.1
|
1.0
|
SG
|
N:CYS130
|
2.3
|
399.2
|
1.0
|
SG
|
N:CYS93
|
2.3
|
401.1
|
1.0
|
SG
|
N:CYS90
|
2.3
|
398.0
|
1.0
|
OD1
|
N:ASP132
|
3.2
|
393.0
|
1.0
|
CB
|
N:CYS93
|
3.4
|
401.1
|
1.0
|
CB
|
N:CYS90
|
3.6
|
398.0
|
1.0
|
N
|
N:CYS130
|
3.7
|
399.2
|
1.0
|
CB
|
N:CYS130
|
3.9
|
399.2
|
1.0
|
N
|
N:CYS93
|
3.9
|
401.1
|
1.0
|
CB
|
N:CYS133
|
4.1
|
395.1
|
1.0
|
CG
|
N:ASP132
|
4.2
|
393.0
|
1.0
|
CA
|
N:CYS130
|
4.2
|
399.2
|
1.0
|
CB
|
N:ALA92
|
4.3
|
399.8
|
1.0
|
CA
|
N:CYS93
|
4.3
|
401.1
|
1.0
|
OG1
|
N:THR129
|
4.4
|
394.1
|
1.0
|
OD2
|
N:ASP132
|
4.4
|
393.0
|
1.0
|
N
|
N:CYS133
|
4.6
|
395.1
|
1.0
|
O
|
N:CYS130
|
4.6
|
399.2
|
1.0
|
C
|
N:CYS130
|
4.7
|
399.2
|
1.0
|
C
|
N:ALA92
|
4.7
|
399.8
|
1.0
|
C
|
N:THR129
|
4.7
|
394.1
|
1.0
|
CA
|
N:THR129
|
4.8
|
394.1
|
1.0
|
CA
|
N:CYS133
|
4.8
|
395.1
|
1.0
|
CA
|
N:ALA92
|
4.9
|
399.8
|
1.0
|
CA
|
N:CYS90
|
5.0
|
398.0
|
1.0
|
|
Zinc binding site 7 out
of 8 in 7vpz
Go back to
Zinc Binding Sites List in 7vpz
Zinc binding site 7 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn202
b:410.9
occ:1.00
|
OD2
|
N:ASP65
|
1.9
|
388.4
|
1.0
|
NE2
|
N:HIS85
|
2.3
|
388.3
|
1.0
|
NE2
|
N:HIS87
|
2.3
|
386.4
|
1.0
|
SG
|
N:CYS79
|
2.3
|
384.6
|
1.0
|
CD2
|
N:HIS85
|
2.7
|
388.3
|
1.0
|
CB
|
N:CYS79
|
2.9
|
384.6
|
1.0
|
CE1
|
N:HIS87
|
3.0
|
386.4
|
1.0
|
CG
|
N:ASP65
|
3.1
|
388.4
|
1.0
|
CD2
|
N:HIS87
|
3.4
|
386.4
|
1.0
|
CE1
|
N:HIS85
|
3.5
|
388.3
|
1.0
|
OE1
|
N:GLU98
|
3.8
|
385.9
|
1.0
|
CB
|
N:ASP65
|
4.0
|
388.4
|
1.0
|
OD1
|
N:ASP65
|
4.0
|
388.4
|
1.0
|
CG
|
N:HIS85
|
4.0
|
388.3
|
1.0
|
ND1
|
N:HIS87
|
4.1
|
386.4
|
1.0
|
CB
|
N:GLU98
|
4.1
|
385.9
|
1.0
|
CA
|
N:CYS79
|
4.3
|
384.6
|
1.0
|
ND1
|
N:HIS85
|
4.4
|
388.3
|
1.0
|
CG
|
N:HIS87
|
4.4
|
386.4
|
1.0
|
CD
|
N:GLU98
|
4.5
|
385.9
|
1.0
|
NH1
|
N:ARG77
|
4.6
|
386.3
|
1.0
|
N
|
N:CYS79
|
4.7
|
384.6
|
1.0
|
CG
|
N:GLU98
|
4.9
|
385.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 7vpz
Go back to
Zinc Binding Sites List in 7vpz
Zinc binding site 8 out
of 8 in the Cryo-Em Structure of Streptomyces Coelicolor Transcription Initial Complex with One Zur Dimer
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 Transcription Initial Complex with One Zur Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn203
b:431.0
occ:1.00
|
OE2
|
N:GLU105
|
1.9
|
401.0
|
1.0
|
NE2
|
N:HIS122
|
2.3
|
381.0
|
1.0
|
NE2
|
N:HIS86
|
2.3
|
387.8
|
1.0
|
NE2
|
N:HIS84
|
2.3
|
383.8
|
1.0
|
CD
|
N:GLU105
|
2.5
|
401.0
|
1.0
|
OE1
|
N:GLU105
|
2.5
|
401.0
|
1.0
|
CE1
|
N:HIS86
|
3.0
|
387.8
|
1.0
|
CE1
|
N:HIS84
|
3.1
|
383.8
|
1.0
|
CD2
|
N:HIS122
|
3.1
|
381.0
|
1.0
|
CE1
|
N:HIS122
|
3.4
|
381.0
|
1.0
|
CD2
|
N:HIS86
|
3.4
|
387.8
|
1.0
|
CD2
|
N:HIS84
|
3.4
|
383.8
|
1.0
|
CG2
|
N:VAL104
|
3.4
|
392.6
|
1.0
|
CG
|
N:GLU105
|
3.8
|
401.0
|
1.0
|
ND1
|
N:HIS86
|
4.1
|
387.8
|
1.0
|
ND1
|
N:HIS84
|
4.3
|
383.8
|
1.0
|
CG
|
N:HIS122
|
4.3
|
381.0
|
1.0
|
CG
|
N:HIS86
|
4.4
|
387.8
|
1.0
|
ND1
|
N:HIS122
|
4.4
|
381.0
|
1.0
|
CG
|
N:HIS84
|
4.5
|
383.8
|
1.0
|
CB
|
N:VAL104
|
4.7
|
392.6
|
1.0
|
N
|
N:GLU105
|
4.7
|
401.0
|
1.0
|
CB
|
N:GLU105
|
4.8
|
401.0
|
1.0
|
CA
|
N:GLU105
|
4.9
|
401.0
|
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 12:45:00 2024
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