Zinc in PDB 4zh3: Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br
Enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br
All present enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br:
2.7.7.6;
Protein crystallography data
The structure of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br, PDB code: 4zh3
was solved by
Y.Feng,
R.H.Ebright,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.75 /
4.08
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
186.339,
205.790,
307.630,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.8 /
26.7
|
Other elements in 4zh3:
The structure of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br
(pdb code 4zh3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br, PDB code: 4zh3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4zh3
Go back to
Zinc Binding Sites List in 4zh3
Zinc binding site 1 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1502
b:90.9
occ:1.00
|
SG
|
D:CYS70
|
2.1
|
76.2
|
1.0
|
SG
|
D:CYS72
|
2.1
|
72.0
|
1.0
|
SG
|
D:CYS85
|
2.3
|
89.1
|
1.0
|
CB
|
D:CYS85
|
3.2
|
96.9
|
1.0
|
CB
|
D:CYS72
|
3.5
|
72.3
|
1.0
|
SG
|
D:CYS88
|
3.6
|
0.9
|
1.0
|
CB
|
D:CYS70
|
3.7
|
79.9
|
1.0
|
CB
|
D:LYS74
|
3.8
|
91.1
|
1.0
|
N
|
D:CYS72
|
3.9
|
0.3
|
1.0
|
O
|
D:CYS88
|
4.1
|
0.8
|
1.0
|
N
|
D:LYS74
|
4.1
|
0.8
|
1.0
|
CA
|
D:CYS72
|
4.2
|
94.6
|
1.0
|
N
|
D:GLY73
|
4.2
|
97.4
|
1.0
|
CB
|
D:LYS87
|
4.3
|
98.6
|
1.0
|
N
|
D:CYS88
|
4.3
|
0.6
|
1.0
|
C
|
D:CYS72
|
4.5
|
0.8
|
1.0
|
CA
|
D:LYS74
|
4.6
|
97.4
|
1.0
|
CA
|
D:CYS85
|
4.7
|
0.4
|
1.0
|
N
|
D:LEU71
|
4.7
|
83.0
|
1.0
|
CA
|
D:CYS70
|
4.9
|
83.9
|
1.0
|
C
|
D:CYS70
|
4.9
|
77.0
|
1.0
|
N
|
D:LYS87
|
4.9
|
0.9
|
1.0
|
C
|
D:CYS88
|
4.9
|
0.5
|
1.0
|
CB
|
D:CYS88
|
5.0
|
0.3
|
1.0
|
C
|
D:LEU71
|
5.0
|
0.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4zh3
Go back to
Zinc Binding Sites List in 4zh3
Zinc binding site 2 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1503
b:49.4
occ:1.00
|
SG
|
D:CYS898
|
2.1
|
0.7
|
1.0
|
SG
|
D:CYS888
|
2.2
|
61.6
|
1.0
|
SG
|
D:CYS814
|
2.3
|
50.3
|
1.0
|
SG
|
D:CYS895
|
2.3
|
94.9
|
1.0
|
CB
|
D:CYS898
|
2.5
|
50.9
|
1.0
|
CB
|
D:CYS888
|
2.9
|
85.2
|
1.0
|
CA
|
D:CYS888
|
3.6
|
81.7
|
1.0
|
CB
|
D:CYS814
|
3.6
|
64.0
|
1.0
|
CA
|
D:CYS898
|
3.7
|
69.7
|
1.0
|
CB
|
D:CYS895
|
3.8
|
51.5
|
1.0
|
N
|
D:CYS898
|
3.9
|
75.3
|
1.0
|
NH2
|
D:ARG883
|
4.2
|
0.6
|
1.0
|
N
|
D:ASP889
|
4.4
|
50.1
|
1.0
|
O
|
D:CYS895
|
4.4
|
45.2
|
1.0
|
N
|
D:CYS895
|
4.4
|
39.5
|
1.0
|
C
|
D:CYS888
|
4.4
|
70.6
|
1.0
|
N
|
D:CYS814
|
4.5
|
57.3
|
1.0
|
CA
|
D:CYS895
|
4.6
|
57.4
|
1.0
|
CG2
|
D:THR816
|
4.6
|
90.5
|
1.0
|
CA
|
D:CYS814
|
4.7
|
58.2
|
1.0
|
N
|
D:CYS888
|
4.7
|
80.1
|
1.0
|
C
|
D:CYS895
|
4.9
|
36.9
|
1.0
|
C
|
D:CYS898
|
4.9
|
59.5
|
1.0
|
NE
|
D:ARG883
|
4.9
|
90.5
|
1.0
|
O
|
D:SER884
|
5.0
|
66.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4zh3
Go back to
Zinc Binding Sites List in 4zh3
Zinc binding site 3 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn1502
b:98.9
occ:1.00
|
SG
|
J:CYS72
|
2.2
|
90.8
|
1.0
|
SG
|
J:CYS70
|
2.2
|
0.8
|
1.0
|
SG
|
J:CYS85
|
2.3
|
65.1
|
1.0
|
CB
|
J:CYS85
|
3.2
|
55.5
|
1.0
|
CB
|
J:CYS72
|
3.4
|
0.4
|
1.0
|
SG
|
J:CYS88
|
3.5
|
0.2
|
1.0
|
CB
|
J:CYS70
|
3.8
|
0.8
|
1.0
|
CB
|
J:LYS74
|
3.9
|
0.1
|
1.0
|
N
|
J:CYS72
|
3.9
|
75.2
|
1.0
|
O
|
J:CYS88
|
4.0
|
0.7
|
1.0
|
CB
|
J:LYS87
|
4.1
|
76.1
|
1.0
|
N
|
J:CYS88
|
4.1
|
0.4
|
1.0
|
CA
|
J:CYS72
|
4.1
|
94.0
|
1.0
|
N
|
J:LYS74
|
4.1
|
92.0
|
1.0
|
N
|
J:GLY73
|
4.2
|
0.5
|
1.0
|
C
|
J:CYS72
|
4.5
|
94.3
|
1.0
|
CA
|
J:LYS74
|
4.6
|
0.2
|
1.0
|
CA
|
J:CYS85
|
4.7
|
79.8
|
1.0
|
N
|
J:LEU71
|
4.7
|
98.7
|
1.0
|
N
|
J:LYS87
|
4.8
|
93.6
|
1.0
|
C
|
J:CYS88
|
4.8
|
0.1
|
1.0
|
CB
|
J:CYS88
|
4.8
|
0.8
|
1.0
|
CA
|
J:CYS88
|
4.8
|
0.7
|
1.0
|
CA
|
J:LYS87
|
4.9
|
96.6
|
1.0
|
C
|
J:LEU71
|
5.0
|
96.9
|
1.0
|
C
|
J:CYS70
|
5.0
|
0.9
|
1.0
|
CA
|
J:CYS70
|
5.0
|
0.7
|
1.0
|
C
|
J:LYS87
|
5.0
|
0.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4zh3
Go back to
Zinc Binding Sites List in 4zh3
Zinc binding site 4 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRH16-Br within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn1503
b:46.5
occ:1.00
|
SG
|
J:CYS898
|
2.3
|
87.3
|
1.0
|
SG
|
J:CYS888
|
2.4
|
88.5
|
1.0
|
SG
|
J:CYS814
|
2.5
|
53.0
|
1.0
|
CB
|
J:CYS888
|
2.8
|
0.2
|
1.0
|
SG
|
J:CYS895
|
2.8
|
36.0
|
1.0
|
CB
|
J:CYS898
|
2.8
|
62.2
|
1.0
|
CA
|
J:CYS888
|
3.1
|
65.9
|
1.0
|
CB
|
J:CYS814
|
3.6
|
44.8
|
1.0
|
N
|
J:ASP889
|
3.9
|
79.7
|
1.0
|
C
|
J:CYS888
|
3.9
|
88.0
|
1.0
|
CA
|
J:CYS898
|
4.2
|
77.1
|
1.0
|
CG2
|
J:THR816
|
4.2
|
88.6
|
1.0
|
CB
|
J:CYS895
|
4.2
|
72.5
|
1.0
|
N
|
J:CYS888
|
4.2
|
42.6
|
1.0
|
NH2
|
J:ARG883
|
4.3
|
80.3
|
1.0
|
N
|
J:CYS898
|
4.4
|
76.8
|
1.0
|
N
|
J:CYS814
|
4.7
|
50.5
|
1.0
|
N
|
J:CYS895
|
4.7
|
78.0
|
1.0
|
CA
|
J:CYS814
|
4.7
|
53.0
|
1.0
|
O
|
J:SER884
|
4.8
|
72.5
|
1.0
|
N
|
J:THR890
|
4.8
|
66.0
|
1.0
|
O
|
J:CYS895
|
4.9
|
69.7
|
1.0
|
CA
|
J:CYS895
|
5.0
|
76.0
|
1.0
|
O
|
J:CYS888
|
5.0
|
98.5
|
1.0
|
|
Reference:
Y.Feng,
D.Degen,
X.Wang,
M.Gigliotti,
S.Liu,
Y.Zhang,
D.Das,
T.Michalchuk,
Y.W.Ebright,
M.Talaue,
N.Connell,
R.H.Ebright.
Structural Basis of Transcription Inhibition By Cbr Hydroxamidines and Cbr Pyrazoles. Structure V. 23 1470 2015.
ISSN: ISSN 0969-2126
PubMed: 26190576
DOI: 10.1016/J.STR.2015.06.009
Page generated: Sun Oct 27 11:47:57 2024
|