Zinc in PDB 4zh4: Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18
Enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18
All present enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18:
2.7.7.6;
Protein crystallography data
The structure of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18, PDB code: 4zh4
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)
|
49.20 /
3.99
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
185.581,
204.105,
308.038,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25 /
28.3
|
Other elements in 4zh4:
The structure of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18 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 CBRP18
(pdb code 4zh4). 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 CBRP18, PDB code: 4zh4:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4zh4
Go back to
Zinc Binding Sites List in 4zh4
Zinc binding site 1 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18
 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 CBRP18 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1502
b:84.7
occ:1.00
|
SG
|
D:CYS70
|
2.1
|
61.9
|
1.0
|
SG
|
D:CYS72
|
2.1
|
56.4
|
1.0
|
SG
|
D:CYS85
|
2.3
|
78.3
|
1.0
|
CB
|
D:CYS85
|
3.3
|
86.1
|
1.0
|
CB
|
D:CYS72
|
3.4
|
56.7
|
1.0
|
SG
|
D:CYS88
|
3.5
|
0.0
|
1.0
|
CB
|
D:CYS70
|
3.7
|
65.5
|
1.0
|
N
|
D:CYS72
|
3.8
|
95.7
|
1.0
|
CB
|
D:LYS74
|
3.9
|
92.1
|
1.0
|
O
|
D:CYS88
|
4.0
|
0.8
|
1.0
|
CA
|
D:CYS72
|
4.1
|
79.0
|
1.0
|
N
|
D:LYS74
|
4.1
|
0.8
|
1.0
|
N
|
D:GLY73
|
4.2
|
0.6
|
1.0
|
CB
|
D:LYS87
|
4.2
|
0.1
|
1.0
|
N
|
D:CYS88
|
4.3
|
0.7
|
1.0
|
C
|
D:CYS72
|
4.5
|
85.2
|
1.0
|
CA
|
D:LYS74
|
4.6
|
98.4
|
1.0
|
N
|
D:LEU71
|
4.6
|
74.5
|
1.0
|
CA
|
D:CYS85
|
4.7
|
0.6
|
1.0
|
C
|
D:CYS70
|
4.8
|
62.7
|
1.0
|
CA
|
D:CYS70
|
4.9
|
69.6
|
1.0
|
C
|
D:LEU71
|
4.9
|
99.0
|
1.0
|
CB
|
D:CYS88
|
4.9
|
0.4
|
1.0
|
C
|
D:CYS88
|
4.9
|
0.6
|
1.0
|
N
|
D:LYS87
|
4.9
|
0.4
|
1.0
|
CA
|
D:CYS88
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4zh4
Go back to
Zinc Binding Sites List in 4zh4
Zinc binding site 2 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18
 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 CBRP18 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1503
b:33.2
occ:1.00
|
SG
|
D:CYS898
|
2.1
|
0.8
|
1.0
|
SG
|
D:CYS888
|
2.2
|
58.4
|
1.0
|
SG
|
D:CYS895
|
2.3
|
98.9
|
1.0
|
SG
|
D:CYS814
|
2.4
|
38.9
|
1.0
|
CB
|
D:CYS898
|
2.4
|
42.0
|
1.0
|
CB
|
D:CYS888
|
2.8
|
82.0
|
1.0
|
CA
|
D:CYS888
|
3.5
|
78.6
|
1.0
|
CB
|
D:CYS814
|
3.7
|
52.5
|
1.0
|
CA
|
D:CYS898
|
3.7
|
60.8
|
1.0
|
CB
|
D:CYS895
|
3.8
|
55.5
|
1.0
|
N
|
D:CYS898
|
4.0
|
66.3
|
1.0
|
NH2
|
D:ARG883
|
4.3
|
96.8
|
1.0
|
C
|
D:CYS888
|
4.3
|
67.4
|
1.0
|
N
|
D:ASP889
|
4.3
|
67.9
|
1.0
|
O
|
D:CYS895
|
4.4
|
49.2
|
1.0
|
N
|
D:CYS895
|
4.4
|
43.5
|
1.0
|
N
|
D:CYS814
|
4.6
|
45.8
|
1.0
|
CA
|
D:CYS895
|
4.6
|
61.4
|
1.0
|
N
|
D:CYS888
|
4.6
|
76.9
|
1.0
|
CG2
|
D:THR816
|
4.6
|
90.3
|
1.0
|
CA
|
D:CYS814
|
4.7
|
46.8
|
1.0
|
C
|
D:CYS895
|
4.9
|
41.0
|
1.0
|
C
|
D:CYS898
|
4.9
|
50.5
|
1.0
|
O
|
D:SER884
|
4.9
|
53.4
|
1.0
|
NE
|
D:ARG883
|
5.0
|
85.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4zh4
Go back to
Zinc Binding Sites List in 4zh4
Zinc binding site 3 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18
 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 CBRP18 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn1502
b:94.9
occ:1.00
|
SG
|
J:CYS70
|
2.1
|
96.7
|
1.0
|
SG
|
J:CYS85
|
2.2
|
50.7
|
1.0
|
SG
|
J:CYS72
|
2.3
|
86.3
|
1.0
|
CB
|
J:CYS85
|
3.1
|
41.1
|
1.0
|
SG
|
J:CYS88
|
3.3
|
0.6
|
1.0
|
CB
|
J:CYS72
|
3.5
|
0.9
|
1.0
|
CB
|
J:CYS70
|
3.7
|
0.8
|
1.0
|
O
|
J:CYS88
|
3.7
|
0.1
|
1.0
|
N
|
J:CYS72
|
3.8
|
70.7
|
1.0
|
CB
|
J:LYS74
|
4.1
|
0.6
|
1.0
|
N
|
J:CYS88
|
4.1
|
0.8
|
1.0
|
CA
|
J:CYS72
|
4.2
|
89.6
|
1.0
|
CB
|
J:LYS87
|
4.3
|
65.5
|
1.0
|
N
|
J:LYS74
|
4.3
|
93.5
|
1.0
|
N
|
J:GLY73
|
4.3
|
0.2
|
1.0
|
N
|
J:LEU71
|
4.5
|
76.0
|
1.0
|
CA
|
J:CYS85
|
4.6
|
65.4
|
1.0
|
C
|
J:CYS88
|
4.6
|
0.4
|
1.0
|
C
|
J:CYS72
|
4.7
|
89.8
|
1.0
|
CB
|
J:CYS88
|
4.7
|
0.1
|
1.0
|
CA
|
J:CYS88
|
4.7
|
0.1
|
1.0
|
C
|
J:CYS70
|
4.8
|
0.8
|
1.0
|
CA
|
J:LYS74
|
4.8
|
0.8
|
1.0
|
CA
|
J:CYS70
|
4.8
|
0.6
|
1.0
|
N
|
J:LYS87
|
4.9
|
83.1
|
1.0
|
C
|
J:LEU71
|
4.9
|
74.2
|
1.0
|
CA
|
J:LYS87
|
5.0
|
86.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4zh4
Go back to
Zinc Binding Sites List in 4zh4
Zinc binding site 4 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with CBRP18
 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 CBRP18 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn1503
b:54.8
occ:1.00
|
SG
|
J:CYS898
|
2.3
|
83.2
|
1.0
|
SG
|
J:CYS814
|
2.4
|
47.5
|
1.0
|
SG
|
J:CYS888
|
2.5
|
66.8
|
1.0
|
SG
|
J:CYS895
|
2.7
|
26.0
|
1.0
|
CB
|
J:CYS888
|
2.8
|
81.5
|
1.0
|
CB
|
J:CYS898
|
2.8
|
58.1
|
1.0
|
CA
|
J:CYS888
|
3.1
|
44.2
|
1.0
|
CB
|
J:CYS814
|
3.5
|
39.4
|
1.0
|
N
|
J:ASP889
|
3.9
|
57.2
|
1.0
|
C
|
J:CYS888
|
4.0
|
66.3
|
1.0
|
CA
|
J:CYS898
|
4.1
|
73.0
|
1.0
|
CG2
|
J:THR816
|
4.1
|
76.8
|
1.0
|
NH2
|
J:ARG883
|
4.2
|
73.7
|
1.0
|
CB
|
J:CYS895
|
4.2
|
62.6
|
1.0
|
N
|
J:CYS888
|
4.3
|
20.9
|
1.0
|
N
|
J:CYS898
|
4.4
|
72.7
|
1.0
|
N
|
J:CYS814
|
4.6
|
45.1
|
1.0
|
CA
|
J:CYS814
|
4.7
|
47.6
|
1.0
|
N
|
J:CYS895
|
4.8
|
68.1
|
1.0
|
O
|
J:SER884
|
4.8
|
81.3
|
1.0
|
N
|
J:THR890
|
4.9
|
49.2
|
1.0
|
O
|
J:CYS895
|
4.9
|
59.7
|
1.0
|
NE
|
J:ARG883
|
5.0
|
77.6
|
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 11:47:56 2024
|