Zinc in PDB 4mey: Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme
Enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme
All present enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme:
2.7.7.6;
Protein crystallography data
The structure of Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme, PDB code: 4mey
was solved by
Y.Feng,
Y.Zhang,
E.Arnold,
R.H.Ebright,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.92 /
3.95
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
186.390,
207.238,
308.302,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
27.6 /
32.5
|
Other elements in 4mey:
The structure of Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme
(pdb code 4mey). 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 Holoenzyme, PDB code: 4mey:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4mey
Go back to
Zinc Binding Sites List in 4mey
Zinc binding site 1 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme
 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 Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn2001
b:83.6
occ:1.00
|
SG
|
D:CYS88
|
2.2
|
0.7
|
1.0
|
SG
|
D:CYS72
|
2.2
|
67.8
|
1.0
|
SG
|
D:CYS85
|
2.3
|
68.0
|
1.0
|
SG
|
D:CYS70
|
2.3
|
88.1
|
1.0
|
CB
|
D:CYS70
|
3.2
|
94.7
|
1.0
|
CB
|
D:CYS85
|
3.2
|
53.9
|
1.0
|
CB
|
D:CYS88
|
3.2
|
0.6
|
1.0
|
N
|
D:CYS72
|
3.5
|
61.8
|
1.0
|
CB
|
D:CYS72
|
3.6
|
63.9
|
1.0
|
N
|
D:CYS88
|
3.8
|
0.8
|
1.0
|
CA
|
D:CYS72
|
4.0
|
67.7
|
1.0
|
N
|
D:GLY73
|
4.0
|
0.0
|
1.0
|
CA
|
D:CYS88
|
4.1
|
0.3
|
1.0
|
CB
|
D:LYS74
|
4.1
|
0.6
|
1.0
|
N
|
D:LYS74
|
4.1
|
0.8
|
1.0
|
N
|
D:LEU71
|
4.1
|
52.3
|
1.0
|
C
|
D:CYS72
|
4.4
|
77.6
|
1.0
|
C
|
D:CYS70
|
4.4
|
81.6
|
1.0
|
CA
|
D:CYS70
|
4.4
|
87.4
|
1.0
|
C
|
D:LEU71
|
4.6
|
72.3
|
1.0
|
CA
|
D:CYS85
|
4.7
|
56.1
|
1.0
|
CB
|
D:LYS87
|
4.7
|
0.7
|
1.0
|
CA
|
D:LYS74
|
4.7
|
0.3
|
1.0
|
CA
|
D:LEU71
|
4.8
|
58.9
|
1.0
|
C
|
D:CYS88
|
4.9
|
0.1
|
1.0
|
C
|
D:LYS87
|
4.9
|
0.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4mey
Go back to
Zinc Binding Sites List in 4mey
Zinc binding site 2 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme
 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 Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn2002
b:68.0
occ:1.00
|
SG
|
D:CYS814
|
2.2
|
86.0
|
1.0
|
SG
|
D:CYS888
|
2.3
|
72.3
|
1.0
|
SG
|
D:CYS898
|
2.3
|
49.5
|
1.0
|
SG
|
D:CYS895
|
2.4
|
48.3
|
1.0
|
CB
|
D:CYS888
|
3.1
|
72.3
|
1.0
|
CB
|
D:CYS814
|
3.3
|
86.0
|
1.0
|
CB
|
D:CYS895
|
3.4
|
48.3
|
1.0
|
CB
|
D:CYS898
|
3.5
|
49.5
|
1.0
|
CA
|
D:CYS888
|
3.5
|
72.3
|
1.0
|
N
|
D:ASP889
|
4.1
|
68.0
|
1.0
|
C
|
D:CYS888
|
4.2
|
72.3
|
1.0
|
N
|
D:CYS814
|
4.3
|
86.0
|
1.0
|
N
|
D:CYS895
|
4.3
|
48.3
|
1.0
|
OG1
|
D:THR890
|
4.3
|
55.8
|
1.0
|
CA
|
D:CYS895
|
4.4
|
48.3
|
1.0
|
CA
|
D:CYS814
|
4.5
|
86.0
|
1.0
|
NH2
|
D:ARG883
|
4.5
|
70.8
|
1.0
|
N
|
D:CYS888
|
4.6
|
72.3
|
1.0
|
CA
|
D:CYS898
|
4.7
|
49.5
|
1.0
|
N
|
D:CYS898
|
4.7
|
49.5
|
1.0
|
N
|
D:THR890
|
4.7
|
55.8
|
1.0
|
CB
|
D:THR890
|
4.9
|
55.8
|
1.0
|
CG2
|
D:THR816
|
4.9
|
0.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4mey
Go back to
Zinc Binding Sites List in 4mey
Zinc binding site 3 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme
 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 Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn2001
b:0.9
occ:1.00
|
SG
|
J:CYS88
|
2.2
|
0.2
|
1.0
|
SG
|
J:CYS72
|
2.3
|
76.2
|
1.0
|
SG
|
J:CYS70
|
2.4
|
0.1
|
1.0
|
SG
|
J:CYS85
|
2.4
|
74.5
|
1.0
|
CB
|
J:CYS88
|
3.1
|
0.1
|
1.0
|
CB
|
J:CYS85
|
3.1
|
60.4
|
1.0
|
CB
|
J:CYS70
|
3.2
|
0.7
|
1.0
|
N
|
J:CYS72
|
3.6
|
70.1
|
1.0
|
CB
|
J:CYS72
|
3.7
|
72.2
|
1.0
|
N
|
J:CYS88
|
3.8
|
0.3
|
1.0
|
CA
|
J:CYS88
|
4.0
|
0.8
|
1.0
|
CA
|
J:CYS72
|
4.1
|
76.0
|
1.0
|
N
|
J:LEU71
|
4.1
|
0.2
|
1.0
|
N
|
J:GLY73
|
4.1
|
92.8
|
1.0
|
N
|
J:LYS74
|
4.2
|
0.5
|
1.0
|
CB
|
J:LYS74
|
4.2
|
0.2
|
1.0
|
C
|
J:CYS70
|
4.4
|
0.6
|
1.0
|
CA
|
J:CYS70
|
4.4
|
0.3
|
1.0
|
C
|
J:CYS72
|
4.5
|
86.0
|
1.0
|
C
|
J:LEU71
|
4.6
|
0.2
|
1.0
|
CA
|
J:CYS85
|
4.6
|
62.7
|
1.0
|
C
|
J:CYS88
|
4.8
|
0.6
|
1.0
|
CA
|
J:LEU71
|
4.8
|
0.8
|
1.0
|
CA
|
J:LYS74
|
4.8
|
0.9
|
1.0
|
N
|
J:GLY89
|
4.9
|
95.0
|
1.0
|
CB
|
J:LYS87
|
4.9
|
0.6
|
1.0
|
C
|
J:LYS87
|
4.9
|
0.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4mey
Go back to
Zinc Binding Sites List in 4mey
Zinc binding site 4 out
of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase Holoenzyme
 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 Holoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn2002
b:63.5
occ:1.00
|
SG
|
J:CYS814
|
2.1
|
0.5
|
1.0
|
SG
|
J:CYS895
|
2.3
|
64.9
|
1.0
|
SG
|
J:CYS898
|
2.3
|
68.1
|
1.0
|
SG
|
J:CYS888
|
2.3
|
0.2
|
1.0
|
CB
|
J:CYS814
|
3.1
|
98.0
|
1.0
|
CB
|
J:CYS898
|
3.3
|
68.1
|
1.0
|
CB
|
J:CYS888
|
3.3
|
0.2
|
1.0
|
CB
|
J:CYS895
|
3.4
|
64.9
|
1.0
|
CA
|
J:CYS888
|
3.6
|
0.2
|
1.0
|
OG1
|
J:THR890
|
3.9
|
78.9
|
1.0
|
N
|
J:ASP889
|
4.0
|
54.6
|
1.0
|
C
|
J:CYS888
|
4.2
|
0.2
|
1.0
|
N
|
J:CYS814
|
4.3
|
0.5
|
1.0
|
CA
|
J:CYS814
|
4.3
|
0.6
|
1.0
|
N
|
J:CYS895
|
4.4
|
64.9
|
1.0
|
CA
|
J:CYS895
|
4.5
|
64.9
|
1.0
|
N
|
J:THR890
|
4.5
|
78.9
|
1.0
|
CA
|
J:CYS898
|
4.5
|
68.1
|
1.0
|
N
|
J:CYS898
|
4.5
|
68.1
|
1.0
|
NH2
|
J:ARG883
|
4.6
|
68.3
|
1.0
|
CB
|
J:THR890
|
4.6
|
78.9
|
1.0
|
CG2
|
J:THR816
|
4.8
|
94.0
|
1.0
|
N
|
J:CYS888
|
4.9
|
0.2
|
1.0
|
|
Reference:
D.Degen,
Y.Feng,
Y.Zhang,
K.Y.Ebright,
Y.W.Ebright,
M.Gigliotti,
H.Vahedian-Movahed,
S.Mandal,
M.Talaue,
N.Connell,
E.Arnold,
W.Fenical,
R.H.Ebright.
Transcription Inhibition By the Depsipeptide Antibiotic Salinamide A. Elife V. 3 02451 2014.
ISSN: ESSN 2050-084X
PubMed: 24843001
DOI: 10.7554/ELIFE.02451
Page generated: Sun Oct 27 02:24:15 2024
|