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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:

Magnesium (Mg) 2 atoms

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

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