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Zinc in PDB 4mex: Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A

Enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A

All present enzymatic activity of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A, PDB code: 4mex 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) 49.87 / 3.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 185.800, 208.188, 308.179, 90.00, 90.00, 90.00
R / Rfree (%) 28.6 / 32.5

Other elements in 4mex:

The structure of Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A 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 in Complex with Salinamide A (pdb code 4mex). 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 Salinamide A, PDB code: 4mex:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4mex

Go back to Zinc Binding Sites List in 4mex
Zinc binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A


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 Salinamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:87.6
occ:1.00
SG D:CYS88 2.2 0.6 1.0
SG D:CYS72 2.2 0.5 1.0
SG D:CYS70 2.3 0.4 1.0
SG D:CYS85 2.6 33.8 1.0
CB D:CYS88 2.9 0.8 1.0
N D:CYS72 3.2 0.3 1.0
CB D:CYS72 3.3 0.6 1.0
CB D:CYS70 3.5 1.0 1.0
CB D:CYS85 3.5 56.3 1.0
N D:CYS88 3.6 0.9 1.0
CA D:CYS72 3.7 0.7 1.0
CA D:CYS88 3.8 0.8 1.0
N D:LEU71 3.9 95.3 1.0
N D:GLY73 3.9 0.8 1.0
C D:CYS70 4.2 97.9 1.0
C D:CYS72 4.2 0.6 1.0
C D:LEU71 4.2 0.5 1.0
N D:LYS74 4.3 0.1 1.0
CB D:LYS74 4.4 0.5 1.0
CA D:LEU71 4.5 94.8 1.0
CA D:CYS70 4.5 0.1 1.0
CB D:LYS87 4.6 73.0 1.0
C D:CYS88 4.7 0.6 1.0
C D:LYS87 4.7 85.1 1.0
O D:CYS70 4.8 98.6 1.0
CB D:LEU71 4.9 86.4 1.0
CA D:CYS85 5.0 54.0 1.0
CA D:LYS74 5.0 0.7 1.0
N D:GLY89 5.0 0.1 1.0

Zinc binding site 2 out of 4 in 4mex

Go back to Zinc Binding Sites List in 4mex
Zinc binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A


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 Salinamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:64.0
occ:1.00
SG D:CYS814 2.2 75.9 1.0
SG D:CYS898 2.3 88.3 1.0
SG D:CYS895 2.3 90.9 1.0
SG D:CYS888 2.3 75.9 1.0
CB D:CYS898 3.2 91.7 1.0
CB D:CYS888 3.2 60.7 1.0
CA D:CYS888 3.6 55.2 1.0
CB D:CYS814 3.6 98.6 1.0
CB D:CYS895 3.6 97.0 1.0
N D:ASP889 4.1 80.1 1.0
N D:CYS814 4.2 91.7 1.0
NH2 D:ARG883 4.3 0.9 1.0
C D:CYS888 4.3 64.8 1.0
N D:CYS895 4.3 76.0 1.0
OG1 D:THR890 4.4 91.1 1.0
CA D:CYS898 4.4 92.8 1.0
N D:CYS898 4.4 83.0 1.0
CA D:CYS895 4.5 82.7 1.0
CA D:CYS814 4.5 100.0 1.0
CG2 D:THR816 4.6 0.9 1.0
N D:CYS888 4.7 65.4 1.0
N D:THR890 4.8 64.8 1.0
O D:CYS895 5.0 85.4 1.0

Zinc binding site 3 out of 4 in 4mex

Go back to Zinc Binding Sites List in 4mex
Zinc binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A


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 Salinamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2001

b:0.8
occ:1.00
SG J:CYS72 2.2 97.9 1.0
SG J:CYS88 2.3 0.5 1.0
SG J:CYS70 2.3 0.5 1.0
SG J:CYS85 2.7 65.8 1.0
CB J:CYS88 3.0 0.5 1.0
N J:CYS72 3.1 0.4 1.0
CB J:CYS70 3.3 0.5 1.0
CB J:CYS72 3.4 0.6 1.0
CB J:CYS85 3.6 78.8 1.0
CA J:CYS72 3.7 0.3 1.0
N J:LEU71 3.8 0.4 1.0
N J:CYS88 3.8 0.6 1.0
N J:GLY73 3.8 0.1 1.0
CA J:CYS88 4.0 0.7 1.0
C J:CYS70 4.1 0.5 1.0
N J:LYS74 4.2 0.4 1.0
C J:CYS72 4.2 0.7 1.0
C J:LEU71 4.2 0.2 1.0
CB J:LYS74 4.3 0.7 1.0
CA J:CYS70 4.4 0.9 1.0
CA J:LEU71 4.4 0.7 1.0
O J:CYS70 4.7 0.2 1.0
CB J:LYS87 4.8 0.5 1.0
CB J:LEU71 4.9 0.7 1.0
CA J:LYS74 4.9 0.1 1.0
C J:CYS88 4.9 0.9 1.0
C J:LYS87 4.9 0.3 1.0
CA J:GLY73 4.9 0.3 1.0

Zinc binding site 4 out of 4 in 4mex

Go back to Zinc Binding Sites List in 4mex
Zinc binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Rna Polymerase in Complex with Salinamide A


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 Salinamide A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:80.2
occ:1.00
SG J:CYS814 2.2 95.4 1.0
SG J:CYS898 2.2 58.3 1.0
SG J:CYS895 2.3 52.3 1.0
SG J:CYS888 2.3 0.4 1.0
CB J:CYS898 3.0 77.3 1.0
CB J:CYS814 3.2 0.8 1.0
CB J:CYS888 3.3 0.4 1.0
CB J:CYS895 3.6 64.4 1.0
CA J:CYS888 3.6 0.4 1.0
OG1 J:THR890 3.9 72.9 1.0
NH2 J:ARG883 4.1 86.1 1.0
N J:ASP889 4.2 87.1 1.0
N J:CYS814 4.2 93.8 1.0
N J:CYS895 4.2 66.1 1.0
CA J:CYS898 4.2 77.1 1.0
N J:CYS898 4.3 79.6 1.0
CA J:CYS814 4.3 0.0 1.0
C J:CYS888 4.4 0.4 1.0
CA J:CYS895 4.4 62.3 1.0
N J:THR890 4.6 73.0 1.0
CB J:THR890 4.7 78.6 1.0
N J:CYS888 4.8 0.4 1.0
O J:CYS895 4.9 67.0 1.0
NE J:ARG883 4.9 94.8 1.0
C J:CYS895 5.0 63.1 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: Wed Dec 16 05:35:10 2020

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