Zinc in PDB 6n61: Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin

All present enzymatic activity of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin:
2.7.7.6;

The structure of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin, PDB code: 6n61 was solved by N.Braffman, J.Hauver, E.A.Campbell, S.A.Darst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 3.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	172.888, 172.888, 385.015, 90.00, 90.00, 90.00
R / Rfree (%)	27.3 / 31.6

The structure of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin (pdb code 6n61). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin, PDB code: 6n61:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:0.7 occ:1.00 SG D:CYS72 2.3 78.7 1.0 SG D:CYS85 2.5 0.0 1.0 SG D:CYS88 2.6 0.3 1.0 CB D:CYS85 2.7 0.8 1.0 SG D:CYS70 2.8 0.1 1.0 CB D:LYS87 3.4 0.6 1.0 CB D:CYS72 3.5 94.9 1.0 N D:CYS88 3.6 0.4 1.0 CB D:CYS88 4.0 0.3 1.0 CA D:CYS85 4.1 0.8 1.0 O D:CYS85 4.1 0.8 1.0 N D:CYS72 4.2 0.8 1.0 CA D:LYS87 4.2 0.1 1.0 N D:LYS87 4.3 0.8 1.0 C D:CYS85 4.3 1.0 1.0 CA D:CYS88 4.3 0.8 1.0 CB D:CYS70 4.4 0.2 1.0 C D:LYS87 4.4 0.1 1.0 CA D:CYS72 4.5 96.8 1.0 CG D:LYS87 4.6 0.6 1.0 N D:GLY89 4.8 0.8 1.0 N D:CYS85 4.9 0.8 1.0 N D:VAL90 4.9 0.0 1.0 C D:CYS88 4.9 0.8 1.0 O D:VAL90 4.9 0.7 1.0 CB D:VAL90 4.9 80.8 1.0

Zinc binding site 2 out of 2 in the Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Capistruin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1503 b:0.0 occ:1.00 SG D:CYS895 2.3 0.1 1.0 SG D:CYS888 2.3 88.7 1.0 CB D:CYS898 2.3 0.7 1.0 SG D:CYS814 2.4 0.2 1.0 SG D:CYS898 3.1 0.9 1.0 CB D:CYS814 3.2 0.4 1.0 CB D:CYS888 3.5 97.6 1.0 CA D:CYS898 3.5 0.1 1.0 N D:CYS898 3.5 0.9 1.0 OG1 D:THR890 3.8 0.9 1.0 CB D:CYS895 3.9 0.4 1.0 N D:CYS814 4.2 0.2 1.0 CA D:CYS888 4.2 0.2 1.0 O D:CYS895 4.3 92.8 1.0 CA D:CYS814 4.3 0.2 1.0 NH2 D:ARG883 4.3 0.8 1.0 N D:CYS895 4.3 95.9 1.0 C D:CYS898 4.5 0.2 1.0 CA D:CYS895 4.5 0.5 1.0 N D:ASP889 4.7 0.7 1.0 N D:TYR899 4.7 83.3 1.0 C D:CYS895 4.7 81.9 1.0 C D:HIS897 4.8 0.4 1.0 C D:CYS888 4.8 0.7 1.0 CG1 D:VAL894 5.0 0.5 1.0

N.R.Braffman, F.J.Piscotta, J.Hauver, E.A.Campbell, A.J.Link, S.A.Darst. Structural Mechanism of Transcription Inhibition By Lasso Peptides Microcin J25 and Capistruin. Proc. Natl. Acad. Sci. V. 116 1273 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30626643
DOI: 10.1073/PNAS.1817352116