Zinc in PDB 6n60: Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25)

Enzymatic activity of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25)

All present enzymatic activity of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25):
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25), PDB code: 6n60 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) 49.55 / 3.68
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 172.906, 172.906, 387.263, 90.00, 90.00, 90.00
R / Rfree (%) 26.3 / 30.6

Other elements in 6n60:

The structure of Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25) (pdb code 6n60). 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 Microcin J25 (MCCJ25), PDB code: 6n60:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6n60

Go back to Zinc Binding Sites List in 6n60
Zinc binding site 1 out of 2 in the Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25)


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 Microcin J25 (MCCJ25) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:0.4
occ:1.00
 SG D:CYS85 2.4 0.6 1.0
SG D:CYS72 2.4 0.1 1.0
SG D:CYS88 2.6 0.2 1.0
CB D:CYS70 2.6 0.4 1.0
SG D:CYS70 3.0 0.1 1.0
CB D:CYS85 3.3 0.7 1.0
CB D:CYS72 3.9 0.0 1.0
N D:GLY73 3.9 0.4 1.0
N D:LYS74 3.9 0.7 1.0
CA D:CYS70 4.0 0.0 1.0
N D:CYS72 4.0 0.9 1.0
CB D:CYS88 4.2 0.1 1.0
N D:TYR75 4.3 0.8 1.0
CA D:CYS72 4.4 0.1 1.0
N D:LEU71 4.4 0.9 1.0
CB D:LYS74 4.4 0.3 1.0
C D:CYS70 4.4 0.2 1.0
N D:CYS88 4.4 0.8 1.0
C D:CYS72 4.6 0.2 1.0
CA D:LYS74 4.7 0.5 1.0
CA D:CYS85 4.7 0.0 1.0
CA D:GLY73 4.8 0.6 1.0
C D:GLY73 4.8 0.3 1.0
CA D:CYS88 4.9 1.0 1.0

Zinc binding site 2 out of 2 in 6n60

Go back to Zinc Binding Sites List in 6n60
Zinc binding site 2 out of 2 in the Escherichia Coli Rna Polymerase SIGMA70-Holoenzyme Bound to Upstream Fork Promoter Dna and Microcin J25 (MCCJ25)


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 Microcin J25 (MCCJ25) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:0.2
occ:1.00
 SG D:CYS888 2.5 0.7 1.0
SG D:CYS814 2.5 0.6 1.0
SG D:CYS895 2.5 0.7 1.0
SG D:CYS898 2.5 0.4 1.0
CB D:CYS895 3.1 1.0 1.0
CB D:CYS898 3.2 0.6 1.0
CB D:CYS888 3.4 0.5 1.0
NH2 D:ARG883 3.4 0.9 1.0
CA D:CYS888 3.6 0.7 1.0
CG2 D:THR816 3.6 0.9 1.0
N D:ASP889 4.0 0.9 1.0
OG1 D:THR890 4.1 0.1 1.0
CB D:CYS814 4.1 0.1 1.0
CA D:CYS895 4.2 0.2 1.0
C D:CYS888 4.3 0.9 1.0
N D:CYS895 4.3 0.7 1.0
N D:CYS898 4.3 0.6 1.0
CA D:CYS898 4.4 0.0 1.0
N D:CYS814 4.5 0.0 1.0
CZ D:ARG883 4.6 0.0 1.0
N D:CYS888 4.8 0.4 1.0
O D:CYS895 4.8 0.5 1.0
N D:THR890 4.8 0.9 1.0
C D:CYS895 4.8 0.5 1.0
CA D:CYS814 4.9 1.0 1.0
NE D:ARG883 4.9 0.1 1.0
CB D:THR816 5.0 0.7 1.0

Reference:

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
Page generated: Wed Dec 16 12:21:21 2020

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