Zinc in PDB 6ca0: Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex

All present enzymatic activity of Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex:
2.7.7.6;

The structure of Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex (pdb code 6ca0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex, PDB code: 6ca0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.8 occ:1.00 N D:CYS72 2.2 0.5 1.0 SG D:CYS88 2.5 0.7 1.0 SG D:CYS70 2.5 0.1 1.0 SG D:CYS72 2.6 0.5 1.0 N D:LEU71 2.8 0.2 1.0 CB D:CYS70 3.0 0.1 1.0 C D:LEU71 3.1 0.2 1.0 CA D:CYS72 3.1 0.5 1.0 CB D:CYS72 3.2 0.5 1.0 CA D:LEU71 3.2 0.2 1.0 C D:CYS70 3.3 0.1 1.0 N D:GLY73 3.4 0.1 1.0 CB D:LEU71 3.5 0.2 1.0 C D:CYS72 3.7 0.5 1.0 CA D:CYS70 3.8 0.1 1.0 O D:CYS70 4.1 0.1 1.0 CB D:CYS88 4.1 0.7 1.0 SG D:CYS85 4.2 0.3 1.0 O D:LEU71 4.2 0.2 1.0 CB D:CYS85 4.5 0.3 1.0 CA D:GLY73 4.7 0.1 1.0 N D:LYS74 4.7 0.9 1.0 CG D:LEU71 4.8 0.2 1.0 N D:CYS70 4.9 0.1 1.0 CD1 D:LEU71 4.9 0.2 1.0 O D:CYS72 4.9 0.5 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of E. Coli Rnap SIGMA70 Open Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2003 b:1.0 occ:1.00 SG D:CYS888 2.5 0.5 1.0 CA D:CYS888 2.6 0.5 1.0 SG D:CYS898 2.6 0.9 1.0 CB D:CYS888 2.8 0.5 1.0 SG D:CYS814 2.9 0.6 1.0 N D:ASP889 3.1 0.3 1.0 CG2 D:THR816 3.2 0.6 1.0 C D:CYS888 3.4 0.5 1.0 NH2 D:ARG883 3.8 0.4 1.0 N D:CYS888 3.8 0.5 1.0 SG D:CYS895 3.9 0.6 1.0 CB D:CYS895 4.2 0.6 1.0 CB D:THR816 4.2 0.6 1.0 CB D:CYS898 4.3 0.9 1.0 OG1 D:THR890 4.4 0.5 1.0 CA D:ASP889 4.4 0.3 1.0 O D:SER887 4.5 0.7 1.0 N D:THR890 4.5 0.5 1.0 C D:SER887 4.5 0.7 1.0 O D:CYS888 4.6 0.5 1.0 O D:SER884 4.7 0.1 1.0 CB D:CYS814 4.7 0.6 1.0 CZ D:ARG883 4.7 0.4 1.0 CB D:ASP889 4.7 0.3 1.0 NE D:ARG883 4.8 0.4 1.0 N D:CYS895 4.9 0.6 1.0 C D:ASP889 5.0 0.3 1.0

A.Narayanan, F.S.Vago, K.Li, M.Z.Qayyum, D.Yernool, W.Jiang, K.S.Murakami. Cryo-Em Structure Ofescherichia COLISIGMA70RNA Polymerase and Promoter Dna Complex Revealed A Role of Sigma Non-Conserved Region During the Open Complex Formation. J. Biol. Chem. V. 293 7367 2018.
ISSN: ESSN 1083-351X
PubMed: 29581236
DOI: 10.1074/JBC.RA118.002161