Zinc in PDB 5ipm: Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna

All present enzymatic activity of Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna:
2.7.7.6;

The structure of Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna, PDB code: 5ipm was solved by B.Liu, Y.Zuo, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	126.46 / 4.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	132.752, 151.967, 228.064, 90.00, 90.00, 90.00
R / Rfree (%)	27 / 33

The structure of Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna (pdb code 5ipm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna, PDB code: 5ipm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1501 b:0.8 occ:1.00 SG D:CYS85 2.1 0.4 1.0 SG D:CYS88 2.2 1.0 1.0 SG D:CYS72 2.4 0.4 1.0 SG D:CYS70 2.6 0.8 1.0 CB D:CYS85 2.9 0.1 1.0 CB D:CYS70 3.3 0.2 1.0 CB D:CYS88 3.4 0.5 1.0 N D:CYS72 3.9 0.4 1.0 CB D:CYS72 3.9 0.2 1.0 CB D:LYS74 3.9 0.6 1.0 N D:CYS88 3.9 0.9 1.0 N D:LYS74 4.1 0.5 1.0 CA D:CYS88 4.3 0.1 1.0 N D:GLY73 4.3 0.1 1.0 CA D:CYS72 4.3 0.5 1.0 N D:LEU71 4.3 1.0 1.0 CA D:CYS85 4.4 0.8 1.0 CA D:CYS70 4.6 0.9 1.0 C D:CYS70 4.6 0.8 1.0 CA D:LYS74 4.6 0.6 1.0 C D:CYS72 4.6 0.9 1.0 CB D:LYS87 4.7 0.8 1.0 C D:LEU71 4.9 0.9 1.0 CD2 D:TYR75 4.9 1.0 1.0 N D:GLY89 5.0 0.2 1.0 C D:CYS85 5.0 0.5 1.0

Zinc binding site 2 out of 2 in the Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:0.7 occ:1.00 SG D:CYS898 1.8 0.3 1.0 SG D:CYS814 1.9 0.9 1.0 SG D:CYS895 2.6 0.8 1.0 SG D:CYS888 2.9 0.9 1.0 CB D:CYS814 2.9 0.2 1.0 CB D:CYS898 3.2 0.0 1.0 CB D:CYS888 3.5 0.5 1.0 CA D:CYS888 3.6 0.3 1.0 CB D:CYS895 3.8 0.8 1.0 NH2 D:ARG883 4.0 0.4 1.0 NE D:ARG883 4.0 0.1 1.0 OG1 D:THR816 4.0 0.6 1.0 CA D:CYS814 4.1 0.4 1.0 N D:CYS814 4.2 0.9 1.0 N D:ASP889 4.2 0.9 1.0 N D:CYS898 4.2 0.7 1.0 CA D:CYS898 4.3 0.4 1.0 OG1 D:THR890 4.4 0.9 1.0 CZ D:ARG883 4.4 0.5 1.0 C D:CYS888 4.5 0.5 1.0 N D:CYS895 4.5 0.8 1.0 N D:CYS888 4.7 0.7 1.0 CA D:CYS895 4.7 1.0 1.0 CB D:THR816 4.7 0.8 1.0

B.Liu, Y.Zuo, T.A.Steitz. Structures of E. Coli Sigma S-Transcription Initiation Complexes Provide New Insights Into Polymerase Mechanism. Proc.Natl.Acad.Sci.Usa V. 113 4051 2016.
ISSN: ESSN 1091-6490
PubMed: 27035955
DOI: 10.1073/PNAS.1520555113