Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the Sigmas-Transcription Initiation Complex with 4-Nt Nascent Rna, PDB code: 5ipm:

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1503 b:0.1 occ:1.00 O3' 3:G16 2.1 0.0 1.0 OD1 D:ASP460 2.1 0.3 1.0 OD1 D:ASP464 2.4 0.4 1.0 OD1 D:ASP462 2.5 0.2 1.0 CG D:ASP460 2.7 0.7 1.0 OP1 3:U17 2.7 0.7 1.0 P 3:U17 2.8 0.2 1.0 OD2 D:ASP460 2.9 0.3 1.0 CG D:ASP462 3.1 0.7 1.0 OD2 D:ASP462 3.1 0.2 1.0 CG D:ASP464 3.2 0.8 1.0 O2' 3:G16 3.2 0.5 1.0 OD2 D:ASP464 3.3 0.6 1.0 C3' 3:G16 3.3 0.9 1.0 O D:ASP460 3.3 0.9 1.0 OP2 3:U17 3.4 0.3 1.0 C2' 3:G16 3.7 0.9 1.0 C4' 3:G16 3.8 0.8 1.0 CB D:ASP460 4.0 0.7 1.0 C D:ASP460 4.1 0.4 1.0 N D:ASP460 4.2 0.4 1.0 O5' 3:U17 4.2 0.6 1.0 CA D:ASP460 4.3 0.0 1.0 NH2 D:ARG425 4.5 0.5 1.0 CB D:ASP462 4.6 0.9 1.0 N D:ASP462 4.6 0.4 1.0 CB D:ASP464 4.6 0.7 1.0 C5' 3:G16 4.8 0.8 1.0 O4' 3:G16 4.9 0.9 1.0 C1' 3:G16 4.9 0.2 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