Magnesium in PDB 5ipl: 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: 5ipl 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)	126.63 / 3.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	131.710, 152.671, 226.698, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 29.3

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

Magnesium 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 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 OD1 D:ASP460 2.1 0.7 1.0 OD1 D:ASP464 2.3 0.9 1.0 OD1 D:ASP462 2.4 0.7 1.0 O3' 3:G16 2.6 0.4 1.0 CG D:ASP460 2.7 0.1 1.0 O2' 3:G16 2.7 0.3 1.0 OD2 D:ASP460 2.8 0.7 1.0 OD2 D:ASP462 3.0 0.1 1.0 CG D:ASP462 3.0 0.3 1.0 CG D:ASP464 3.1 0.5 1.0 C3' 3:G16 3.1 1.0 1.0 C4' 3:G16 3.2 0.7 1.0 O D:ASP460 3.3 1.0 1.0 OD2 D:ASP464 3.3 0.6 1.0 C2' 3:G16 3.5 0.4 1.0 CB D:ASP460 4.0 0.6 1.0 C5' 3:G16 4.1 0.2 1.0 C D:ASP460 4.1 0.5 1.0 N D:ASP460 4.2 0.9 1.0 O4' 3:G16 4.3 0.5 1.0 CA D:ASP460 4.3 0.1 1.0 CB D:ASP462 4.5 0.7 1.0 NH2 D:ARG425 4.5 0.9 1.0 CB D:ASP464 4.5 0.4 1.0 C1' 3:G16 4.5 1.0 1.0 N D:ASP462 4.5 0.8 1.0 O2 C:DPO1401 4.9 0.4 1.0 C5' 3:U17 5.0 0.9 1.0 CA D:ASP462 5.0 0.9 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1504 b:0.0 occ:1.00 OD2 D:ASP460 2.2 0.7 1.0 O5 C:DPO1401 2.5 0.9 1.0 CB D:ASP460 2.7 0.6 1.0 CG D:ASP460 2.7 0.1 1.0 OE1 C:GLU813 2.9 1.0 1.0 O2 C:DPO1401 3.4 0.4 1.0 NH2 C:ARG1106 3.7 0.7 1.0 P2 C:DPO1401 3.8 0.3 1.0 OD1 D:ASP460 3.9 0.7 1.0 O7 C:DPO1401 3.9 0.8 1.0 CD C:GLU813 4.0 0.6 1.0 OD2 C:ASP814 4.0 0.2 1.0 CA D:ASP460 4.2 0.1 1.0 P1 C:DPO1401 4.3 0.7 1.0 O4 C:DPO1401 4.4 0.1 1.0 OE2 C:GLU813 4.5 0.1 1.0 OD2 D:ASP462 4.6 0.1 1.0 CZ C:ARG1106 4.6 0.2 1.0 O3 C:DPO1401 4.8 0.2 1.0 CB C:GLU813 4.9 0.0 1.0 CG C:ASP814 5.0 0.7 1.0 C D:ASP460 5.0 0.5 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