Magnesium in PDB 4ylp: E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna

All present enzymatic activity of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna:
2.7.7.6;

The structure of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna, PDB code: 4ylp was solved by Y.Zuo, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.98 / 5.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	237.674, 204.988, 248.838, 90.00, 116.86, 90.00
R / Rfree (%)	23.1 / 31.3

The structure of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium atom in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna (pdb code 4ylp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna, PDB code: 4ylp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1503 b:0.5 occ:1.00 O3' 3:U16 1.9 0.4 1.0 OP1 3:C17 2.2 0.2 1.0 OD1 D:ASP460 2.2 0.6 1.0 OD1 D:ASP464 2.2 0.7 1.0 OD1 D:ASP462 2.4 0.2 1.0 P 3:C17 2.5 0.0 1.0 OD2 D:ASP464 2.8 0.7 1.0 CG D:ASP464 2.8 0.7 1.0 C3' 3:U16 3.0 0.3 1.0 C4' 3:U16 3.2 1.0 1.0 CG D:ASP460 3.2 0.6 1.0 CG D:ASP462 3.4 0.1 1.0 O D:ASP460 3.5 0.2 1.0 O5' 3:C17 3.6 0.8 1.0 C5' 3:U16 3.6 0.9 1.0 OP2 3:C17 3.7 0.9 1.0 C5' 3:C17 3.7 0.3 1.0 O2' 3:U16 3.8 0.1 1.0 OD2 D:ASP462 3.8 0.4 1.0 OD2 D:ASP460 3.8 0.7 1.0 C2' 3:U16 4.0 0.8 1.0 C D:ASP460 4.1 0.6 1.0 CB D:ASP460 4.3 0.8 1.0 CB D:ASP464 4.3 0.5 1.0 N D:ASP460 4.4 0.2 1.0 CA D:ASP460 4.4 0.6 1.0 O5' 3:U16 4.5 0.3 1.0 O4' 3:U16 4.6 0.9 1.0 NH2 D:ARG425 4.6 0.3 1.0 N D:ASP462 4.6 0.0 1.0 CB D:ASP462 4.7 0.8 1.0 O D:ASP462 4.7 1.0 1.0 N D:ASP464 4.7 0.2 1.0 C D:ASP462 4.8 0.0 1.0 C4' 3:C17 4.9 0.4 1.0 O4' 3:C17 4.9 0.3 1.0 CA D:ASP464 4.9 0.9 1.0 C1' 3:U16 5.0 0.3 1.0 CA D:ASP462 5.0 0.2 1.0

Magnesium binding site 2 out of 3 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg1503 b:0.8 occ:1.00 OP1 6:C17 1.1 0.5 1.0 P 6:C17 2.2 0.1 1.0 OD1 J:ASP462 2.3 0.8 1.0 O3' 6:U16 2.5 0.6 1.0 OD1 J:ASP460 2.7 0.6 1.0 OD2 J:ASP460 2.8 0.9 1.0 CG J:ASP462 2.9 0.0 1.0 OD2 J:ASP462 2.9 0.9 1.0 CG J:ASP460 3.0 0.9 1.0 OP2 6:C17 3.1 0.9 1.0 NZ I:LYS1073 3.4 0.2 1.0 O5' 6:C17 3.4 0.9 1.0 OD1 J:ASP464 3.7 0.5 1.0 C3' 6:U16 3.7 0.6 1.0 C5' 6:C17 3.9 0.5 1.0 C5' 6:U16 4.0 0.6 1.0 C4' 6:U16 4.1 0.9 1.0 CE I:LYS1073 4.2 0.9 1.0 CB J:ASP462 4.3 0.4 1.0 OD2 J:ASP464 4.3 0.8 1.0 CB J:ASP460 4.3 0.7 1.0 CG J:ASP464 4.4 0.2 1.0 O J:ASP460 4.4 0.5 1.0 O5' 6:U16 4.7 0.8 1.0 NH2 I:ARG1106 4.7 0.8 1.0 O J:ASP462 4.8 0.8 1.0 C J:ASP460 4.8 0.1 1.0 N J:ASP462 4.9 0.2 1.0 C2' 6:U16 5.0 0.1 1.0 CA J:ASP462 5.0 0.7 1.0

Magnesium binding site 3 out of 3 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg1503 b:1.0 occ:1.00 OD2 P:ASP462 1.6 0.5 1.0 OD2 P:ASP460 2.4 0.5 1.0 CG P:ASP462 2.6 0.7 1.0 OP1 9:C17 2.6 0.8 1.0 OD1 P:ASP462 3.0 0.3 1.0 CG P:ASP460 3.2 0.5 1.0 NH2 O:ARG1106 3.2 0.4 1.0 OD1 P:ASP460 3.6 0.8 1.0 P 9:C17 3.9 0.9 1.0 CB P:ASP462 3.9 0.4 1.0 CE O:LYS1073 4.1 0.3 1.0 CZ O:ARG1106 4.1 0.7 1.0 OD2 O:ASP814 4.3 1.0 1.0 CB P:ASP460 4.3 0.7 1.0 O3' 9:U16 4.5 0.8 1.0 OP2 9:C17 4.5 0.6 1.0 NZ O:LYS1073 4.7 0.0 1.0 NE O:ARG1106 4.8 0.7 1.0 NH1 O:ARG1106 4.8 0.3 1.0 N P:ASP462 4.9 0.0 1.0

Y.Zuo, T.A.Steitz. Crystal Structures of the E. Coli Transcription Initiation Complexes with A Complete Bubble. Mol.Cell V. 58 534 2015.
ISSN: ISSN 1097-2765
PubMed: 25866247
DOI: 10.1016/J.MOLCEL.2015.03.010