Magnesium in PDB 8dh5: T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch

All present enzymatic activity of T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch:
2.7.7.6;

The structure of T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch, PDB code: 8dh5 was solved by J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.43 / 2.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.544, 86.305, 201.199, 89.79, 85.39, 69.49
R / Rfree (%)	23.4 / 26.7

The binding sites of Magnesium atom in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch (pdb code 8dh5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch, PDB code: 8dh5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:107.3 occ:1.00 O1G B:ATP901 2.2 101.7 1.0 O2B B:ATP901 2.8 106.3 1.0 OD2 B:ASP471 3.4 65.3 1.0 PG B:ATP901 3.4 68.6 1.0 O1A B:ATP901 3.8 70.0 1.0 O2G B:ATP901 3.9 93.5 1.0 O3B B:ATP901 3.9 84.0 1.0 PB B:ATP901 4.0 86.3 1.0 CG B:ASP471 4.2 56.9 1.0 OD1 B:ASP471 4.2 66.0 1.0 NZ B:LYS472 4.6 79.6 1.0 O3A B:ATP901 4.6 57.1 1.0 PA B:ATP901 4.7 84.2 1.0 O3G B:ATP901 4.7 78.2 1.0 CE B:LYS472 4.9 55.6 1.0

Magnesium binding site 2 out of 2 in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Atp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg902 b:58.9 occ:1.00 O1G E:ATP901 2.2 80.7 1.0 O2B E:ATP901 2.7 99.0 1.0 O2A E:ATP901 3.1 114.9 1.0 PG E:ATP901 3.4 81.3 1.0 OD1 E:ASP471 3.5 100.9 1.0 O3B E:ATP901 3.6 91.8 1.0 PB E:ATP901 3.7 81.5 1.0 PA E:ATP901 4.0 106.1 1.0 O3A E:ATP901 4.1 72.1 1.0 CG E:ASP471 4.2 71.7 1.0 OD2 E:ASP471 4.2 69.7 1.0 O3G E:ATP901 4.3 44.0 1.0 O1A E:ATP901 4.3 102.2 1.0 O2G E:ATP901 4.5 65.9 1.0 NZ E:LYS472 4.9 67.5 1.0

J.Oh, M.Kimoto, H.Xu, J.Chong, I.Hirao, D.Wang. Structural Basis of Transcription Recognition of A Hydrophobic Unnatural Base Pair By T7 Rna Polymerase. Nat Commun V. 14 195 2023.
ISSN: ESSN 2041-1723
PubMed: 36635281
DOI: 10.1038/S41467-022-35755-8