Magnesium in PDB 8dh4: T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Dstp Pair

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

The structure of T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Dstp Pair, PDB code: 8dh4 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)	43.20 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.779, 86.23, 201.463, 89.85, 85.39, 69.59
R / Rfree (%)	23.3 / 27.5

The binding sites of Magnesium atom in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dpa-Dstp Pair (pdb code 8dh4). 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-Dstp Pair, PDB code: 8dh4:
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-Dstp Pair


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-Dstp Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:79.7 occ:1.00 O12 B:S96901 2.0 134.2 1.0 O03 B:S96901 2.4 92.9 1.0 O06 B:S96901 3.1 126.9 1.0 P09 B:S96901 3.3 123.6 1.0 O10 B:S96901 3.7 124.2 1.0 OD2 B:ASP471 3.7 96.3 1.0 P01 B:S96901 3.7 121.7 1.0 P05 B:S96901 4.0 123.6 1.0 OD1 B:ASP506 4.1 100.6 1.0 O08 B:S96901 4.1 83.7 1.0 O13 B:S96901 4.2 121.6 1.0 OD1 B:ASP471 4.3 95.0 1.0 O04 B:S96901 4.3 109.6 1.0 CG B:ASP471 4.4 85.6 1.0 O11 B:S96901 4.4 130.8 1.0 C14 B:S96901 4.5 114.1 1.0 NZ B:LYS472 4.8 116.7 1.0 O02 B:S96901 4.9 99.3 1.0 CG B:ASP506 4.9 100.6 1.0

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


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-Dstp Pair within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg902 b:103.7 occ:1.00 O10 E:S96901 2.1 135.1 1.0 OD2 E:ASP471 3.1 88.2 1.0 P09 E:S96901 3.6 134.6 1.0 C14 E:S96901 3.6 131.5 1.0 O03 E:S96901 3.8 118.2 1.0 CG E:ASP471 3.9 78.8 1.0 OD1 E:ASP471 4.0 91.6 1.0 O13 E:S96901 4.1 127.1 1.0 O12 E:S96901 4.2 131.0 1.0 O11 E:S96901 4.2 96.3 1.0 O06 E:S96901 4.2 136.5 1.0 OD2 E:ASP506 4.5 91.0 1.0 P01 E:S96901 4.6 124.9 1.0 O08 E:S96901 4.6 115.9 1.0 P05 E:S96901 4.9 140.6 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