Magnesium in PDB 8dh1: T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Patp Pair

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

The structure of T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Patp Pair, PDB code: 8dh1 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)	39.34 / 2.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.866, 86.156, 201.676, 89.85, 85.09, 69.56
R / Rfree (%)	23 / 27.2

The binding sites of Magnesium atom in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Patp Pair (pdb code 8dh1). 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 Dds-Patp Pair, PDB code: 8dh1:
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 Dds-Patp 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 Dds-Patp Pair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:97.3 occ:1.00 O08 B:S8L902 2.3 118.8 1.0 O12 B:S8L902 2.4 108.8 1.0 P09 B:S8L902 2.5 150.2 1.0 O13 B:S8L902 2.8 129.6 1.0 O10 B:S8L902 2.9 117.3 1.0 C14 B:S8L902 3.2 110.2 1.0 O03 B:S8L902 3.4 118.4 1.0 OD2 B:ASP471 3.4 68.5 1.0 P01 B:S8L902 3.4 128.4 1.0 P05 B:S8L902 3.6 97.0 1.0 O04 B:S8L902 3.6 99.6 1.0 O11 B:S8L902 3.9 119.9 1.0 NZ B:LYS472 4.3 80.6 1.0 CG B:ASP471 4.4 65.0 1.0 O06 B:S8L902 4.4 81.1 1.0 C15 B:S8L902 4.6 97.5 1.0 OD1 B:ASP471 4.7 64.3 1.0 O07 B:S8L902 4.7 91.6 1.0 O02 B:S8L902 4.9 88.5 1.0

Magnesium binding site 2 out of 2 in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Patp 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 Dds-Patp Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:143.2 occ:1.00 O23 B:S8L902 2.1 68.0 1.0 C22 B:S8L902 2.9 83.5 1.0 C2' C:U8 3.5 50.6 1.0 OH B:TYR639 3.7 68.9 1.0 N1 C:U8 3.8 54.8 1.0 C3' C:U8 3.8 54.7 1.0 C6 C:U8 3.9 49.4 1.0 C2 C:U8 4.0 49.8 1.0 C5 C:U8 4.1 44.0 1.0 N3 C:U8 4.2 58.4 1.0 O3' C:U8 4.2 60.2 1.0 C1' C:U8 4.3 53.4 1.0 C21 B:S8L902 4.3 99.6 1.0 C4 C:U8 4.3 58.4 1.0 O2 C:U8 4.5 50.3 1.0 O2' C:U8 4.6 38.8 1.0 CZ B:TYR639 5.0 59.8 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