Magnesium in PDB 8dh2: T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch

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

The structure of T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch, PDB code: 8dh2 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)	47.37 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.702, 85.047, 200.477, 89.87, 85.38, 69.51
R / Rfree (%)	26 / 30.8

The binding sites of Magnesium atom in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch (pdb code 8dh2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch, PDB code: 8dh2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-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 Dds-Atp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:66.7 occ:1.00 O1G B:3PO902 2.2 107.0 1.0 O2A B:3PO902 3.1 107.2 1.0 PG B:3PO902 3.5 104.6 1.0 OD2 B:ASP471 3.8 65.5 1.0 O2G B:3PO902 3.8 90.7 1.0 OD2 B:ASP506 4.1 81.0 1.0 NZ B:LYS472 4.2 94.9 1.0 PA B:3PO902 4.3 111.7 1.0 O3A B:3PO902 4.3 106.4 1.0 O3B B:3PO902 4.4 93.2 1.0 O2B B:3PO902 4.6 89.4 1.0 OD1 B:ASP471 4.6 60.5 1.0 O3G B:3PO902 4.6 72.8 1.0 CG B:ASP471 4.6 48.7 1.0 PB B:3PO902 4.7 105.7 1.0

Magnesium binding site 2 out of 4 in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-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 Dds-Atp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg902 b:74.8 occ:1.00 O1B E:3PO901 2.1 125.7 1.0 O2A E:3PO901 2.1 101.0 1.0 PA E:3PO901 3.2 108.8 1.0 PB E:3PO901 3.2 121.2 1.0 O3A E:3PO901 3.4 107.0 1.0 NZ E:LYS472 3.4 104.6 1.0 OD2 E:ASP471 3.8 65.9 1.0 OD1 E:ASP471 3.9 65.0 1.0 O5' E:3PO901 4.0 77.0 1.0 O2B E:3PO901 4.1 82.4 1.0 CG E:ASP471 4.1 58.4 1.0 O1A E:3PO901 4.4 85.4 1.0 O3B E:3PO901 4.5 118.8 1.0 CE E:LYS472 4.5 106.2 1.0 O1G E:3PO901 5.0 121.0 1.0 O2G E:3PO901 5.0 138.3 1.0

Magnesium binding site 3 out of 4 in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg903 b:125.9 occ:1.00 O5' I:3PO902 2.2 148.9 1.0 O3G I:3PO902 2.8 165.2 1.0 PA I:3PO902 3.1 170.4 1.0 O1A I:3PO902 3.2 166.4 1.0 O3A I:3PO902 3.7 172.8 1.0 OD2 I:ASP471 3.9 159.1 1.0 PG I:3PO902 4.0 176.7 1.0 O3B I:3PO902 4.2 168.2 1.0 O2A I:3PO902 4.5 165.4 1.0 PB I:3PO902 4.5 176.1 1.0 O1G I:3PO902 4.5 167.3 1.0 O2B I:3PO902 4.7 169.8 1.0 CG I:ASP471 4.8 163.2 1.0 OD1 I:ASP471 4.9 170.1 1.0

Magnesium binding site 4 out of 4 in the T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T7 Rna Polymerase Elongation Complex with Unnatural Base Dds-Atp Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg902 b:124.9 occ:1.00 O1B L:3PO901 2.1 158.2 1.0 O5' L:3PO901 3.3 151.8 1.0 PB L:3PO901 3.5 168.3 1.0 O3B L:3PO901 3.9 159.1 1.0 PA L:3PO901 4.1 163.1 1.0 OD1 L:ASP471 4.1 106.0 1.0 O1A L:3PO901 4.2 159.3 1.0 CG L:ASP471 4.2 104.6 1.0 O3A L:3PO901 4.3 155.3 1.0 OD2 L:ASP471 4.3 104.5 1.0 O2B L:3PO901 4.5 148.6 1.0 CB L:ASP471 4.9 115.1 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