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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 8dh5

Go back to Magnesium Binding Sites List in 8dh5
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 8dh5

Go back to Magnesium Binding Sites List in 8dh5
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

Reference:

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
Page generated: Fri Oct 4 00:42:41 2024

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