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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 8dh2

Go back to Magnesium Binding Sites List in 8dh2
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 8dh2

Go back to Magnesium Binding Sites List in 8dh2
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 8dh2

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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 8dh2

Go back to Magnesium Binding Sites List in 8dh2
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

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 00:42:34 2024

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