Atomistry » Magnesium » PDB 8d9r-8diq » 8dh2
Atomistry »
  Magnesium »
    PDB 8d9r-8diq »
      8dh2 »

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

Go back to Magnesium Binding Sites List in 8dh2
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

Last articles

Na in 7Q78
Na in 7Q77
Na in 7Q76
Na in 7Q6Q
Na in 7Q75
Na in 7Q5F
Na in 7Q47
Na in 7Q3Z
Na in 7Q5E
Na in 7Q36
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy