Magnesium in PDB 5omq: Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site

All present enzymatic activity of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site:
2.7.7.7;

The structure of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site, PDB code: 5omq was solved by K.Betz, A.Marx, K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.84 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.793, 93.678, 158.205, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.8

The structure of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site (pdb code 5omq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site, PDB code: 5omq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:44.5 occ:1.00 OD2 A:ASP404 2.1 58.9 1.0 OD1 A:ASP542 2.2 47.5 1.0 O A:HOH960 2.3 44.3 1.0 O2A A:DTP806 2.5 35.6 1.0 O A:HOH951 2.6 61.5 1.0 CG A:ASP404 3.1 53.6 1.0 CG A:ASP542 3.2 43.0 1.0 OD1 A:ASP404 3.4 57.7 1.0 C3' P:DC12 3.5 42.4 1.0 MN A:MN805 3.5 41.8 1.0 PA A:DTP806 3.5 40.8 1.0 OD2 A:ASP542 3.7 49.1 1.0 H5'1 A:DTP806 3.7 52.0 1.0 OH A:TYR402 3.8 50.1 1.0 H5'2 A:DTP806 3.8 52.0 1.0 O5' A:DTP806 3.9 42.7 1.0 N A:GLY543 4.0 45.8 1.0 C5' A:DTP806 4.1 43.2 1.0 O1A A:DTP806 4.1 30.2 1.0 C4' P:DC12 4.1 44.3 1.0 C5' P:DC12 4.1 50.9 1.0 O A:HOH936 4.2 50.2 1.0 C A:ASP542 4.2 44.8 1.0 CA A:GLY543 4.3 44.9 1.0 O A:ASP540 4.4 45.0 1.0 CB A:ASP404 4.5 47.1 1.0 CB A:ASP542 4.5 39.7 1.0 O A:ASP542 4.5 38.0 1.0 N A:ASP542 4.6 42.1 1.0 CA A:ASP542 4.7 40.8 1.0 O3G A:DTP806 4.7 42.4 1.0 C2' P:DC12 4.7 43.2 1.0 O3A A:DTP806 4.9 31.2 1.0 O P:HOH104 4.9 47.9 1.0 CZ A:TYR402 5.0 55.2 1.0 O2B A:DTP806 5.0 47.0 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:43.6 occ:1.00 O A:HOH923 2.0 48.4 1.0 O A:HOH936 2.1 50.2 1.0 O3G A:DTP806 2.2 42.4 1.0 O A:HOH934 2.3 58.4 1.0 OE1 A:GLU580 2.4 70.1 1.0 OD1 A:ASP404 2.6 57.7 1.0 CG A:ASP404 3.1 53.6 1.0 PG A:DTP806 3.2 39.7 1.0 CD A:GLU580 3.4 69.8 1.0 MN A:MN805 3.4 41.8 1.0 O2G A:DTP806 3.5 39.7 1.0 CB A:ASP404 3.6 47.1 1.0 OE2 A:GLU580 3.7 66.2 1.0 O1G A:DTP806 3.7 35.7 1.0 O A:PHE405 3.8 43.9 1.0 OD2 A:ASP404 3.9 58.9 1.0 O A:ASP404 4.3 50.7 1.0 O2A A:DTP806 4.3 35.6 1.0 OE1 A:GLU578 4.4 64.4 1.0 C A:ASP404 4.4 50.2 1.0 C A:PHE405 4.5 54.4 1.0 O3B A:DTP806 4.6 49.2 1.0 CA A:ASP404 4.7 46.5 1.0 CG A:GLU580 4.8 71.3 1.0 O A:HOH951 4.8 61.5 1.0 O2B A:DTP806 4.9 47.0 1.0 N A:PHE405 4.9 49.3 1.0 CA A:ARG406 5.0 52.3 1.0

H.M.Kropp, K.Betz, J.Wirth, K.Diederichs, A.Marx. Crystal Structures of Ternary Complexes of Archaeal B-Family Dna Polymerases. Plos One V. 12 88005 2017.
ISSN: ESSN 1932-6203
PubMed: 29211756
DOI: 10.1371/JOURNAL.PONE.0188005