Magnesium in PDB 7omg: Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template

All present enzymatic activity of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template:
2.7.7.7;

The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template, PDB code: 7omg was solved by K.Betz, H.M.Kropp, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.25 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	108.403, 147.138, 71.129, 90, 90, 90
R / Rfree (%)	21 / 24.8

The structure of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom
Manganese	(Mn)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template (pdb code 7omg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template, PDB code: 7omg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:57.2 occ:1.00 O A:HOH965 2.0 59.0 1.0 O2G A:DTP801 2.2 50.7 1.0 OE2 A:GLU580 2.4 85.3 1.0 OD2 A:ASP404 2.4 58.4 1.0 O A:HOH939 2.6 60.3 1.0 O A:HOH959 2.6 56.1 1.0 OE1 A:GLU580 2.7 83.9 1.0 CD A:GLU580 2.8 87.2 1.0 PG A:DTP801 3.2 49.8 1.0 CG A:ASP404 3.3 57.3 1.0 O3G A:DTP801 3.5 53.4 1.0 CB A:ASP404 3.6 60.0 1.0 MN A:MN804 3.6 51.6 1.0 O1G A:DTP801 3.7 51.0 1.0 O A:PHE405 3.9 52.9 1.0 CG A:GLU580 4.3 83.2 1.0 O A:HOH909 4.3 54.5 1.0 OE1 A:GLU578 4.4 63.2 1.0 OD1 A:ASP404 4.4 55.0 1.0 O3B A:DTP801 4.6 49.6 1.0 O1A A:DTP801 4.6 54.0 1.0 O A:ASP404 4.6 57.5 1.0 C A:ASP404 4.6 53.3 1.0 C A:PHE405 4.7 52.8 1.0 CA A:ASP404 4.8 55.2 1.0 O A:HOH913 4.8 56.0 1.0 CB A:GLU580 5.0 80.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Kod Dna Polymerase in A Ternary Complex with An Uracil Containing Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:45.8 occ:1.00 OD1 A:ASP542 2.1 51.0 1.0 OD1 A:ASP404 2.1 55.0 1.0 O A:HOH913 2.2 56.0 1.0 O A:HOH956 2.2 51.2 1.0 O1A A:DTP801 2.2 54.0 1.0 CG A:ASP404 2.9 57.3 1.0 CG A:ASP542 3.0 50.2 1.0 OD2 A:ASP404 3.0 58.4 1.0 OD2 A:ASP542 3.2 52.0 1.0 MN A:MN804 3.4 51.6 1.0 PA A:DTP801 3.5 50.8 1.0 O A:HOH959 3.7 56.1 1.0 OH A:TYR402 3.8 64.0 1.0 C3' P:DOC12 3.9 48.6 1.0 O2A A:DTP801 4.0 54.8 1.0 O5' A:DTP801 4.1 46.9 1.0 C5' A:DTP801 4.2 49.1 1.0 CB A:ASP404 4.3 60.0 1.0 N A:GLY543 4.3 53.0 1.0 C A:ASP542 4.3 50.7 1.0 C5' P:DOC12 4.4 52.2 1.0 CB A:ASP542 4.4 49.7 1.0 O A:ASP540 4.4 54.8 1.0 C4' P:DOC12 4.5 51.3 1.0 O A:HOH952 4.5 58.8 1.0 O A:ASP542 4.6 49.2 1.0 O2G A:DTP801 4.6 50.7 1.0 CA A:GLY543 4.7 56.3 1.0 CA A:ASP542 4.7 51.3 1.0 N A:ASP542 4.7 51.5 1.0 O3A A:DTP801 4.8 48.3 1.0 CZ A:TYR402 4.9 65.5 1.0 O1B A:DTP801 4.9 51.8 1.0

H.M.Kropp, S.Ludmann, K.Diederichs, K.Betz, A.Marx. Structural Basis For the Recognition of Deaminated Nucleobases By An Archaeal Dna Polymerase. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 34486208
DOI: 10.1002/CBIC.202100306