Magnesium in PDB 7s9q: Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog:
2.7.7.7;

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog, PDB code: 7s9q was solved by B.D.Freudenthal, B.J.Ryan, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.15 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.624, 78.583, 54.916, 90, 112.44, 90
R / Rfree (%)	19.3 / 24.7

The structure of Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog also contains other interesting chemical elements:

Sodium	(Na)	3 atoms
Manganese	(Mn)	3 atoms

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog (pdb code 7s9q). 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 Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog, PDB code: 7s9q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


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 Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:39.9 occ:1.00 O A:HOH638 2.0 46.5 1.0 O A:HOH763 2.1 48.5 1.0 NE2 A:HIS51 2.4 29.7 1.0 O A:HOH779 2.6 36.5 1.0 O A:HOH817 2.9 52.5 1.0 CD2 A:HIS51 3.3 31.8 1.0 CE1 A:HIS51 3.4 32.2 1.0 CG A:HIS51 4.4 24.1 1.0 ND1 A:HIS51 4.5 22.9 1.0 O A:HOH760 4.6 38.5 1.0 CG A:PRO50 4.8 24.7 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog


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 Dna Polymerase Beta with Template Fapy-Dg and An Incoming Datp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:41.1 occ:1.00 O A:HOH592 2.0 43.3 1.0 O A:HOH751 2.0 39.8 1.0 NE2 A:HIS252 2.4 32.6 1.0 CE1 A:HIS252 2.4 27.3 1.0 O A:HOH664 2.7 34.8 1.0 O A:HOH761 3.1 47.4 1.0 NE2 A:GLN240 3.5 31.5 1.0 OE1 A:GLN240 3.6 40.1 1.0 CD2 A:HIS252 3.7 27.8 1.0 ND1 A:HIS252 3.8 36.9 1.0 OE2 A:GLU249 3.8 50.0 1.0 CD A:GLN240 3.9 32.0 1.0 CG A:HIS252 4.4 20.1 1.0 CD A:GLU249 4.5 44.8 1.0 OE1 A:GLU249 4.6 61.4 1.0 OH A:TYR142 4.9 23.9 1.0

B.J.Ryan, H.Yang, J.H.T.Bacurio, M.R.Smith, A.K.Basu, M.M.Greenberg, B.D.Freudenthal. Structural Dynamics of A Common Mutagenic Oxidative Dna Lesion in Duplex Dna and During Dna Replication. J.Am.Chem.Soc. V. 144 8054 2022.
ISSN: ESSN 1520-5126
PubMed: 35499923
DOI: 10.1021/JACS.2C00193