Magnesium in PDB 6ph6: Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream, PDB code: 6ph6 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.93 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.510, 79.675, 55.428, 90.00, 107.52, 90.00
R / Rfree (%)	18.5 / 27.6

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream (pdb code 6ph6). 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 Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream, PDB code: 6ph6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:29.1 occ:1.00 OD1 A:ASP190 2.0 30.5 1.0 O3G A:DCP401 2.1 31.1 1.0 OD2 A:ASP192 2.2 26.1 1.0 O2B A:DCP401 2.4 23.7 1.0 O2A A:DCP401 2.5 23.8 1.0 O A:ASP190 3.0 31.6 1.0 CG A:ASP190 3.3 28.2 1.0 CG A:ASP192 3.3 32.4 1.0 PG A:DCP401 3.3 44.0 1.0 PB A:DCP401 3.5 29.1 1.0 O A:HOH540 3.5 29.0 1.0 C A:ASP190 3.6 30.2 1.0 O1G A:DCP401 3.6 27.8 1.0 N A:ASP190 3.8 23.8 1.0 O3B A:DCP401 3.8 37.4 1.0 PA A:DCP401 3.9 31.7 1.0 OG A:SER180 3.9 25.0 1.0 OD1 A:ASP192 3.9 30.2 1.0 OD2 A:ASP190 4.1 31.0 1.0 CA A:ASP190 4.1 23.4 1.0 O3A A:DCP401 4.2 28.7 1.0 CB A:ASP190 4.2 22.4 1.0 CB A:ASP192 4.4 23.9 1.0 N A:MET191 4.4 27.6 1.0 N A:SER180 4.4 23.2 1.0 CA A:GLY179 4.5 21.5 1.0 MG A:MG403 4.5 34.3 1.0 O2G A:DCP401 4.6 33.0 1.0 N A:ASP192 4.6 26.3 1.0 C5' A:DCP401 4.7 21.1 1.0 C A:MET191 4.7 25.7 1.0 CA A:MET191 4.8 28.6 1.0 O1B A:DCP401 4.8 26.2 1.0 O1A A:DCP401 4.8 26.8 1.0 O5' A:DCP401 4.8 27.0 1.0 N A:GLY189 4.9 30.5 1.0 C A:GLY189 4.9 27.4 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with 2NT-Gap with Dctp Bound Downstream within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:34.3 occ:1.00 OD2 A:ASP256 2.5 30.3 1.0 OD1 A:ASP192 2.5 30.2 1.0 OD2 A:ASP190 2.6 31.0 1.0 O2A A:DCP401 2.8 23.8 1.0 O1A A:DCP401 3.3 26.8 1.0 PA A:DCP401 3.3 31.7 1.0 CG A:ASP190 3.4 28.2 1.0 CG A:ASP192 3.4 32.4 1.0 OD1 A:ASP190 3.4 30.5 1.0 O5' A:DCP401 3.5 27.0 1.0 OD2 A:ASP192 3.6 26.1 1.0 CG A:ASP256 3.6 30.0 1.0 C5' A:DCP401 4.0 21.1 1.0 CB A:ASP256 4.1 28.1 1.0 MG A:MG402 4.5 29.1 1.0 NH2 A:ARG254 4.5 36.4 1.0 OD1 A:ASP256 4.6 36.8 1.0 O A:HOH543 4.6 31.2 1.0 CB A:ASP190 4.8 22.4 1.0 CB A:ASP192 4.8 23.9 1.0 O3A A:DCP401 4.8 28.7 1.0 O3G A:DCP401 4.9 31.1 1.0

M.J.Howard, N.A.Cavanaugh, V.K.Batra, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Beta Nucleotide-Stabilized Template Misalignment Fidelity Depends on Local Sequence Context. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31801827
DOI: 10.1074/JBC.RA119.010594