Magnesium in PDB 4dqp: Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template)

All present enzymatic activity of Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template):
2.7.7.7;

The structure of Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template), PDB code: 4dqp was solved by W.Wang, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.45 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.220, 109.340, 149.930, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.5

The binding sites of Magnesium atom in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template) (pdb code 4dqp). 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 Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template), PDB code: 4dqp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template)


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 Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:40.9 occ:1.00 O2G A:DCT901 2.1 45.8 1.0 O2B A:DCT901 2.1 39.7 1.0 O2A A:DCT901 2.2 33.8 1.0 OD2 A:ASP830 2.5 47.4 1.0 PB A:DCT901 3.3 38.2 1.0 H A:GLN656 3.3 64.0 1.0 PG A:DCT901 3.3 50.4 1.0 O A:TYR654 3.3 42.4 1.0 PA A:DCT901 3.5 31.9 1.0 CG A:ASP830 3.7 47.1 1.0 OD1 A:ASP653 3.7 60.3 1.0 O A:HOH1246 3.8 42.9 1.0 O3B A:DCT901 3.8 46.4 1.0 O3A A:DCT901 3.9 32.9 1.0 O3G A:DCT901 3.9 51.1 1.0 HA A:SER655 3.9 76.4 1.0 N A:GLN656 4.2 53.3 1.0 HB2 A:ASP653 4.2 56.6 1.0 OD1 A:ASP830 4.2 44.5 1.0 O A:HOH1211 4.3 46.8 1.0 O1A A:DCT901 4.5 29.3 1.0 C A:TYR654 4.5 47.5 1.0 C5' A:DCT901 4.5 31.3 1.0 HA A:GLN656 4.5 54.8 1.0 O5' A:DCT901 4.6 32.2 1.0 O1G A:DCT901 4.6 52.1 1.0 O1B A:DCT901 4.6 36.4 1.0 HB2 A:ASP830 4.6 52.9 1.0 CG A:ASP653 4.6 58.6 1.0 CA A:SER655 4.8 63.7 1.0 CB A:ASP830 4.8 44.1 1.0 HG3 A:GLN656 4.8 67.6 1.0 CB A:ASP653 4.9 47.2 1.0 CA A:GLN656 4.9 45.6 1.0 H A:ILE657 5.0 46.5 1.0 C A:SER655 5.0 59.1 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template)


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 Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Ddctp (Paired with Dg of Template) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:18.9 occ:1.00 O D:HOH1690 2.0 24.8 1.0 O2A D:DCT901 2.0 12.5 1.0 O2G D:DCT901 2.0 20.3 1.0 O2B D:DCT901 2.1 14.4 1.0 OD2 D:ASP830 2.1 19.9 1.0 O D:HOH1033 2.1 18.4 1.0 PB D:DCT901 3.1 14.0 1.0 CG D:ASP830 3.2 22.4 1.0 PA D:DCT901 3.3 14.1 1.0 PG D:DCT901 3.3 18.9 1.0 O3A D:DCT901 3.5 15.1 1.0 O3B D:DCT901 3.5 16.6 1.0 H D:GLN656 3.6 16.6 0.8 H D:GLN656 3.6 16.6 0.2 OD1 D:ASP830 3.7 19.8 1.0 O D:HOH1308 3.8 31.9 1.0 O D:HOH1424 4.0 27.7 1.0 C5' D:DCT901 4.1 11.1 1.0 O D:TYR654 4.2 18.5 1.0 O5' D:DCT901 4.2 11.7 1.0 OD1 D:ASP653 4.3 26.7 1.0 O3G D:DCT901 4.3 20.7 1.0 HA D:SER655 4.4 19.3 0.8 O D:HOH1065 4.4 15.5 1.0 O1G D:DCT901 4.4 18.7 1.0 HB2 D:ASP830 4.4 15.2 1.0 CB D:ASP830 4.4 12.7 1.0 HA D:SER655 4.4 17.9 0.2 N D:GLN656 4.4 13.8 1.0 O1A D:DCT901 4.5 15.8 1.0 O E:HOH130 4.5 53.1 1.0 O1B D:DCT901 4.5 12.5 1.0 HA D:GLN656 4.6 12.6 1.0 HB2 D:ASP653 4.7 31.4 1.0 HB3 D:ASP830 4.7 15.2 1.0 HZ3 D:LYS706 4.9 23.1 1.0 HG3 D:GLN656 5.0 21.3 1.0

W.Wang, E.Y.Wu, H.W.Hellinga, L.S.Beese. Structural Factors That Determine Selectivity of A High Fidelity Dna Polymerase For Deoxy-, Dideoxy-, and Ribonucleotides. J.Biol.Chem. V. 287 28215 2012.
ISSN: ISSN 0021-9258
PubMed: 22648417
DOI: 10.1074/JBC.M112.366609