Magnesium in PDB 3pv8: Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation

All present enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation:
2.7.7.7;

The structure of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation, PDB code: 3pv8 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)	88.42 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.890, 109.300, 150.420, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.1

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation (pdb code 3pv8). 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 Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation, PDB code: 3pv8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation


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 Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:23.0 occ:1.00 OD2 A:ASP830 2.1 22.1 1.0 O2B A:D3T201 2.2 21.4 1.0 O2G A:D3T201 2.2 24.8 1.0 O2A A:D3T201 2.3 18.2 1.0 O A:TYR654 2.3 25.8 1.0 OD1 A:ASP653 2.4 28.7 0.5 PB A:D3T201 3.2 20.8 1.0 CG A:ASP830 3.2 26.1 1.0 PG A:D3T201 3.3 24.4 1.0 CG A:ASP653 3.3 33.2 0.5 PA A:D3T201 3.5 21.2 1.0 O3B A:D3T201 3.5 19.4 1.0 C A:TYR654 3.5 24.3 1.0 H5'2 A:D3T201 3.6 27.0 1.0 OD2 A:ASP653 3.6 35.0 0.5 OD1 A:ASP830 3.6 22.2 1.0 HB2 A:ASP653 3.7 34.0 0.5 O3A A:D3T201 3.7 20.5 1.0 HG22 A:ILE657 3.7 33.2 1.0 HA A:SER655 3.9 29.4 1.0 H A:ILE657 3.9 26.9 1.0 O A:HOH1785 4.0 28.8 1.0 H A:GLN656 4.1 26.7 1.0 HB2 A:TYR654 4.2 23.1 1.0 O3G A:D3T201 4.2 27.6 1.0 C5' A:D3T201 4.3 22.5 1.0 HB A:ILE657 4.3 27.0 1.0 N A:TYR654 4.3 24.2 1.0 O5' A:D3T201 4.4 18.7 1.0 H A:TYR654 4.4 29.0 1.0 HB2 A:ASP830 4.4 26.0 1.0 HG21 A:ILE657 4.4 33.2 1.0 CB A:ASP830 4.4 21.7 1.0 H5'1 A:D3T201 4.4 27.0 1.0 CA A:TYR654 4.4 22.7 1.0 O1G A:D3T201 4.4 22.0 1.0 N A:SER655 4.4 27.3 1.0 CG2 A:ILE657 4.5 27.7 1.0 N A:GLN656 4.5 22.3 1.0 CA A:SER655 4.5 24.5 1.0 O1B A:D3T201 4.5 23.8 1.0 O1A A:D3T201 4.6 17.2 1.0 CB A:ASP653 4.6 28.4 0.5 OD1 A:ASP653 4.6 40.4 0.5 O A:HOH1311 4.7 40.5 1.0 CB A:ASP653 4.7 27.7 0.5 C A:SER655 4.7 25.5 1.0 C A:ASP653 4.7 27.4 1.0 CB A:TYR654 4.7 19.3 1.0 N A:ILE657 4.8 22.4 1.0 O A:ASP830 4.8 24.5 1.0 HB3 A:ASP830 4.8 26.0 1.0 HB3 A:TYR654 4.8 23.1 1.0 HZ3 A:LYS706 4.8 31.4 1.0 CB A:ILE657 4.9 22.5 1.0 HB3 A:ASP653 5.0 33.3 0.5

Magnesium binding site 2 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation


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 Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddttp-Da in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2 b:14.4 occ:1.00 OD2 D:ASP830 2.0 12.8 1.0 O D:HOH1823 2.0 25.9 1.0 O2B D:D3T202 2.2 16.3 1.0 O2G D:D3T202 2.2 15.8 1.0 O D:TYR654 2.2 12.5 1.0 O2A D:D3T202 2.3 13.6 1.0 CG D:ASP830 3.1 11.6 1.0 PB D:D3T202 3.2 13.9 1.0 PG D:D3T202 3.4 16.9 1.0 C D:TYR654 3.5 10.9 1.0 PA D:D3T202 3.6 12.4 1.0 HA D:SER655 3.6 14.7 0.4 O D:HOH1820 3.6 30.8 1.0 O3B D:D3T202 3.6 12.4 1.0 H5'2 D:D3T202 3.6 10.7 1.0 OD1 D:ASP830 3.7 14.3 1.0 HA D:SER655 3.7 14.6 0.6 O3A D:D3T202 3.7 9.4 1.0 H D:GLN656 3.9 17.6 0.5 H D:GLN656 3.9 17.6 0.5 H D:ILE657 4.0 22.6 1.0 HG22 D:ILE657 4.0 24.9 1.0 HB2 D:ASP653 4.1 15.7 1.0 OD2 D:ASP653 4.1 24.7 1.0 HB D:ILE657 4.1 19.8 1.0 HB2 D:ASP830 4.2 10.3 1.0 CB D:ASP830 4.3 8.6 1.0 CA D:SER655 4.3 12.2 0.4 O3G D:D3T202 4.3 22.7 1.0 CA D:SER655 4.3 12.2 0.6 N D:SER655 4.3 11.3 1.0 HB2 D:TYR654 4.3 13.5 1.0 N D:GLN656 4.4 14.7 1.0 C5' D:D3T202 4.4 8.9 1.0 O D:HOH1690 4.4 30.9 1.0 O1G D:D3T202 4.4 13.1 1.0 O5' D:D3T202 4.4 10.8 1.0 O D:HOH902 4.5 29.9 1.0 HG21 D:ILE657 4.5 24.9 1.0 CA D:TYR654 4.5 9.4 1.0 H5'1 D:D3T202 4.5 10.7 1.0 CG2 D:ILE657 4.6 20.8 1.0 O1B D:D3T202 4.6 12.5 1.0 N D:TYR654 4.6 10.0 1.0 H D:TYR654 4.6 11.9 1.0 C D:SER655 4.6 11.1 1.0 HB3 D:ASP830 4.7 10.3 1.0 O1A D:D3T202 4.7 13.1 1.0 N D:ILE657 4.8 18.8 1.0 CB D:ILE657 4.8 16.5 1.0 CB D:TYR654 4.8 11.2 1.0 CB D:ASP653 4.9 13.1 1.0 HB3 D:TYR654 5.0 13.5 1.0

W.Wang, H.W.Hellinga, L.S.Beese. Structural Evidence For the Rare Tautomer Hypothesis of Spontaneous Mutagenesis. Proc.Natl.Acad.Sci.Usa V. 108 17644 2011.
ISSN: ISSN 0027-8424
PubMed: 22006298
DOI: 10.1073/PNAS.1114496108