Magnesium in PDB 3ti0: Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddgtp-Dc in Closed Conformation

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

The structure of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddgtp-Dc in Closed Conformation, PDB code: 3ti0 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)	42.96 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.500, 108.920, 149.570, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddgtp-Dc in Closed Conformation (pdb code 3ti0). 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 Ddgtp-Dc in Closed Conformation, PDB code: 3ti0:
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 Ddgtp-Dc 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 Ddgtp-Dc in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:25.8 occ:1.00 OD2 A:ASP830 2.1 25.2 1.0 O2G A:DG3201 2.2 27.2 1.0 O A:TYR654 2.2 29.8 1.0 O2A A:DG3201 2.2 20.1 1.0 O2B A:DG3201 2.3 22.5 1.0 OD1 A:ASP653 2.3 33.3 1.0 PB A:DG3201 3.2 27.4 1.0 CG A:ASP830 3.2 27.7 1.0 PG A:DG3201 3.3 26.4 1.0 CG A:ASP653 3.3 42.2 1.0 C A:TYR654 3.4 34.3 1.0 PA A:DG3201 3.4 21.2 1.0 H5'2 A:DG3201 3.4 26.3 1.0 O3B A:DG3201 3.6 25.5 1.0 OD2 A:ASP653 3.7 41.4 1.0 OD1 A:ASP830 3.7 25.4 1.0 HG22 A:ILE657 3.8 27.2 1.0 O3A A:DG3201 3.8 22.1 1.0 HA A:SER655 3.8 39.4 1.0 O A:HOH1151 3.9 28.8 1.0 H A:ILE657 4.0 31.9 1.0 O A:HOH1011 4.0 35.2 1.0 H A:GLN656 4.0 32.9 1.0 HB2 A:TYR654 4.1 32.7 1.0 O3G A:DG3201 4.2 33.6 1.0 N A:TYR654 4.2 34.5 1.0 C5' A:DG3201 4.2 22.0 1.0 H A:TYR654 4.2 41.2 1.0 H5'1 A:DG3201 4.2 26.3 1.0 CA A:TYR654 4.3 30.4 1.0 HB A:ILE657 4.3 35.3 1.0 O5' A:DG3201 4.3 18.1 1.0 N A:SER655 4.3 27.2 1.0 HB2 A:ASP830 4.4 26.7 1.0 O1G A:DG3201 4.4 28.3 1.0 CA A:SER655 4.4 32.9 1.0 N A:GLN656 4.4 27.5 1.0 HG21 A:ILE657 4.4 27.2 1.0 O A:HOH1070 4.4 37.7 1.0 CB A:ASP830 4.4 22.3 1.0 CG2 A:ILE657 4.5 22.8 1.0 CB A:TYR654 4.6 27.4 1.0 O1A A:DG3201 4.6 24.4 1.0 O1B A:DG3201 4.6 23.8 1.0 C A:ASP653 4.6 35.0 1.0 HB3 A:TYR654 4.6 32.7 1.0 C A:SER655 4.6 29.0 1.0 CB A:ASP653 4.7 34.6 1.0 N A:ILE657 4.8 26.6 1.0 HZ3 A:LYS706 4.8 37.1 1.0 O A:ASP830 4.8 27.3 1.0 CB A:ILE657 4.9 29.5 1.0 HB3 A:ASP830 4.9 26.7 1.0 HB3 A:ASP653 4.9 41.5 1.0 O A:HOH1288 4.9 33.8 1.0 HA A:ASP653 5.0 30.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddgtp-Dc 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 Ddgtp-Dc in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2 b:13.6 occ:1.00 OD2 D:ASP830 2.1 14.7 1.0 O2A D:DG3202 2.2 13.4 1.0 O D:TYR654 2.2 14.3 1.0 O2B D:DG3202 2.2 14.6 1.0 O2G D:DG3202 2.2 13.8 1.0 O D:HOH1687 2.3 28.8 1.0 CG D:ASP830 3.2 14.6 1.0 PB D:DG3202 3.2 12.9 1.0 PG D:DG3202 3.4 17.6 1.0 C D:TYR654 3.4 15.8 1.0 H5'2 D:DG3202 3.4 15.1 1.0 PA D:DG3202 3.5 14.0 1.0 O3B D:DG3202 3.6 13.2 1.0 OD1 D:ASP830 3.7 13.1 1.0 HA D:SER655 3.7 16.4 0.3 O D:HOH890 3.7 19.8 1.0 HA D:SER655 3.7 16.3 0.7 O3A D:DG3202 3.8 11.2 1.0 HG22 D:ILE657 3.8 16.3 1.0 H D:GLN656 4.0 16.2 0.5 H D:GLN656 4.0 16.2 0.5 H D:ILE657 4.0 20.2 1.0 HB2 D:ASP653 4.0 22.3 1.0 O D:HOH1178 4.1 33.4 1.0 OD2 D:ASP653 4.1 32.5 1.0 C5' D:DG3202 4.2 12.7 1.0 O D:HOH1686 4.2 32.4 1.0 HB2 D:TYR654 4.3 13.9 1.0 N D:SER655 4.3 11.4 0.7 N D:SER655 4.3 11.6 0.3 HB2 D:ASP830 4.3 14.2 1.0 CA D:SER655 4.3 13.7 0.3 O3G D:DG3202 4.3 20.5 1.0 CA D:SER655 4.3 13.7 0.7 O5' D:DG3202 4.3 11.4 1.0 O1G D:DG3202 4.4 16.1 1.0 HB D:ILE657 4.4 18.1 1.0 N D:GLN656 4.4 13.5 1.0 CB D:ASP830 4.4 11.9 1.0 CA D:TYR654 4.4 10.0 1.0 H5'1 D:DG3202 4.4 15.1 1.0 N D:TYR654 4.4 10.7 1.0 H D:TYR654 4.4 12.7 1.0 HG21 D:ILE657 4.5 16.3 1.0 CG2 D:ILE657 4.5 13.6 1.0 O D:HOH973 4.6 26.4 1.0 O1B D:DG3202 4.6 12.3 1.0 C D:SER655 4.6 11.8 0.3 C D:SER655 4.6 11.7 0.7 O1A D:DG3202 4.6 16.3 1.0 CB D:TYR654 4.8 11.6 1.0 HZ2 D:LYS706 4.8 23.6 1.0 HB3 D:ASP830 4.8 14.2 1.0 N D:ILE657 4.8 16.9 1.0 CB D:ASP653 4.8 18.6 1.0 HB3 D:TYR654 4.9 13.9 1.0 CB D:ILE657 4.9 15.2 1.0 C D:ASP653 4.9 18.8 1.0 CG D:ASP653 5.0 22.5 1.0 O D:ASP830 5.0 12.9 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