Magnesium in PDB 3thv: Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddatp-Dt in Closed Conformation

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

The structure of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddatp-Dt in Closed Conformation, PDB code: 3thv 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)	88.41 / 1.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.810, 109.270, 150.430, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.4

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddatp-Dt in Closed Conformation (pdb code 3thv). 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 Ddatp-Dt in Closed Conformation, PDB code: 3thv:
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 Ddatp-Dt 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 Ddatp-Dt in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:26.5 occ:1.00 O2B A:DDS201 2.1 24.3 1.0 O2G A:DDS201 2.1 28.9 1.0 O2A A:DDS201 2.2 24.3 1.0 O A:TYR654 2.3 28.2 1.0 OD2 A:ASP830 2.3 31.7 1.0 OD1 A:ASP653 2.4 31.7 1.0 PB A:DDS201 3.1 29.2 1.0 PG A:DDS201 3.3 27.2 1.0 CG A:ASP653 3.4 41.6 1.0 CG A:ASP830 3.4 30.5 1.0 PA A:DDS201 3.4 23.3 1.0 H5'A A:DDS201 3.4 25.3 1.0 C A:TYR654 3.5 34.7 1.0 O3B A:DDS201 3.5 23.1 1.0 O3A A:DDS201 3.6 20.6 1.0 OD2 A:ASP653 3.7 43.0 1.0 HG22 A:ILE657 3.7 32.5 1.0 OD1 A:ASP830 3.8 26.2 1.0 O A:HOH899 3.8 32.8 1.0 H A:ILE657 3.9 32.9 1.0 HA A:SER655 4.0 43.2 1.0 H A:GLN656 4.0 36.1 1.0 HB2 A:TYR654 4.1 36.5 1.0 O3G A:DDS201 4.2 32.0 1.0 H A:TYR654 4.2 39.7 1.0 N A:TYR654 4.2 33.1 1.0 C5' A:DDS201 4.2 21.1 1.0 O A:HOH1194 4.3 40.1 1.0 HB A:ILE657 4.3 30.9 1.0 CA A:TYR654 4.3 32.2 1.0 O5' A:DDS201 4.3 19.7 1.0 O1G A:DDS201 4.3 25.6 1.0 O A:HOH1040 4.4 39.6 1.0 N A:GLN656 4.4 30.1 1.0 H5' A:DDS201 4.4 25.3 1.0 N A:SER655 4.4 31.7 1.0 HG21 A:ILE657 4.4 32.5 1.0 O1B A:DDS201 4.5 25.4 1.0 CG2 A:ILE657 4.5 27.1 1.0 O1A A:DDS201 4.5 23.1 1.0 CA A:SER655 4.5 36.0 1.0 CB A:TYR654 4.6 30.5 1.0 HB2 A:ASP830 4.6 34.2 1.0 CB A:ASP830 4.7 28.6 1.0 HB3 A:TYR654 4.7 36.5 1.0 C A:SER655 4.7 30.3 1.0 N A:ILE657 4.7 27.4 1.0 C A:ASP653 4.7 32.4 1.0 CB A:ASP653 4.7 37.6 1.0 O A:HOH1280 4.8 37.4 1.0 CB A:ILE657 4.9 25.8 1.0 O A:ASP830 4.9 28.6 1.0 HB3 A:ASP653 4.9 45.0 1.0 HA A:GLN656 5.0 39.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Ddatp-Dt 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 Ddatp-Dt in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2 b:13.0 occ:1.00 OD2 D:ASP830 2.0 13.0 1.0 O2B D:DDS202 2.2 13.0 1.0 O2A D:DDS202 2.2 14.5 1.0 O D:TYR654 2.2 11.3 1.0 O2G D:DDS202 2.3 15.5 1.0 O D:HOH1696 2.3 24.2 1.0 CG D:ASP830 3.2 12.0 1.0 PB D:DDS202 3.2 13.5 1.0 PA D:DDS202 3.4 12.8 1.0 PG D:DDS202 3.4 15.0 1.0 C D:TYR654 3.4 13.7 1.0 H5'A D:DDS202 3.5 12.0 1.0 O3B D:DDS202 3.6 14.1 1.0 OD1 D:ASP830 3.7 13.2 1.0 O3A D:DDS202 3.7 9.6 1.0 HG22 D:ILE657 3.7 13.6 1.0 HA D:SER655 3.8 15.2 0.4 O D:HOH148 3.8 22.1 1.0 HA D:SER655 3.9 15.2 0.6 HB2 D:ASP653 3.9 18.5 1.0 H D:ILE657 3.9 15.7 1.0 H D:GLN656 4.0 13.6 0.5 H D:GLN656 4.0 13.6 0.5 OD2 D:ASP653 4.1 30.5 1.0 O D:HOH1149 4.1 32.9 1.0 O D:HOH1695 4.2 31.0 1.0 HB2 D:TYR654 4.2 9.2 1.0 C5' D:DDS202 4.3 10.1 1.0 HB D:ILE657 4.3 18.2 1.0 O3G D:DDS202 4.3 14.6 1.0 HB2 D:ASP830 4.3 11.5 1.0 HG21 D:ILE657 4.3 13.6 1.0 O5' D:DDS202 4.3 9.7 1.0 N D:SER655 4.4 10.9 0.4 N D:SER655 4.4 10.9 0.6 CB D:ASP830 4.4 9.7 1.0 CA D:TYR654 4.4 8.2 1.0 CA D:SER655 4.4 12.7 0.4 N D:TYR654 4.4 9.0 1.0 CG2 D:ILE657 4.4 11.4 1.0 N D:GLN656 4.4 11.4 1.0 CA D:SER655 4.4 12.7 0.6 O1G D:DDS202 4.4 14.5 1.0 H D:TYR654 4.4 10.8 1.0 H5' D:DDS202 4.5 12.0 1.0 O1B D:DDS202 4.5 11.7 1.0 O1A D:DDS202 4.6 13.3 1.0 O D:HOH972 4.7 28.9 1.0 C D:SER655 4.7 12.4 0.6 C D:SER655 4.7 12.4 0.4 CB D:TYR654 4.7 7.7 1.0 N D:ILE657 4.8 13.2 1.0 HB3 D:ASP830 4.8 11.5 1.0 HZ2 D:LYS706 4.8 23.6 1.0 CB D:ASP653 4.8 15.4 1.0 HB3 D:TYR654 4.9 9.2 1.0 CB D:ILE657 4.9 15.2 1.0 C D:ASP653 4.9 17.8 1.0 CG D:ASP653 4.9 21.3 1.0 O D:ASP830 5.0 12.8 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