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

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

The structure of Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Dctp (Paired with Dg of Template), PDB code: 4dqi 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)	28.77 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.680, 109.360, 150.320, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.5

The binding sites of Magnesium atom in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Dctp (Paired with Dg of Template) (pdb code 4dqi). 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 Dctp (Paired with Dg of Template), PDB code: 4dqi:
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 Dctp (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 Dctp (Paired with Dg of Template) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:23.1 occ:1.00 O2G A:DCP902 2.0 23.5 1.0 OD2 A:ASP830 2.1 23.5 1.0 OD1 A:ASP653 2.2 31.3 1.0 O2B A:DCP902 2.2 17.6 1.0 O A:TYR654 2.2 23.7 1.0 O2A A:DCP902 2.2 16.4 1.0 CG A:ASP830 3.2 22.9 1.0 PB A:DCP902 3.2 21.2 1.0 CG A:ASP653 3.2 41.5 1.0 PG A:DCP902 3.4 24.8 1.0 C A:TYR654 3.4 29.1 1.0 PA A:DCP902 3.4 19.4 1.0 H5'2 A:DCP902 3.4 18.6 1.0 OD2 A:ASP653 3.6 53.0 1.0 O A:HOH1003 3.6 20.5 1.0 OD1 A:ASP830 3.6 19.8 1.0 O3B A:DCP902 3.6 25.4 1.0 O3A A:DCP902 3.7 21.3 1.0 O A:HOH1273 3.8 31.2 1.0 H A:ILE657 3.9 29.0 1.0 HA A:SER655 4.0 38.0 1.0 HG22 A:ILE657 4.0 26.0 1.0 H A:TYR654 4.0 27.9 1.0 H A:GLN656 4.1 31.0 1.0 N A:TYR654 4.1 23.3 1.0 O A:HOH1241 4.1 31.9 1.0 C5' A:DCP902 4.1 15.5 1.0 HB2 A:TYR654 4.1 28.5 1.0 H5'1 A:DCP902 4.2 18.6 1.0 CA A:TYR654 4.2 24.2 1.0 O5' A:DCP902 4.3 17.6 1.0 O3G A:DCP902 4.3 35.8 1.0 N A:SER655 4.4 28.8 1.0 O1G A:DCP902 4.4 21.2 1.0 N A:GLN656 4.4 25.8 1.0 HB2 A:ASP830 4.4 24.5 1.0 CB A:ASP830 4.4 20.4 1.0 CA A:SER655 4.5 31.6 1.0 O1B A:DCP902 4.5 17.9 1.0 HB A:ILE657 4.5 27.6 1.0 O1A A:DCP902 4.5 21.1 1.0 CB A:ASP653 4.5 25.3 1.0 C A:ASP653 4.6 23.8 1.0 CB A:TYR654 4.6 23.7 1.0 C A:SER655 4.7 31.2 1.0 CG2 A:ILE657 4.7 21.6 1.0 HB3 A:ASP653 4.7 30.4 1.0 N A:ILE657 4.7 24.2 1.0 HG21 A:ILE657 4.8 26.0 1.0 HB3 A:TYR654 4.8 28.5 1.0 HB3 A:ASP830 4.8 24.5 1.0 HZ3 A:LYS706 4.9 33.2 1.0 O A:ASP830 4.9 24.5 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment, Dna Duplex, and Dctp (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 Dctp (Paired with Dg of Template) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:17.0 occ:1.00 OD2 D:ASP830 2.0 17.5 1.0 O2G D:DCP902 2.0 27.6 1.0 O D:HOH1741 2.1 37.0 1.0 O2A D:DCP902 2.2 16.5 1.0 O D:TYR654 2.3 15.9 1.0 O2B D:DCP902 2.3 17.8 1.0 CG D:ASP830 3.1 15.2 1.0 PB D:DCP902 3.3 18.0 1.0 PG D:DCP902 3.4 24.4 1.0 H5'1 D:DCP902 3.4 12.1 1.0 C D:TYR654 3.5 15.9 1.0 PA D:DCP902 3.5 15.6 1.0 O D:HOH1124 3.6 18.6 1.0 OD1 D:ASP830 3.6 13.1 1.0 H D:GLN656 3.7 17.0 1.0 O3B D:DCP902 3.8 20.8 1.0 HB2 D:ASP653 3.8 17.5 1.0 O3A D:DCP902 3.8 15.1 1.0 HA D:SER655 3.9 12.2 1.0 HG22 D:ILE657 4.0 25.3 1.0 H D:ILE657 4.0 18.6 1.0 O D:HOH1389 4.1 29.7 1.0 OD2 D:ASP653 4.1 30.8 1.0 HB2 D:ASP830 4.2 15.3 1.0 C5' D:DCP902 4.2 10.1 1.0 N D:GLN656 4.3 14.2 1.0 CB D:ASP830 4.3 12.8 1.0 HB2 D:TYR654 4.3 11.9 1.0 O3G D:DCP902 4.3 25.3 1.0 O5' D:DCP902 4.4 10.8 1.0 H5'2 D:DCP902 4.4 12.1 1.0 O1G D:DCP902 4.4 15.9 1.0 N D:SER655 4.4 11.8 1.0 H D:TYR654 4.4 12.0 1.0 N D:TYR654 4.4 10.0 1.0 CA D:TYR654 4.5 10.0 1.0 CA D:SER655 4.5 10.2 1.0 HB D:ILE657 4.5 22.6 1.0 C D:SER655 4.7 12.4 1.0 O1B D:DCP902 4.7 16.6 1.0 O D:HOH1275 4.7 30.5 1.0 HB3 D:ASP830 4.7 15.3 1.0 HG21 D:ILE657 4.7 25.3 1.0 O1A D:DCP902 4.7 18.2 1.0 CB D:ASP653 4.7 14.6 1.0 CG2 D:ILE657 4.7 21.1 1.0 O E:HOH112 4.8 24.0 1.0 CB D:TYR654 4.8 9.9 1.0 N D:ILE657 4.9 15.5 1.0 O D:ASP830 4.9 11.5 1.0 CG D:ASP653 4.9 31.7 1.0 C D:ASP653 4.9 10.3 1.0 HA D:GLN656 5.0 16.2 1.0 HZ3 D:LYS706 5.0 26.7 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