Manganese in PDB 3px0: Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation

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

The structure of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation, PDB code: 3px0 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)	34.24 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.910, 108.960, 150.130, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.4

The binding sites of Manganese atom in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation (pdb code 3px0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation, PDB code: 3px0:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1 b:37.6 occ:1.00 OD2 A:ASP830 2.0 35.6 1.0 O A:TYR654 2.1 31.9 1.0 O2G A:DCP201 2.1 36.3 1.0 OD1 A:ASP653 2.3 32.4 0.5 O1B A:DCP201 2.4 34.8 1.0 O2A A:DCP201 2.4 31.2 1.0 CG A:ASP830 3.1 40.0 1.0 CG A:ASP653 3.2 34.4 0.5 C A:TYR654 3.2 35.8 1.0 PB A:DCP201 3.4 42.3 1.0 PG A:DCP201 3.4 37.5 1.0 OD2 A:ASP653 3.5 39.0 0.5 HB2 A:ASP653 3.5 39.5 0.5 H5'1 A:DCP201 3.5 44.0 1.0 PA A:DCP201 3.6 30.7 1.0 OD1 A:ASP830 3.7 28.5 1.0 O A:HOH901 3.7 33.9 1.0 HB2 A:TYR654 3.7 34.8 1.0 O3B A:DCP201 3.7 30.1 1.0 H A:GLN656 3.8 40.3 1.0 O3A A:DCP201 3.9 37.6 1.0 OD1 A:ASP653 3.9 40.9 0.5 H A:TYR654 3.9 41.9 0.5 N A:TYR654 3.9 35.0 1.0 H A:TYR654 3.9 41.9 0.5 HA A:SER655 3.9 49.7 1.0 H A:ILE657 4.0 37.5 1.0 CA A:TYR654 4.0 34.8 1.0 O3G A:DCP201 4.1 45.1 1.0 HB2 A:ASP830 4.2 30.7 1.0 CB A:TYR654 4.2 29.1 1.0 N A:SER655 4.3 37.5 1.0 HG22 A:ILE657 4.3 38.3 1.0 CB A:ASP830 4.3 25.7 1.0 C5' A:DCP201 4.3 36.7 1.0 CB A:ASP653 4.3 33.0 0.5 N A:GLN656 4.3 33.6 1.0 HB3 A:TYR654 4.4 34.8 1.0 C A:ASP653 4.4 37.9 0.5 C A:ASP653 4.4 37.9 0.5 O5' A:DCP201 4.4 26.8 1.0 CA A:SER655 4.5 41.5 1.0 H5'2 A:DCP201 4.5 44.0 1.0 O1G A:DCP201 4.5 33.4 1.0 CB A:ASP653 4.5 33.3 0.5 O A:ASP830 4.5 32.1 1.0 HB A:ILE657 4.5 44.2 1.0 CG A:ASP653 4.6 33.7 0.5 O A:HOH1112 4.6 43.4 1.0 C A:SER655 4.7 35.1 1.0 O1A A:DCP201 4.7 38.6 1.0 O2B A:DCP201 4.7 34.6 1.0 HB3 A:ASP653 4.7 39.8 0.5 HB3 A:ASP830 4.8 30.7 1.0 HG2 A:GLU831 4.8 41.7 1.0 N A:ILE657 4.8 31.3 1.0 CA A:ASP653 4.9 34.4 0.5 HA A:ASP653 4.9 41.2 0.5 O A:ASP653 4.9 38.0 0.5 CA A:ASP653 4.9 34.4 0.5 HA A:TYR654 4.9 41.7 1.0 O A:HOH1106 4.9 39.4 1.0 HA A:ASP653 4.9 41.2 0.5 O A:ASP653 5.0 38.0 0.5 CG2 A:ILE657 5.0 32.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Bacillus Dna Polymerase I Large Fragment Bound to Dna and Dctp-Da Mismatch (Tautomer) in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn2 b:20.7 occ:1.00 OD2 D:ASP830 2.1 22.1 1.0 O2G D:DCP202 2.2 22.4 1.0 O D:TYR654 2.2 15.4 1.0 O2A D:DCP202 2.3 18.7 1.0 O1B D:DCP202 2.3 20.1 1.0 OD1 D:ASP653 2.4 20.0 0.5 CG D:ASP830 3.2 16.5 1.0 PB D:DCP202 3.3 22.7 1.0 CG D:ASP653 3.4 21.8 0.5 C D:TYR654 3.4 15.9 1.0 PG D:DCP202 3.4 27.0 1.0 H5'1 D:DCP202 3.5 30.6 1.0 PA D:DCP202 3.5 20.9 1.0 O D:HOH244 3.6 24.1 1.0 O3B D:DCP202 3.7 21.0 1.0 OD1 D:ASP830 3.7 16.3 1.0 OD2 D:ASP653 3.7 27.7 0.5 HB2 D:ASP653 3.8 21.4 0.5 O3A D:DCP202 3.8 21.5 1.0 HA D:SER655 3.8 14.7 1.0 H D:GLN656 3.8 13.4 1.0 H D:ILE657 4.0 19.9 1.0 OD2 D:ASP653 4.0 22.8 0.5 HG22 D:ILE657 4.0 29.7 1.0 HB2 D:ASP830 4.2 17.7 1.0 HB2 D:TYR654 4.2 12.0 1.0 C5' D:DCP202 4.3 25.6 1.0 N D:GLN656 4.3 11.2 1.0 N D:SER655 4.3 12.1 1.0 CB D:ASP830 4.3 14.8 1.0 O3G D:DCP202 4.3 24.4 1.0 N D:TYR654 4.3 9.8 1.0 CA D:TYR654 4.4 10.5 1.0 O D:HOH1246 4.4 32.5 1.0 CA D:SER655 4.4 12.3 1.0 O5' D:DCP202 4.4 16.2 1.0 H D:TYR654 4.4 11.7 1.0 H5'2 D:DCP202 4.4 30.6 1.0 O1G D:DCP202 4.5 20.5 1.0 C D:SER655 4.6 11.7 1.0 CB D:ASP653 4.6 17.9 0.5 O2B D:DCP202 4.6 22.4 1.0 O1A D:DCP202 4.6 20.6 1.0 HB D:ILE657 4.7 21.6 1.0 CB D:ASP653 4.7 18.0 0.5 O D:HOH139 4.7 30.1 1.0 C D:ASP653 4.8 17.1 1.0 CB D:TYR654 4.8 10.1 1.0 HB3 D:ASP830 4.8 17.7 1.0 CG2 D:ILE657 4.8 24.8 1.0 CG D:ASP653 4.8 18.0 0.5 N D:ILE657 4.8 16.7 1.0 O D:ASP830 4.8 13.6 1.0 HG21 D:ILE657 4.8 29.7 1.0 HB3 D:ASP653 4.9 21.5 0.5 HB3 D:TYR654 4.9 12.0 1.0 HA D:GLN656 4.9 13.8 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