Manganese in PDB 4f3o: Dna Polymerase I Large Fragment Complex 5

All present enzymatic activity of Dna Polymerase I Large Fragment Complex 5:
2.7.7.7;

The structure of Dna Polymerase I Large Fragment Complex 5, PDB code: 4f3o 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)	79.56 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.830, 109.330, 150.110, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.4

The binding sites of Manganese atom in the Dna Polymerase I Large Fragment Complex 5 (pdb code 4f3o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dna Polymerase I Large Fragment Complex 5, PDB code: 4f3o:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dna Polymerase I Large Fragment Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase I Large Fragment Complex 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn904 b:16.5 occ:0.33 O A:TYR654 1.8 40.4 1.0 C A:TYR654 3.0 41.9 1.0 OD2 A:ASP830 3.2 43.9 1.0 HA A:SER655 3.3 55.6 1.0 HB2 A:ASP653 3.4 46.1 1.0 CG A:ASP830 3.5 41.7 1.0 OD1 A:ASP653 3.6 56.4 1.0 O A:HOH1025 3.7 30.1 1.0 H A:GLN656 3.7 57.6 1.0 HB2 A:TYR654 3.7 48.0 1.0 OD1 A:ASP830 3.8 34.2 1.0 HB2 A:ASP830 3.8 41.5 1.0 N A:TYR654 3.9 40.0 1.0 CA A:TYR654 3.9 41.3 1.0 N A:SER655 3.9 44.1 1.0 H A:ILE657 3.9 48.9 1.0 CA A:SER655 4.0 46.3 1.0 H A:TYR654 4.0 48.0 1.0 N A:GLN656 4.2 48.0 1.0 CB A:ASP653 4.2 38.4 1.0 C A:ASP653 4.2 40.8 1.0 CB A:ASP830 4.3 34.6 1.0 CB A:TYR654 4.3 40.0 1.0 HG22 A:ILE657 4.3 43.6 1.0 CG A:ASP653 4.4 47.9 1.0 C A:SER655 4.4 44.6 1.0 HB3 A:TYR654 4.4 48.0 1.0 O A:ASP830 4.5 35.2 1.0 HB A:ILE657 4.6 46.7 1.0 O A:ASP653 4.7 42.9 1.0 H A:SER655 4.8 53.0 1.0 N A:ILE657 4.8 40.7 1.0 CA A:ASP653 4.8 39.2 1.0 HA A:TYR654 4.8 49.6 1.0 HB3 A:ASP830 4.8 41.5 1.0 HA A:ASP653 4.9 47.1 1.0 HB3 A:ASP653 5.0 46.1 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase I Large Fragment Complex 5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase I Large Fragment Complex 5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn904 b:8.9 occ:0.20 O D:TYR654 2.1 16.3 1.0 O D:HOH1034 2.3 15.8 1.0 O2B D:D3T901 2.4 17.0 0.8 OD2 D:ASP830 2.8 24.0 1.0 HA D:SER655 3.3 12.3 1.0 C D:TYR654 3.3 12.9 1.0 H D:GLN656 3.4 17.6 1.0 O2A D:D3T901 3.4 21.6 0.8 CG D:ASP830 3.4 13.1 1.0 O D:HOH1486 3.6 25.6 1.0 PB D:D3T901 3.7 15.1 0.8 C5' D:D3T901 3.8 13.9 0.8 HB2 D:ASP653 3.8 19.8 1.0 OD1 D:ASP830 3.9 13.4 1.0 OD2 D:ASP653 3.9 26.7 1.0 HB2 D:ASP830 4.0 15.6 1.0 N D:GLN656 4.0 14.7 1.0 CA D:SER655 4.0 10.3 1.0 N D:SER655 4.1 13.0 1.0 H D:ILE657 4.2 14.0 1.0 O3A D:D3T901 4.2 15.7 0.8 PA D:D3T901 4.2 19.6 0.8 HB2 D:TYR654 4.3 13.1 1.0 CB D:ASP830 4.3 13.0 1.0 HG22 D:ILE657 4.4 20.1 1.0 O1G D:D3T901 4.4 20.2 0.8 CA D:TYR654 4.4 9.4 1.0 C D:SER655 4.4 13.7 1.0 N D:TYR654 4.5 11.4 1.0 H D:TYR654 4.6 13.6 1.0 O5' D:D3T901 4.6 16.2 0.8 O D:HOH1309 4.7 29.3 1.0 CB D:ASP653 4.7 16.5 1.0 O1B D:D3T901 4.7 20.8 0.8 O3B D:D3T901 4.7 21.9 0.8 HA D:GLN656 4.8 17.6 1.0 CB D:TYR654 4.8 10.9 1.0 HB3 D:ASP830 4.8 15.6 1.0 CG D:ASP653 4.8 19.2 1.0 C4' D:D3T901 4.8 14.1 0.8 O D:HOH1065 4.9 15.3 1.0 HB3 D:TYR654 4.9 13.1 1.0 O D:ASP830 4.9 13.3 1.0 C D:ASP653 4.9 11.0 1.0 H D:SER655 5.0 15.6 1.0 CA D:GLN656 5.0 14.7 1.0

W.Wang, H.W.Hellinga, L.S.Beese. Structures of A High-Fidelity Dna Polymerase To Be Published.