Manganese in PDB 6us5: Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+

All present enzymatic activity of Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+:
2.7.7.7;

The structure of Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+, PDB code: 6us5 was solved by W.Zhang, V.S.Lelyveld, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.06 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.761, 108.805, 149.969, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.8

The binding sites of Manganese atom in the Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+ (pdb code 6us5). 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 From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+, PDB code: 6us5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+


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 From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn902 b:93.2 occ:1.00 O1B A:XG4901 2.2 62.5 1.0 O A:TYR654 2.3 37.5 1.0 O1A A:XG4901 2.4 57.5 1.0 O1G A:XG4901 2.4 70.5 1.0 OD2 A:ASP830 2.5 40.9 1.0 CG A:ASP830 3.5 28.0 1.0 PB A:XG4901 3.5 40.4 1.0 C A:TYR654 3.6 30.7 1.0 PA A:XG4901 3.8 43.5 1.0 PG A:XG4901 3.8 56.1 1.0 O A:HOH1144 3.8 42.9 1.0 OD1 A:ASP830 4.0 39.0 1.0 OD1 A:ASP653 4.1 57.0 1.0 O3B A:XG4901 4.1 44.3 1.0 N3A A:XG4901 4.1 56.9 1.0 CB A:ASP653 4.2 38.1 1.0 N A:TYR654 4.3 27.8 1.0 CG A:ASP653 4.5 47.6 1.0 N A:SER655 4.5 33.8 1.0 CA A:TYR654 4.5 32.7 1.0 N A:GLN656 4.5 29.4 1.0 CA A:SER655 4.6 35.3 1.0 N B:C429 4.6 43.4 1.0 CB A:ASP830 4.6 38.3 1.0 O2G A:XG4901 4.7 60.9 1.0 C A:ASP653 4.7 36.2 1.0 O2B A:XG4901 4.7 46.6 1.0 O2A A:XG4901 4.8 58.4 1.0 O5' A:XG4901 4.8 44.1 1.0 O3G A:XG4901 4.8 38.4 1.0 O A:ASP830 4.8 32.3 1.0 C5' A:XG4901 5.0 29.1 1.0

Manganese binding site 2 out of 2 in the Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+


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 From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn902 b:0.9 occ:1.00 O D:TYR654 2.1 88.2 1.0 O2B D:XG4901 2.3 91.0 1.0 OD2 D:ASP830 2.3 88.7 1.0 O2G D:XG4901 2.5 0.2 1.0 O2A D:XG4901 2.5 0.1 1.0 C D:TYR654 3.3 73.2 1.0 PB D:XG4901 3.4 0.3 1.0 CG D:ASP830 3.4 68.3 1.0 PA D:XG4901 3.5 0.9 1.0 OD2 D:ASP653 3.6 77.9 1.0 PG D:XG4901 3.6 0.3 1.0 O5' D:XG4901 3.8 89.7 1.0 CB D:ASP653 3.8 63.7 1.0 N3A D:XG4901 3.8 0.2 1.0 O3B D:XG4901 3.9 99.1 1.0 OD1 D:ASP830 3.9 61.4 1.0 N D:TYR654 4.0 71.3 1.0 CG D:ASP653 4.2 82.1 1.0 CA D:TYR654 4.2 62.1 1.0 N D:SER655 4.2 64.1 1.0 O1G D:XG4901 4.2 0.4 1.0 CA D:SER655 4.3 64.7 1.0 C D:ASP653 4.3 72.5 1.0 C5' D:XG4901 4.5 84.5 1.0 CB D:ASP830 4.6 59.1 1.0 CA D:ASP653 4.6 58.7 1.0 N D:GLN656 4.6 70.3 1.0 O1B D:XG4901 4.7 93.1 1.0 O D:ASP830 4.7 67.8 1.0 CB D:TYR654 4.7 58.5 1.0 N E:C429 4.7 75.2 1.0 O1A D:XG4901 4.8 0.1 1.0 C D:SER655 4.8 60.8 1.0 O3G D:XG4901 4.9 0.2 1.0 O D:ASP653 4.9 64.5 1.0

V.S.Lelyveld, W.Zhang, J.W.Szostak. Dna Polymerase I Large Fragment From Bacillus Stearothermophilus with Dna Template, 3'-Amino Primer, Dgpnhpp Analog, and MN2+ To Be Published.