Calcium in PDB 8sci: Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H

All present enzymatic activity of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H:
2.7.7.7;

The structure of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H, PDB code: 8sci was solved by Z.Fang, 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)	42.81 / 2.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.163, 108.541, 148.783, 90, 90, 90
R / Rfree (%)	18.4 / 25.6

The binding sites of Calcium atom in the Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H (pdb code 8sci). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H, PDB code: 8sci:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:43.6 occ:1.00 OP2 B:DG10 2.5 27.8 0.2 OD2 A:ASP830 2.5 32.4 1.0 O2B A:DGT902 2.7 30.5 0.8 O2A A:DGT902 2.7 25.9 0.8 O6 A:DPO901 2.8 30.5 0.2 O2 A:DPO901 2.8 31.8 0.2 O2G A:DGT902 2.8 31.7 0.8 O A:TYR654 2.8 20.5 1.0 OD2 A:ASP653 2.8 56.7 1.0 O A:HOH1014 3.2 39.8 1.0 O A:HOH1005 3.6 27.1 1.0 CG A:ASP830 3.6 28.1 1.0 P B:DG10 3.8 25.0 0.2 PB A:DGT902 3.9 32.6 0.8 P2 A:DPO901 3.9 32.5 0.2 CG A:ASP653 4.0 40.1 1.0 PA A:DGT902 4.0 27.2 0.8 C A:TYR654 4.0 24.6 1.0 O5 A:DPO901 4.1 34.9 0.2 O3A A:DGT902 4.1 35.7 0.8 P1 A:DPO901 4.1 36.0 0.2 O5' B:DG10 4.2 25.6 0.2 PG A:DGT902 4.2 36.4 0.8 OD1 A:ASP830 4.2 31.4 1.0 N B:C429 4.2 23.9 0.8 CB A:ASP653 4.4 26.5 1.0 O4 A:DPO901 4.4 33.3 0.2 O3B A:DGT902 4.4 33.6 0.8 N B:C429 4.5 24.7 0.2 CA A:SER655 4.6 21.6 1.0 N A:GLN656 4.8 24.6 1.0 N A:SER655 4.8 23.4 1.0 CB A:ASP830 4.8 18.3 1.0 N A:TYR654 4.8 26.6 1.0 C5' A:DGT902 4.8 25.9 0.8 O1A A:DGT902 5.0 30.8 0.8 OP1 B:DG10 5.0 26.3 0.2 O5' A:DGT902 5.0 27.9 0.8 CA A:TYR654 5.0 21.1 1.0

Calcium binding site 2 out of 2 in the Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:57.5 occ:1.00 O D:TYR654 2.3 54.2 1.0 OP2 E:DG10 2.4 43.4 0.1 OD2 D:ASP830 2.5 48.8 1.0 O2 D:DPO901 2.7 53.8 0.1 O2G D:DGT902 2.7 54.1 0.9 O6 D:DPO901 2.8 48.6 0.1 O2B D:DGT902 2.8 48.7 0.9 O2A D:DGT902 2.8 40.8 0.9 OD2 D:ASP653 3.3 69.1 1.0 CG D:ASP830 3.4 39.7 1.0 C D:TYR654 3.5 47.5 1.0 OD1 D:ASP830 3.8 39.7 1.0 CB D:ASP653 3.8 44.7 1.0 P E:DG10 3.9 38.6 0.1 CG D:ASP653 3.9 52.4 1.0 P2 D:DPO901 4.0 50.2 0.1 PB D:DGT902 4.0 50.5 0.9 PG D:DGT902 4.0 53.4 0.9 P1 D:DPO901 4.1 53.3 0.1 PA D:DGT902 4.1 46.3 0.9 O3B D:DGT902 4.3 52.3 0.9 N D:TYR654 4.3 42.3 1.0 O5 D:DPO901 4.3 47.7 0.1 O4 D:DPO901 4.3 52.2 0.1 N D:SER655 4.4 48.5 1.0 CA D:SER655 4.4 50.8 1.0 O3A D:DGT902 4.4 47.8 0.9 N E:C429 4.4 38.5 0.9 CA D:TYR654 4.5 43.1 1.0 C D:ASP653 4.5 42.2 1.0 O5' E:DG10 4.6 40.1 0.1 CB D:ASP830 4.6 37.0 1.0 N E:C429 4.6 37.3 0.1 OE1 D:GLU831 4.6 57.0 1.0 N D:GLN656 4.7 43.7 1.0 O D:ASP830 4.7 45.4 1.0 C5' E:DG10 4.8 39.4 0.1 C5' D:DGT902 4.8 40.9 0.9 CA D:ASP653 4.8 46.2 1.0 O5' D:DGT902 4.8 43.1 0.9 O3G D:DGT902 4.9 59.2 0.9 OP1 E:DG10 4.9 39.0 0.1 O3 D:DPO901 4.9 58.7 0.1 O D:ASP653 5.0 44.5 1.0

V.S.Lelyveld, Z.Fang, J.W.Szostak. Trivalent Rare Earth Metal Cofactors Confer Rapid Np-Dna Polymerase Activity Science 2023.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADH5339