Calcium in PDB 8sct: Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H

The structure of Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H, PDB code: 8sct 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)	47.16 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.32, 108.774, 149.571, 90, 90, 90
R / Rfree (%)	18.7 / 23.2

The binding sites of Calcium atom in the Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H (pdb code 8sct). 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 Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H, PDB code: 8sct:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H


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 Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:36.9 occ:1.00 OD2 A:ASP653 2.2 51.4 1.0 OP2 B:DG10 2.3 22.5 0.6 O2A A:DGT902 2.3 23.2 0.4 O A:TYR654 2.4 30.6 1.0 OD2 A:ASP830 2.4 29.0 1.0 O2G A:DGT902 2.5 31.4 0.4 O2 A:DPO901 2.6 31.4 0.6 O2B A:DGT902 3.0 30.9 0.4 O6 A:DPO901 3.3 31.8 0.6 CG A:ASP653 3.4 39.7 1.0 CG A:ASP830 3.4 26.7 1.0 PA A:DGT902 3.6 23.2 0.4 C A:TYR654 3.6 27.0 1.0 P B:DG10 3.7 24.6 0.6 O3A A:DGT902 3.8 31.9 0.4 P1 A:DPO901 3.9 30.1 0.6 PB A:DGT902 3.9 33.9 0.4 OD1 A:ASP830 3.9 30.2 1.0 PG A:DGT902 3.9 30.1 0.4 CB A:ASP653 4.2 25.5 1.0 P2 A:DPO901 4.2 34.7 0.6 O3B A:DGT902 4.3 34.5 0.4 N B:C429 4.3 18.6 0.6 O4 A:DPO901 4.3 34.7 0.6 OD1 A:ASP653 4.3 49.2 1.0 N B:C429 4.4 19.9 0.4 C5' A:DGT902 4.4 24.1 0.4 CA A:SER655 4.5 28.2 1.0 N A:SER655 4.5 24.8 1.0 N A:TYR654 4.5 23.4 1.0 O5 A:DPO901 4.5 35.5 0.6 O1 A:DPO901 4.5 35.9 0.6 O5' B:DG10 4.6 21.9 0.6 O5' A:DGT902 4.6 22.0 0.4 CA A:TYR654 4.6 25.1 1.0 O1A A:DGT902 4.6 23.9 0.4 OP1 B:DG10 4.6 22.8 0.6 CB A:ASP830 4.7 31.1 1.0 O1G A:DGT902 4.7 35.1 0.4 N A:GLN656 4.7 27.2 1.0 C5' B:DG10 4.7 24.1 0.6 C A:ASP653 4.7 26.2 1.0 O3G A:DGT902 4.9 31.6 0.4 O3 A:DPO901 5.0 32.1 0.6

Calcium binding site 2 out of 2 in the Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H


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 Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:40.0 occ:1.00 OD2 D:ASP830 2.2 35.2 1.0 OP2 E:DG10 2.2 33.0 0.2 OD2 D:ASP653 2.2 49.5 1.0 O2A D:DGT902 2.3 30.0 0.8 O D:TYR654 2.4 41.2 1.0 O2 D:DPO901 2.4 43.3 0.2 O2G D:DGT902 2.4 43.6 0.8 O6 D:DPO901 2.6 36.6 0.2 O2B D:DGT902 2.6 36.5 0.8 CG D:ASP653 3.2 50.8 1.0 CG D:ASP830 3.3 33.8 1.0 P2 D:DPO901 3.4 40.3 0.2 O5 D:DPO901 3.5 42.0 0.2 C D:TYR654 3.6 39.6 1.0 PA D:DGT902 3.6 27.4 0.8 P E:DG10 3.6 30.5 0.2 OD1 D:ASP653 3.6 59.9 1.0 PB D:DGT902 3.7 41.1 0.8 OD1 D:ASP830 3.7 36.4 1.0 P1 D:DPO901 3.7 40.1 0.2 PG D:DGT902 3.8 38.0 0.8 O4 D:DPO901 3.8 43.0 0.2 O3A D:DGT902 3.9 45.4 0.8 O3B D:DGT902 4.1 45.7 0.8 C5' E:DG10 4.1 31.9 0.2 O5' E:DG10 4.1 32.1 0.2 C5' D:DGT902 4.2 31.5 0.8 N E:C429 4.3 32.3 0.8 N D:TYR654 4.3 41.0 1.0 N E:C429 4.4 32.1 0.2 CB D:ASP653 4.4 40.2 1.0 O5' D:DGT902 4.4 32.0 0.8 CA D:TYR654 4.5 35.0 1.0 CB D:ASP830 4.5 30.6 1.0 C D:ASP653 4.6 37.6 1.0 N D:SER655 4.6 41.3 1.0 O3 D:DPO901 4.6 46.2 0.2 O1 D:DPO901 4.6 42.4 0.2 O D:ASP830 4.7 34.3 1.0 OP1 E:DG10 4.7 33.3 0.2 O3G D:DGT902 4.7 47.8 0.8 O1G D:DGT902 4.7 42.5 0.8 CA D:SER655 4.7 42.9 1.0 N D:GLN656 4.7 34.5 1.0 O1A D:DGT902 4.7 31.0 0.8 O7 D:DPO901 4.8 39.0 0.2 CB D:TYR654 4.9 29.0 1.0 O D:ASP653 5.0 40.2 1.0 CA D:ASP653 5.0 40.0 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