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

The structure of Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 8H, PDB code: 8scs 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)	45.24 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.623, 108.676, 149.254, 90, 90, 90
R / Rfree (%)	19 / 23.3

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 8H (pdb code 8scs). 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 8H, PDB code: 8scs:
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 8H


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 8H within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:27.5 occ:1.00 OP2 B:DG10 2.1 18.2 0.3 OD2 A:ASP830 2.3 22.5 1.0 O A:TYR654 2.4 19.5 1.0 O2G A:DGT902 2.5 26.0 0.7 O2A A:DGT902 2.5 17.0 0.7 O2 A:DPO901 2.6 25.6 0.3 OD2 A:ASP653 2.7 40.9 1.0 O2B A:DGT902 2.7 23.1 0.7 O6 A:DPO901 2.8 22.5 0.3 CG A:ASP830 3.4 21.4 1.0 P B:DG10 3.5 17.5 0.3 C A:TYR654 3.6 22.5 1.0 PB A:DGT902 3.7 22.3 0.7 PA A:DGT902 3.8 16.0 0.7 PG A:DGT902 3.8 23.0 0.7 CG A:ASP653 3.8 35.7 1.0 P1 A:DPO901 3.9 22.1 0.3 P2 A:DPO901 3.9 21.9 0.3 O3A A:DGT902 3.9 24.1 0.7 O3B A:DGT902 4.0 23.7 0.7 OD1 A:ASP830 4.0 24.6 1.0 C5' A:DGT902 4.2 16.4 0.7 N B:C429 4.2 15.7 0.7 N B:C429 4.3 16.9 0.3 O5 A:DPO901 4.3 21.4 0.3 O4 A:DPO901 4.3 23.0 0.3 O5' B:DG10 4.3 16.6 0.3 C5' B:DG10 4.4 16.9 0.3 CB A:ASP653 4.4 21.2 1.0 OP1 B:DG10 4.4 18.0 0.3 N A:TYR654 4.4 16.1 1.0 O1 A:DPO901 4.5 23.7 0.3 CA A:SER655 4.5 20.6 1.0 N A:SER655 4.5 18.4 1.0 O5' A:DGT902 4.5 16.7 0.7 N A:GLN656 4.6 15.9 1.0 CA A:TYR654 4.6 17.8 1.0 CB A:ASP830 4.6 17.8 1.0 O1G A:DGT902 4.7 21.5 0.7 O3G A:DGT902 4.7 25.1 0.7 OD1 A:ASP653 4.8 43.1 1.0 C A:ASP653 4.9 21.8 1.0 C A:SER655 4.9 16.4 1.0 O1A A:DGT902 5.0 17.6 0.7 OE2 A:GLU831 5.0 36.4 1.0

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 8H


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 8H within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:30.4 occ:1.00 OD2 D:ASP653 2.1 40.0 1.0 OD2 D:ASP830 2.2 33.4 1.0 O2 D:DPO901 2.3 30.1 0.1 OP2 E:DG10 2.3 26.5 0.1 O2G D:DGT902 2.3 29.9 0.9 O D:TYR654 2.3 33.9 1.0 O2A D:DGT902 2.4 22.7 0.9 O2B D:DGT902 2.4 27.7 0.9 O6 D:DPO901 2.5 28.0 0.1 CG D:ASP653 3.1 39.7 1.0 CG D:ASP830 3.3 32.3 1.0 OD1 D:ASP653 3.4 47.6 1.0 C D:TYR654 3.5 33.6 1.0 PB D:DGT902 3.5 31.7 0.9 P2 D:DPO901 3.6 31.6 0.1 P1 D:DPO901 3.6 31.5 0.1 PG D:DGT902 3.6 31.3 0.9 PA D:DGT902 3.6 26.2 0.9 P E:DG10 3.7 25.6 0.1 O5 D:DPO901 3.9 33.5 0.1 OD1 D:ASP830 3.9 29.1 1.0 O4 D:DPO901 4.0 33.4 0.1 O3A D:DGT902 4.0 36.1 0.9 O3B D:DGT902 4.0 34.1 0.9 C5' D:DGT902 4.1 24.4 0.9 C5' E:DG10 4.1 24.9 0.1 O5' E:DG10 4.1 25.1 0.1 N E:C429 4.2 25.2 0.9 N D:TYR654 4.3 27.8 1.0 O5' D:DGT902 4.4 24.8 0.9 N E:C429 4.4 25.4 0.1 CA D:TYR654 4.4 33.2 1.0 O1 D:DPO901 4.4 30.8 0.1 CB D:ASP653 4.4 32.3 1.0 N D:SER655 4.5 37.0 1.0 CA D:SER655 4.5 34.2 1.0 O3G D:DGT902 4.5 37.2 0.9 N D:GLN656 4.5 26.8 1.0 CB D:ASP830 4.5 25.9 1.0 O1G D:DGT902 4.5 30.5 0.9 C D:ASP653 4.6 35.5 1.0 O3 D:DPO901 4.6 36.3 0.1 CG2 D:ILE657 4.8 27.7 1.0 OP1 E:DG10 4.8 25.6 0.1 CB D:TYR654 4.8 30.9 1.0 O1A D:DGT902 4.8 22.2 0.9 C D:SER655 4.8 33.5 1.0 O1B D:DGT902 4.9 30.3 0.9 O7 D:DPO901 4.9 30.2 0.1 O D:ASP830 4.9 29.6 1.0 CA D:ASP653 5.0 32.1 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