Calcium in PDB 8scq: Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 2H

The structure of Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 2H, PDB code: 8scq 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)	46.83 / 2.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.657, 108.549, 148.248, 90, 90, 90
R / Rfree (%)	18.8 / 23.6

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 2H (pdb code 8scq). 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 2H, PDB code: 8scq:
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 2H


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 2H within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:29.8 occ:1.00 OP2 B:DG10 2.2 24.2 0.1 OD2 A:ASP830 2.3 26.2 1.0 O A:TYR654 2.4 25.9 1.0 O2A A:DGT902 2.4 23.4 0.9 O2 A:DPO901 2.5 26.9 0.1 O2G A:DGT902 2.5 26.9 0.9 O2B A:DGT902 2.6 24.9 0.9 O6 A:DPO901 2.6 24.8 0.1 OD2 A:ASP653 2.7 43.8 1.0 OD1 A:ASP653 2.8 49.4 1.0 CG A:ASP653 3.1 41.3 1.0 CG A:ASP830 3.4 24.9 1.0 PB A:DGT902 3.6 23.3 0.9 C A:TYR654 3.6 23.4 1.0 P B:DG10 3.6 22.7 0.1 P2 A:DPO901 3.6 23.6 0.1 PA A:DGT902 3.7 20.9 0.9 P1 A:DPO901 3.8 25.9 0.1 PG A:DGT902 3.8 25.9 0.9 O5 A:DPO901 3.8 25.5 0.1 O3A A:DGT902 3.9 26.0 0.9 O3B A:DGT902 4.0 27.5 0.9 OD1 A:ASP830 4.0 25.3 1.0 O4 A:DPO901 4.1 26.6 0.1 C5' B:DG10 4.2 22.9 0.1 C5' A:DGT902 4.2 23.4 0.9 O5' B:DG10 4.2 22.4 0.1 N B:C429 4.2 21.8 0.9 N B:C429 4.3 22.4 0.1 O1 A:DPO901 4.3 26.9 0.1 CA A:SER655 4.5 24.8 1.0 N A:TYR654 4.5 23.1 1.0 N A:SER655 4.5 25.8 1.0 O5' A:DGT902 4.5 21.4 0.9 CB A:ASP653 4.6 26.4 1.0 N A:GLN656 4.6 20.2 1.0 CA A:TYR654 4.6 22.8 1.0 CB A:ASP830 4.6 21.2 1.0 O1G A:DGT902 4.7 28.2 0.9 OP1 B:DG10 4.7 22.3 0.1 O1A A:DGT902 4.8 24.1 0.9 O3G A:DGT902 4.8 27.4 0.9 C A:ASP653 4.9 26.4 1.0 C A:SER655 4.9 20.5 1.0 O1B A:DGT902 4.9 23.1 0.9 O3 A:DPO901 5.0 26.8 0.1 O7 A:DPO901 5.0 23.2 0.1

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 2H


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 2H within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:33.5 occ:1.00 OD2 D:ASP653 2.1 43.5 1.0 OD2 D:ASP830 2.2 30.2 1.0 O2A D:DGT902 2.3 23.2 1.0 O2B D:DGT902 2.3 28.0 1.0 O D:TYR654 2.3 36.5 1.0 O2 D:DPO901 2.4 32.3 0.0 O2G D:DGT902 2.4 32.2 1.0 O6 D:DPO901 2.4 28.4 0.0 OP2 E:DG10 2.5 28.2 0.0 CG D:ASP653 3.1 39.4 1.0 OD1 D:ASP653 3.3 49.0 1.0 CG D:ASP830 3.4 36.4 1.0 PB D:DGT902 3.5 28.8 1.0 P2 D:DPO901 3.5 29.6 0.0 C D:TYR654 3.5 33.3 1.0 PA D:DGT902 3.6 29.1 1.0 P1 D:DPO901 3.7 33.6 0.0 PG D:DGT902 3.7 33.5 1.0 O5 D:DPO901 3.7 32.3 0.0 P E:DG10 3.8 28.1 0.0 OD1 D:ASP830 3.9 32.9 1.0 O4 D:DPO901 3.9 34.1 0.0 C5' E:DG10 3.9 28.3 0.0 O3B D:DGT902 3.9 34.4 1.0 O3A D:DGT902 3.9 34.3 1.0 C5' D:DGT902 4.0 28.4 1.0 O5' E:DG10 4.1 28.2 0.0 N E:C429 4.2 27.5 1.0 N D:TYR654 4.3 36.6 1.0 O5' D:DGT902 4.3 28.3 1.0 CA D:TYR654 4.4 32.2 1.0 CB D:ASP653 4.4 34.8 1.0 N E:C429 4.4 28.0 0.0 O1 D:DPO901 4.5 35.0 0.0 N D:SER655 4.5 34.9 1.0 N D:GLN656 4.5 30.4 1.0 CA D:SER655 4.6 33.8 1.0 O1G D:DGT902 4.6 35.5 1.0 CB D:ASP830 4.6 25.0 1.0 C D:ASP653 4.6 38.8 1.0 O3G D:DGT902 4.6 39.2 1.0 O3 D:DPO901 4.7 37.3 0.0 CG2 D:ILE657 4.7 23.9 1.0 CB D:TYR654 4.8 32.1 1.0 O1B D:DGT902 4.8 31.9 1.0 O1A D:DGT902 4.8 24.5 1.0 C D:SER655 4.8 34.2 1.0 O7 D:DPO901 4.8 31.6 0.0 N D:ILE657 5.0 34.2 1.0 CA D:ASP653 5.0 34.2 1.0 O D:ASP830 5.0 29.9 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