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

The structure of Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 1H, PDB code: 8scp 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)	39.86 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.864, 108.751, 149.986, 90, 90, 90
R / Rfree (%)	18.9 / 23.8

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 1H (pdb code 8scp). 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 1H, PDB code: 8scp:
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 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 Wildtype 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:20.1 occ:1.00 OP2 B:DG10 2.2 17.7 0.0 OD2 A:ASP830 2.3 19.5 1.0 OD1 A:ASP653 2.3 34.7 1.0 O A:TYR654 2.3 15.0 1.0 O2A A:DGT902 2.4 16.0 1.0 O2G A:DGT902 2.4 20.3 1.0 O2 A:DPO901 2.4 20.2 0.0 O6 A:DPO901 2.5 16.1 0.0 O2B A:DGT902 2.5 15.8 1.0 CG A:ASP653 3.1 31.9 1.0 OD2 A:ASP653 3.2 39.7 1.0 CG A:ASP830 3.4 18.5 1.0 C A:TYR654 3.5 17.9 1.0 PB A:DGT902 3.5 16.6 1.0 P B:DG10 3.6 17.0 0.0 P2 A:DPO901 3.6 16.7 0.0 PA A:DGT902 3.7 17.1 1.0 PG A:DGT902 3.7 19.4 1.0 P1 A:DPO901 3.8 19.4 0.0 O5 A:DPO901 3.9 18.5 0.0 O3B A:DGT902 4.0 18.6 1.0 O3A A:DGT902 4.0 18.9 1.0 OD1 A:ASP830 4.0 20.8 1.0 O4 A:DPO901 4.0 18.5 0.0 C5' A:DGT902 4.1 14.5 1.0 O5' B:DG10 4.1 15.8 0.0 C5' B:DG10 4.1 15.4 0.0 N B:C429 4.3 16.7 1.0 N A:TYR654 4.3 15.3 1.0 N A:SER655 4.4 14.6 1.0 O5' A:DGT902 4.4 15.4 1.0 N A:GLN656 4.4 15.1 1.0 N B:C429 4.4 16.8 0.0 CA A:SER655 4.4 17.3 1.0 CA A:TYR654 4.5 16.4 1.0 O1 A:DPO901 4.6 20.6 0.0 O3G A:DGT902 4.6 19.3 1.0 CB A:ASP653 4.6 20.7 1.0 CB A:ASP830 4.6 15.5 1.0 OP1 B:DG10 4.6 17.3 0.0 O1G A:DGT902 4.7 21.7 1.0 C A:ASP653 4.8 20.9 1.0 C A:SER655 4.8 14.6 1.0 O3 A:DPO901 4.8 19.6 0.0 O1A A:DGT902 4.8 17.3 1.0 CG2 A:ILE657 4.9 13.6 1.0 O1B A:DGT902 4.9 15.5 1.0 O B:HOH201 4.9 27.7 1.0 O7 A:DPO901 4.9 15.8 0.0 CB A:TYR654 4.9 13.3 1.0 N A:ILE657 5.0 12.8 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 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 Wildtype 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:32.4 occ:1.00 OD2 D:ASP830 2.2 31.7 1.0 OD2 D:ASP653 2.2 40.8 1.0 OP2 E:DG10 2.3 29.0 0.0 O2 D:DPO901 2.3 33.7 0.0 O D:TYR654 2.3 32.5 1.0 O2G D:DGT902 2.3 33.7 1.0 O2B D:DGT902 2.4 28.8 1.0 O2A D:DGT902 2.4 24.5 1.0 O6 D:DPO901 2.5 29.1 0.0 CG D:ASP653 3.1 38.6 1.0 CG D:ASP830 3.3 30.0 1.0 OD1 D:ASP653 3.4 44.6 1.0 P2 D:DPO901 3.5 30.6 0.0 C D:TYR654 3.5 33.1 1.0 PB D:DGT902 3.5 30.0 1.0 P1 D:DPO901 3.6 33.9 0.0 PA D:DGT902 3.6 28.1 1.0 PG D:DGT902 3.7 33.8 1.0 P E:DG10 3.7 27.8 0.0 O5 D:DPO901 3.7 33.3 0.0 OD1 D:ASP830 3.9 31.4 1.0 O4 D:DPO901 3.9 36.1 0.0 O3A D:DGT902 4.0 35.8 1.0 C5' E:DG10 4.0 28.1 0.0 O3B D:DGT902 4.0 37.4 1.0 C5' D:DGT902 4.0 28.1 1.0 O5' E:DG10 4.1 28.0 0.0 N D:TYR654 4.3 31.5 1.0 N E:C429 4.3 27.3 1.0 O5' D:DGT902 4.3 28.6 1.0 CA D:TYR654 4.4 33.9 1.0 N D:SER655 4.5 32.9 1.0 N E:C429 4.5 26.9 0.0 CB D:ASP653 4.5 32.1 1.0 N D:GLN656 4.5 26.8 1.0 CA D:SER655 4.5 35.0 1.0 O3G D:DGT902 4.5 38.4 1.0 CB D:ASP830 4.5 25.8 1.0 O1 D:DPO901 4.6 32.7 0.0 O3 D:DPO901 4.6 37.0 0.0 C D:ASP653 4.6 34.2 1.0 O1G D:DGT902 4.6 32.4 1.0 C D:SER655 4.7 33.6 1.0 OP1 E:DG10 4.8 27.1 0.0 CB D:TYR654 4.8 31.5 1.0 O1B D:DGT902 4.8 34.0 1.0 O7 D:DPO901 4.8 32.8 0.0 O1A D:DGT902 4.9 28.8 1.0 CG2 D:ILE657 4.9 29.0 1.0 O D:ASP830 4.9 32.6 1.0 N D:ILE657 5.0 27.2 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