Calcium in PDB 8scu: Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 48H (Product State)

The structure of Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 48H (Product State), PDB code: 8scu 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)	47.04 / 2.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.082, 109.164, 150.591, 90, 90, 90
R / Rfree (%)	18.7 / 23.9

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 48H (Product State) (pdb code 8scu). 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 48H (Product State), PDB code: 8scu:
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 48H (Product State)


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 48H (Product State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:40.5 occ:1.00 OD2 A:ASP830 2.4 38.3 1.0 OP2 B:DG10 2.5 23.8 1.0 O2 A:DPO901 2.5 42.4 1.0 O A:TYR654 2.6 28.1 1.0 OD2 A:ASP653 2.6 42.7 1.0 O A:HOH1105 2.7 34.8 1.0 O A:HOH1001 3.2 36.4 1.0 O6 A:DPO901 3.3 46.1 1.0 CG A:ASP830 3.4 33.4 1.0 CG A:ASP653 3.7 33.5 1.0 C A:TYR654 3.7 30.0 1.0 OD1 A:ASP830 3.8 30.7 1.0 P1 A:DPO901 3.9 40.9 1.0 P B:DG10 3.9 27.1 1.0 CB A:ASP653 4.1 29.6 1.0 P2 A:DPO901 4.3 57.7 1.0 N B:C429 4.3 27.4 1.0 O1 A:DPO901 4.3 46.8 1.0 N A:TYR654 4.4 28.5 1.0 O5 A:DPO901 4.5 53.9 1.0 O4 A:DPO901 4.5 38.0 1.0 N A:SER655 4.6 28.5 1.0 CA A:SER655 4.6 30.9 1.0 CB A:ASP830 4.6 28.9 1.0 CA A:TYR654 4.7 27.5 1.0 C A:ASP653 4.7 29.1 1.0 OD1 A:ASP653 4.7 39.6 1.0 O5' B:DG10 4.8 27.8 1.0 OP1 B:DG10 4.8 24.6 1.0 N A:GLN656 4.9 27.8 1.0 C5' B:DG10 4.9 27.8 1.0 O3 A:DPO901 4.9 37.6 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 48H (Product State)


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 48H (Product State) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:56.2 occ:1.00 OP2 E:DG10 2.1 43.3 0.4 OD2 D:ASP830 2.2 47.5 1.0 O2 D:DPO901 2.4 51.0 0.4 O2A D:DGT902 2.5 41.9 0.6 O2G D:DGT902 2.5 50.7 0.6 OD2 D:ASP653 2.5 55.6 1.0 O D:TYR654 2.5 53.5 1.0 O6 D:DPO901 3.0 48.5 0.4 O2B D:DGT902 3.1 48.7 0.6 CG D:ASP830 3.2 48.4 1.0 CG D:ASP653 3.5 51.6 1.0 OD1 D:ASP830 3.5 44.9 1.0 P E:DG10 3.6 39.9 0.4 O5 D:DPO901 3.6 53.2 0.4 C D:TYR654 3.7 50.6 1.0 P2 D:DPO901 3.8 55.0 0.4 CB D:ASP653 3.8 47.1 1.0 P1 D:DPO901 3.8 51.6 0.4 PA D:DGT902 3.9 41.6 0.6 PG D:DGT902 3.9 45.3 0.6 O4 D:DPO901 4.1 50.5 0.4 PB D:DGT902 4.1 55.7 0.6 N E:C429 4.2 41.3 0.6 N E:C429 4.2 40.5 0.4 O3A D:DGT902 4.3 52.7 0.6 O5' E:DG10 4.3 43.3 0.4 N D:TYR654 4.4 50.5 1.0 O3B D:DGT902 4.5 53.0 0.6 C5' E:DG10 4.5 40.1 0.4 C D:ASP653 4.5 54.0 1.0 OP1 E:DG10 4.5 41.6 0.4 CB D:ASP830 4.6 44.9 1.0 C5' D:DGT902 4.6 39.9 0.6 O3 D:DPO901 4.6 58.1 0.4 CA D:TYR654 4.6 51.5 1.0 OD1 D:ASP653 4.6 58.2 1.0 N D:SER655 4.7 52.6 1.0 O D:ASP830 4.7 44.2 1.0 O1 D:DPO901 4.7 53.8 0.4 CA D:SER655 4.7 53.6 1.0 O5' D:DGT902 4.7 43.5 0.6 O1G D:DGT902 4.7 52.5 0.6 CA D:ASP653 4.8 47.5 1.0 O3G D:DGT902 4.8 58.5 0.6 O1A D:DGT902 4.8 41.0 0.6 O D:ASP653 5.0 52.2 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