Calcium in PDB 8sco: Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 0H (Ground State)

The structure of Bst Dna Polymerase I Large Fragment Wildtype D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 0H (Ground State), PDB code: 8sco 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)	41.52 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.051, 109.038, 150.945, 90, 90, 90
R / Rfree (%)	18.9 / 23.4

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 0H (Ground State) (pdb code 8sco). 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 0H (Ground State), PDB code: 8sco:
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 0H (Ground 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 0H (Ground State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:15.3 occ:1.00 OD2 A:ASP830 2.3 15.0 1.0 O2G A:DGT901 2.3 14.5 1.0 O A:TYR654 2.3 9.6 1.0 O2A A:DGT901 2.4 15.0 1.0 O2B A:DGT901 2.5 12.8 1.0 OD2 A:ASP653 2.6 28.9 1.0 OD1 A:ASP653 2.8 35.8 1.0 CG A:ASP653 3.0 26.4 1.0 CG A:ASP830 3.4 12.5 1.0 PB A:DGT901 3.5 13.8 1.0 C A:TYR654 3.5 10.2 1.0 PG A:DGT901 3.6 16.6 1.0 PA A:DGT901 3.6 15.4 1.0 O3B A:DGT901 3.9 13.7 1.0 O3A A:DGT901 3.9 18.7 1.0 O A:HOH1421 4.0 25.5 0.8 OD1 A:ASP830 4.0 15.2 1.0 C5' A:DGT901 4.2 10.7 1.0 O A:HOH1039 4.2 26.0 0.7 N A:GLN656 4.3 8.9 1.0 N A:TYR654 4.4 9.7 1.0 N B:C429 4.4 13.1 1.0 N A:SER655 4.4 9.9 1.0 O5' A:DGT901 4.4 10.9 1.0 CA A:SER655 4.5 9.6 1.0 O3G A:DGT901 4.5 16.8 1.0 CA A:TYR654 4.5 11.3 1.0 CB A:ASP653 4.5 16.7 1.0 CB A:ASP830 4.5 10.2 1.0 O1G A:DGT901 4.6 16.6 1.0 C A:SER655 4.7 11.1 1.0 C A:ASP653 4.8 13.7 1.0 O1A A:DGT901 4.8 15.2 1.0 O1B A:DGT901 4.8 10.6 1.0 CG2 A:ILE657 4.9 10.4 1.0 N A:ILE657 4.9 9.8 1.0 O A:HOH1340 4.9 17.4 0.8 CB A:TYR654 5.0 9.2 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 0H (Ground 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 0H (Ground State) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:27.6 occ:1.00 OD2 D:ASP830 2.2 32.8 1.0 OD2 D:ASP653 2.2 41.4 1.0 O2A D:DGT901 2.3 22.7 1.0 O D:TYR654 2.3 31.4 1.0 O2G D:DGT901 2.4 32.3 1.0 O2B D:DGT901 2.5 25.1 1.0 CG D:ASP653 3.3 36.1 1.0 CG D:ASP830 3.4 28.1 1.0 C D:TYR654 3.5 30.8 1.0 PA D:DGT901 3.6 23.2 1.0 PB D:DGT901 3.6 28.1 1.0 PG D:DGT901 3.7 30.0 1.0 OD1 D:ASP653 3.8 42.5 1.0 O D:HOH1192 3.8 38.3 1.0 C5' D:DGT901 4.0 24.3 1.0 OD1 D:ASP830 4.0 29.0 1.0 O3A D:DGT901 4.0 32.9 1.0 O3B D:DGT901 4.1 36.9 1.0 O D:HOH1145 4.1 31.1 0.9 N D:TYR654 4.2 33.9 1.0 O5' D:DGT901 4.3 27.2 1.0 CA D:TYR654 4.4 35.3 1.0 N E:C429 4.4 24.9 1.0 O3G D:DGT901 4.4 37.3 1.0 N D:GLN656 4.4 26.4 1.0 N D:SER655 4.5 33.9 1.0 CB D:ASP830 4.5 21.1 1.0 CA D:SER655 4.6 29.0 1.0 C D:ASP653 4.6 36.2 1.0 CB D:ASP653 4.6 32.6 1.0 CB D:TYR654 4.7 28.6 1.0 CG2 D:ILE657 4.7 24.4 1.0 O1G D:DGT901 4.7 26.9 1.0 C D:SER655 4.7 30.1 1.0 O1A D:DGT901 4.8 25.1 1.0 N D:ILE657 4.8 27.9 1.0 O D:ASP830 4.9 27.8 1.0 O1B D:DGT901 4.9 28.7 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