Calcium in PDB 8scj: Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 2H

All present enzymatic activity of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 2H:
2.7.7.7;

The structure of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 2H, PDB code: 8scj 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)	37.46 / 2.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.034, 109.696, 149.845, 90, 90, 90
R / Rfree (%)	20.4 / 26

The binding sites of Calcium atom in the Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 2H (pdb code 8scj). 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 Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 2H, PDB code: 8scj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bst Dna Polymerase I Large Fragment Mutant F710Y/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 Mutant F710Y/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:48.5 occ:1.00 OP2 B:DG10 2.2 30.3 0.4 OD2 A:ASP830 2.6 32.9 1.0 O6 A:DPO901 2.7 33.5 0.4 O2 A:DPO901 2.7 36.6 0.4 O A:TYR654 2.8 22.9 1.0 O2G A:DGT902 2.8 36.5 0.6 O2A A:DGT902 2.8 28.3 0.6 O2B A:DGT902 2.8 33.5 0.6 OD2 A:ASP653 3.0 50.5 1.0 O A:HOH1002 3.3 41.1 1.0 O A:HOH1001 3.4 27.7 1.0 P B:DG10 3.7 25.1 0.4 CG A:ASP830 3.8 32.3 1.0 P2 A:DPO901 3.8 38.2 0.4 C A:TYR654 4.0 29.6 1.0 PB A:DGT902 4.0 38.5 0.6 O5 A:DPO901 4.1 38.0 0.4 CG A:ASP653 4.1 43.4 1.0 PA A:DGT902 4.1 29.6 0.6 P1 A:DPO901 4.1 38.2 0.4 PG A:DGT902 4.1 38.3 0.6 O3A A:DGT902 4.3 38.4 0.6 N B:C429 4.3 29.5 0.6 O5' B:DG10 4.3 27.9 0.4 N B:C429 4.3 29.0 0.4 OD1 A:ASP830 4.3 34.5 1.0 O4 A:DPO901 4.4 39.4 0.4 CB A:ASP653 4.4 30.2 1.0 O3B A:DGT902 4.5 39.6 0.6 CA A:SER655 4.6 28.5 1.0 OP1 B:DG10 4.7 31.2 0.4 N A:GLN656 4.7 28.2 1.0 C5' B:DG10 4.7 28.0 0.4 N A:SER655 4.7 24.7 1.0 N A:TYR654 4.9 26.7 1.0 O1 A:DPO901 4.9 36.7 0.4 CB A:ASP830 4.9 25.9 1.0 C5' A:DGT902 4.9 28.2 0.6 O3G A:DGT902 5.0 37.9 0.6

Calcium binding site 2 out of 2 in the Bst Dna Polymerase I Large Fragment Mutant F710Y/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 Mutant F710Y/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:58.2 occ:1.00 OP2 E:DG10 2.3 44.4 0.2 OD2 D:ASP830 2.4 53.9 1.0 O D:TYR654 2.5 54.2 1.0 O2A D:DGT902 2.5 48.0 0.8 O2 D:DPO901 2.6 54.7 0.2 O2G D:DGT902 2.6 54.9 0.8 O6 D:DPO901 2.7 47.3 0.2 O2B D:DGT902 2.7 47.1 0.8 OD2 D:ASP653 3.0 67.8 1.0 CG D:ASP830 3.5 46.2 1.0 PA D:DGT902 3.6 43.0 0.8 C D:TYR654 3.7 46.1 1.0 P E:DG10 3.7 40.1 0.2 P2 D:DPO901 3.7 53.3 0.2 O5' D:DGT902 3.8 42.2 0.8 PB D:DGT902 3.8 55.0 0.8 O5 D:DPO901 3.9 49.1 0.2 P1 D:DPO901 3.9 52.3 0.2 CG D:ASP653 3.9 59.0 1.0 PG D:DGT902 4.0 51.1 0.8 OD1 D:ASP830 4.1 46.2 1.0 O3A D:DGT902 4.1 49.8 0.8 O4 D:DPO901 4.2 51.6 0.2 O5' E:DG10 4.3 41.1 0.2 O3B D:DGT902 4.3 51.9 0.8 N E:C429 4.3 39.9 0.8 CB D:ASP653 4.4 47.8 1.0 C5' E:DG10 4.4 39.5 0.2 N E:C429 4.4 39.8 0.2 CA D:SER655 4.4 47.1 1.0 N D:SER655 4.5 45.4 1.0 N D:TYR654 4.6 45.8 1.0 N D:GLN656 4.7 41.5 1.0 CB D:ASP830 4.7 36.3 1.0 CA D:TYR654 4.7 48.7 1.0 O1G D:DGT902 4.7 49.8 0.8 OP1 E:DG10 4.8 40.7 0.2 O3 D:DPO901 4.8 56.7 0.2 C5' D:DGT902 4.8 38.0 0.8 C D:ASP653 4.9 43.9 1.0 OD1 D:ASP653 4.9 61.2 1.0 O1A D:DGT902 4.9 42.9 0.8 O1 D:DPO901 4.9 51.4 0.2 O3G D:DGT902 5.0 61.5 0.8 O D:ASP830 5.0 41.2 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