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

All present enzymatic activity of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 8H:
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 8H, PDB code: 8scm 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)	44.10 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.966, 109.484, 149.824, 90, 90, 90
R / Rfree (%)	19.3 / 25

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 8H (pdb code 8scm). 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 8H, PDB code: 8scm:
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 8H


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 8H within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:40.5 occ:1.00 OP2 B:DG10 2.5 22.8 0.9 O2A A:DGT902 2.5 25.2 0.1 OD2 A:ASP830 2.5 34.1 1.0 O A:TYR654 2.7 17.6 1.0 OD2 A:ASP653 2.8 41.9 1.0 O2G A:DGT902 2.9 34.9 0.1 O2 A:DPO901 3.1 35.7 0.9 O2B A:DGT902 3.2 29.4 0.1 O A:HOH1118 3.2 30.0 1.0 O6 A:DPO901 3.4 30.4 0.9 CG A:ASP830 3.6 27.5 1.0 O A:HOH1002 3.6 21.2 1.0 CG A:ASP653 3.8 26.8 1.0 C A:TYR654 3.9 18.0 1.0 O A:HOH1020 3.9 31.5 1.0 P B:DG10 3.9 20.0 0.9 PA A:DGT902 3.9 25.1 0.1 CB A:ASP653 4.0 21.0 1.0 OD1 A:ASP830 4.1 29.7 1.0 O A:HOH1024 4.1 30.5 1.0 PB A:DGT902 4.3 36.4 0.1 PG A:DGT902 4.3 37.2 0.1 N B:C429 4.3 18.6 0.1 N B:C429 4.4 16.5 0.9 P1 A:DPO901 4.4 39.6 0.9 O3A A:DGT902 4.4 33.9 0.1 P2 A:DPO901 4.4 38.6 0.9 O5 A:DPO901 4.6 35.6 0.9 N A:TYR654 4.6 16.2 1.0 CA A:SER655 4.7 22.5 1.0 O4 A:DPO901 4.7 36.0 0.9 N A:SER655 4.7 17.4 1.0 C5' A:DGT902 4.7 20.7 0.1 CB A:ASP830 4.7 22.6 1.0 OP1 B:DG10 4.8 22.2 0.9 O3B A:DGT902 4.8 35.9 0.1 C A:ASP653 4.8 17.1 1.0 O1A A:DGT902 4.8 23.4 0.1 O1 A:DPO901 4.8 42.2 0.9 CA A:TYR654 4.9 17.0 1.0 OD1 A:ASP653 4.9 36.9 1.0 O5' B:DG10 4.9 19.3 0.9 O5' A:DGT902 4.9 20.6 0.1 N A:GLN656 5.0 16.0 1.0

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 8H


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 8H within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:48.8 occ:1.00 OP2 E:DG10 2.2 34.9 0.5 O2 D:DPO901 2.5 49.1 0.5 O2A D:DGT902 2.5 34.5 0.5 OD2 D:ASP830 2.6 39.9 1.0 O D:TYR654 2.6 39.4 1.0 O2G D:DGT902 2.8 47.6 0.5 O6 D:DPO901 2.9 41.3 0.5 OD2 D:ASP653 2.9 44.8 1.0 O2B D:DGT902 2.9 41.5 0.5 CG D:ASP830 3.6 35.5 1.0 P E:DG10 3.7 27.6 0.5 P2 D:DPO901 3.8 48.4 0.5 O5 D:DPO901 3.8 44.7 0.5 PA D:DGT902 3.8 29.6 0.5 CG D:ASP653 3.9 43.1 1.0 C D:TYR654 3.9 37.2 1.0 P1 D:DPO901 3.9 48.7 0.5 PB D:DGT902 4.0 46.5 0.5 OD1 D:ASP830 4.0 32.9 1.0 CB D:ASP653 4.0 34.8 1.0 O3A D:DGT902 4.1 42.5 0.5 PG D:DGT902 4.2 45.5 0.5 O4 D:DPO901 4.2 44.7 0.5 N E:C429 4.2 27.9 0.5 N E:C429 4.3 29.8 0.5 OP1 E:DG10 4.5 30.5 0.5 O3B D:DGT902 4.5 46.3 0.5 O5' E:DG10 4.6 29.4 0.5 N D:TYR654 4.6 30.9 1.0 CA D:SER655 4.7 39.6 1.0 N D:SER655 4.7 38.3 1.0 C D:ASP653 4.8 34.0 1.0 O5' D:DGT902 4.8 30.2 0.5 O3 D:DPO901 4.8 48.9 0.5 O1 D:DPO901 4.8 47.9 0.5 C5' E:DG10 4.8 28.2 0.5 O1G D:DGT902 4.8 46.6 0.5 CA D:TYR654 4.8 32.4 1.0 CB D:ASP830 4.9 26.8 1.0 O1A D:DGT902 4.9 31.4 0.5 N D:GLN656 4.9 32.5 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