Calcium in PDB 8sck: Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 4H

All present enzymatic activity of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 4H:
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 4H, PDB code: 8sck 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)	39.63 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.5, 108.932, 149.356, 90, 90, 90
R / Rfree (%)	19.4 / 24.8

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 4H (pdb code 8sck). 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 4H, PDB code: 8sck:
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 4H


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 4H within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:43.9 occ:1.00 OP2 B:DG10 2.3 29.6 0.7 O2A A:DGT902 2.5 29.0 0.3 O A:TYR654 2.6 21.9 1.0 OD2 A:ASP830 2.7 33.3 1.0 OD2 A:ASP653 2.8 44.0 1.0 O2 A:DPO901 2.8 37.3 0.7 O2G A:DGT902 2.9 37.1 0.3 O A:HOH1051 3.0 35.2 1.0 O6 A:DPO901 3.1 32.8 0.7 O2B A:DGT902 3.2 32.3 0.3 O A:HOH1002 3.6 24.9 1.0 CG A:ASP830 3.7 27.3 1.0 P B:DG10 3.7 24.2 0.7 CG A:ASP653 3.8 32.2 1.0 C A:TYR654 3.8 21.9 1.0 PA A:DGT902 3.9 26.9 0.3 OD1 A:ASP830 4.1 29.3 1.0 P2 A:DPO901 4.1 38.8 0.7 P1 A:DPO901 4.2 40.0 0.7 N B:C429 4.2 21.8 0.7 CB A:ASP653 4.2 23.3 1.0 O5 A:DPO901 4.2 38.1 0.7 PB A:DGT902 4.2 37.6 0.3 PG A:DGT902 4.3 39.4 0.3 N B:C429 4.3 23.0 0.3 CA A:SER655 4.3 26.5 1.0 O3A A:DGT902 4.4 37.3 0.3 O4 A:DPO901 4.4 37.7 0.7 N A:SER655 4.6 21.8 1.0 OP1 B:DG10 4.6 25.7 0.7 O5' B:DG10 4.6 22.7 0.7 O3B A:DGT902 4.7 37.0 0.3 N A:TYR654 4.7 22.9 1.0 O1A A:DGT902 4.8 26.5 0.3 O3G A:DGT902 4.8 36.3 0.3 CB A:ASP830 4.8 21.4 1.0 N A:GLN656 4.9 23.1 1.0 OD1 A:ASP653 4.9 37.8 1.0 CA A:TYR654 4.9 22.1 1.0 C A:ASP653 4.9 24.4 1.0 C5' A:DGT902 4.9 23.6 0.3 C5' B:DG10 4.9 23.3 0.7 O5' A:DGT902 5.0 24.6 0.3

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 4H


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 4H within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:51.6 occ:1.00 OP2 E:DG10 2.2 37.6 0.3 O D:TYR654 2.5 41.4 1.0 OD2 D:ASP830 2.5 45.0 1.0 O2 D:DPO901 2.7 52.1 0.3 O2A D:DGT902 2.7 35.8 0.7 O2G D:DGT902 2.7 52.3 0.7 O2B D:DGT902 2.9 44.3 0.7 OD2 D:ASP653 2.9 49.4 1.0 O6 D:DPO901 3.0 44.3 0.3 O D:HOH1003 3.1 36.3 1.0 CG D:ASP830 3.6 35.3 1.0 P E:DG10 3.7 32.4 0.3 C D:TYR654 3.7 40.2 1.0 PA D:DGT902 3.9 34.5 0.7 CG D:ASP653 3.9 46.8 1.0 PB D:DGT902 3.9 51.7 0.7 P2 D:DPO901 4.0 50.7 0.3 P1 D:DPO901 4.0 52.3 0.3 O3A D:DGT902 4.0 49.5 0.7 O5 D:DPO901 4.1 48.8 0.3 PG D:DGT902 4.1 52.4 0.7 CB D:ASP653 4.1 36.6 1.0 OD1 D:ASP830 4.2 34.2 1.0 N E:C429 4.2 32.9 0.7 O4 D:DPO901 4.3 51.0 0.3 N E:C429 4.4 32.7 0.3 O3B D:DGT902 4.4 51.7 0.7 O5' E:DG10 4.5 34.8 0.3 N D:TYR654 4.5 33.6 1.0 CA D:SER655 4.6 43.0 1.0 N D:SER655 4.6 38.8 1.0 OP1 E:DG10 4.6 37.0 0.3 CA D:TYR654 4.7 35.3 1.0 CB D:ASP830 4.7 31.9 1.0 C D:ASP653 4.7 36.2 1.0 N D:GLN656 4.7 40.5 1.0 C5' E:DG10 4.7 33.5 0.3 O3G D:DGT902 4.9 54.9 0.7 O3 D:DPO901 4.9 54.4 0.3 O5' D:DGT902 4.9 38.6 0.7 O1A D:DGT902 4.9 39.3 0.7 C5' D:DGT902 4.9 36.0 0.7 O1 D:DPO901 4.9 51.7 0.3

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