Calcium in PDB 8scn: Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H (Product State)

All present enzymatic activity of Bst Dna Polymerase I Large Fragment Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H (Product State):
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 24H (Product State), PDB code: 8scn 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)	44.11 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.844, 108.793, 149.905, 90, 90, 90
R / Rfree (%)	18.6 / 24.3

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 24H (Product State) (pdb code 8scn). 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 24H (Product State), PDB code: 8scn:
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 24H (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 Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H (Product State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:38.6 occ:1.00 OP2 B:DG10 2.4 21.7 1.0 OD2 A:ASP830 2.5 33.2 1.0 O A:TYR654 2.6 19.8 1.0 OD2 A:ASP653 2.6 32.2 1.0 O2 A:DPO901 2.7 42.5 1.0 O A:HOH1211 3.1 29.8 1.0 O7 A:DPO901 3.5 35.9 1.0 O A:HOH1001 3.5 23.1 1.0 CG A:ASP830 3.6 25.5 1.0 CG A:ASP653 3.7 26.4 1.0 C A:TYR654 3.8 21.5 1.0 P B:DG10 3.8 21.1 1.0 O5 A:DPO901 4.0 48.1 1.0 O B:HOH118 4.1 28.5 1.0 OD1 A:ASP830 4.1 28.0 1.0 CB A:ASP653 4.1 20.9 1.0 P1 A:DPO901 4.1 41.2 1.0 P2 A:DPO901 4.2 54.1 1.0 N B:C429 4.3 15.1 1.0 O4 A:DPO901 4.5 38.7 1.0 CA A:SER655 4.5 25.1 1.0 N A:SER655 4.6 18.3 1.0 OP1 B:DG10 4.6 19.2 1.0 N A:TYR654 4.7 17.9 1.0 CB A:ASP830 4.8 21.1 1.0 C A:ASP653 4.8 20.6 1.0 CA A:TYR654 4.8 18.4 1.0 OD1 A:ASP653 4.8 29.7 1.0 O5' B:DG10 4.9 20.4 1.0 O1 A:DPO901 4.9 47.6 1.0 N A:GLN656 5.0 15.5 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 24H (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 Mutant F710Y/D598A with 3'-Amino Primer, Dgtp, and Calcium Time-Resolved 24H (Product State) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:47.6 occ:1.00 OP2 E:DG10 2.3 27.0 1.0 O7 D:DPO901 2.4 58.4 1.0 OD2 D:ASP830 2.5 40.7 1.0 OD2 D:ASP653 2.6 39.0 1.0 O D:TYR654 2.7 39.0 1.0 O3 D:DPO901 3.3 46.8 1.0 CG D:ASP830 3.5 37.0 1.0 CG D:ASP653 3.6 41.0 1.0 P E:DG10 3.7 27.8 1.0 CB D:ASP653 3.8 32.9 1.0 P2 D:DPO901 3.8 51.3 1.0 OD1 D:ASP830 3.9 33.1 1.0 C D:TYR654 3.9 38.0 1.0 O1 D:DPO901 4.0 60.3 1.0 P1 D:DPO901 4.0 67.5 1.0 N E:C429 4.3 24.0 1.0 O4 D:DPO901 4.3 55.9 1.0 O5 D:DPO901 4.6 52.9 1.0 OP1 E:DG10 4.6 31.8 1.0 N D:TYR654 4.6 33.2 1.0 C D:ASP653 4.7 34.6 1.0 OD1 D:ASP653 4.7 44.9 1.0 O5' E:DG10 4.7 31.5 1.0 CA D:SER655 4.8 45.4 1.0 N D:SER655 4.8 39.1 1.0 O6 D:DPO901 4.8 62.5 1.0 CB D:ASP830 4.8 33.4 1.0 CA D:TYR654 4.9 35.9 1.0 CA D:ASP653 4.9 36.1 1.0 C5' E:DG10 5.0 27.9 1.0 O D:ASP830 5.0 35.6 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