Calcium in PDB 9ddr: Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp

All present enzymatic activity of Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp:
2.7.7.7;

The structure of Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp, PDB code: 9ddr was solved by Z.Frevert, D.Reusch, B.Freudenthal, M.T.Washington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.42 / 2.15
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.556, 97.556, 202.148, 90, 90, 120
R / Rfree (%)	23.7 / 28

The binding sites of Calcium atom in the Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp (pdb code 9ddr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp, PDB code: 9ddr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:33.8 occ:1.00 O2A A:TTP501 2.2 34.8 1.0 OD1 A:ASP34 2.2 39.5 1.0 O1G A:TTP501 2.2 35.4 1.0 O A:LEU35 2.2 37.0 1.0 O1B A:TTP501 2.3 31.3 1.0 OD2 A:ASP126 2.3 34.1 1.0 CA A:CA503 2.9 66.5 1.0 CG A:ASP34 3.3 41.8 1.0 H5'2 A:TTP501 3.4 45.3 1.0 C A:LEU35 3.4 33.3 1.0 PB A:TTP501 3.4 37.3 1.0 PA A:TTP501 3.5 40.8 1.0 PG A:TTP501 3.5 41.2 1.0 CG A:ASP126 3.5 36.7 1.0 H A:LEU35 3.8 41.5 1.0 O3A A:TTP501 3.8 38.9 1.0 N A:LEU35 3.8 34.5 1.0 OD2 A:ASP34 3.8 52.9 1.0 O3B A:TTP501 3.9 41.8 1.0 O A:HOH679 4.0 47.0 1.0 OD1 A:ASP126 4.0 33.8 1.0 O2G A:TTP501 4.1 36.7 1.0 C A:ASP34 4.1 36.4 1.0 H A:PHE38 4.2 42.4 1.0 HA A:ASP36 4.2 42.0 1.0 CA A:LEU35 4.2 38.3 1.0 C5' A:TTP501 4.2 37.8 1.0 HB2 A:PHE38 4.3 38.4 1.0 H A:CYS37 4.3 41.4 1.0 HB2 A:LEU35 4.3 41.8 1.0 O5' A:TTP501 4.4 43.3 1.0 H5'1 A:TTP501 4.4 45.3 1.0 N A:ASP36 4.4 35.2 1.0 O1A A:TTP501 4.5 40.4 1.0 O A:ASP34 4.5 35.9 1.0 CB A:ASP34 4.5 41.4 1.0 HA A:ASP34 4.5 47.6 1.0 N A:CYS37 4.6 34.5 1.0 HB2 A:ASP126 4.6 40.0 1.0 O3G A:TTP501 4.6 44.7 1.0 CA A:ASP36 4.7 35.0 1.0 CA A:ASP34 4.7 39.6 1.0 CB A:ASP126 4.7 33.4 1.0 O2B A:TTP501 4.7 38.5 1.0 C A:ASP36 4.8 36.6 1.0 CB A:LEU35 4.8 34.9 1.0 N A:PHE38 4.9 35.3 1.0 HB3 A:ASP34 4.9 49.6 1.0 HA A:LEU35 5.0 45.9 1.0

Calcium binding site 2 out of 2 in the Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Substrate Complex of Dna Polymerase Iota with Dna (Template A), CA2+, and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.5 occ:1.00 O2A A:TTP501 2.1 34.8 1.0 O3' B:DC18 2.7 37.5 1.0 OD1 A:ASP126 2.7 33.8 1.0 OD1 A:ASP34 2.7 39.5 1.0 OE2 A:GLU127 2.8 33.8 1.0 HG3 A:GLU127 2.9 36.8 1.0 CA A:CA502 2.9 33.8 1.0 OD2 A:ASP126 3.0 34.1 1.0 OD2 A:ASP34 3.1 52.9 1.0 CG A:ASP34 3.1 41.8 1.0 CG A:ASP126 3.2 36.7 1.0 PA A:TTP501 3.2 40.8 1.0 HG2 A:GLU127 3.3 36.8 1.0 CG A:GLU127 3.4 30.7 1.0 O1A A:TTP501 3.5 40.4 1.0 CD A:GLU127 3.5 34.9 1.0 H5'1 A:TTP501 3.7 45.3 1.0 O A:HOH679 3.9 47.0 1.0 H5'2 A:TTP501 3.9 45.3 1.0 O5' A:TTP501 4.0 43.3 1.0 C3' B:DC18 4.0 37.8 1.0 C5' A:TTP501 4.1 37.8 1.0 O1G A:TTP501 4.2 35.4 1.0 O A:HOH629 4.3 35.3 1.0 HA A:ASP34 4.4 47.6 1.0 CB A:ASP34 4.4 41.4 1.0 O1B A:TTP501 4.4 31.3 1.0 C4' B:DC18 4.5 38.7 1.0 HB2 A:ASP34 4.5 49.6 1.0 O3A A:TTP501 4.6 38.9 1.0 O A:ASP126 4.7 33.8 1.0 CB A:ASP126 4.7 33.4 1.0 C2' B:DC18 4.7 36.9 1.0 OE1 A:GLU127 4.8 35.5 1.0 H A:LEU35 4.8 41.5 1.0 CA A:ASP34 4.8 39.6 1.0 CB A:GLU127 4.8 29.7 1.0 C A:ASP126 4.9 32.5 1.0 O A:LEU35 4.9 37.0 1.0

Z.Frevert, D.T.Reusch, M.S.Gildenberg, S.M.Jordan, B.J.Ryan, B.D.Freudenthal, M.T.Washington. Visualizing Dna Polymerase Iota Catalyze Hoogsteen-Directed Dna Synthesis Nat Commun V. 16 5979 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-61245-8