Calcium in PDB 9drc: Ternary Substrate Complex of Dna Polymerase Iota R71A Mutant with Dna (Template A) and Dttp

All present enzymatic activity of Ternary Substrate Complex of Dna Polymerase Iota R71A Mutant with Dna (Template A) and Dttp:
2.7.7.7;

The structure of Ternary Substrate Complex of Dna Polymerase Iota R71A Mutant with Dna (Template A) and Dttp, PDB code: 9drc 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)	24.89 / 2.45
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.278, 97.278, 202.828, 90, 90, 120
R / Rfree (%)	24.9 / 29.4

The binding sites of Calcium atom in the Ternary Substrate Complex of Dna Polymerase Iota R71A Mutant with Dna (Template A) and Dttp (pdb code 9drc). 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 R71A Mutant with Dna (Template A) and Dttp, PDB code: 9drc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ternary Substrate Complex of Dna Polymerase Iota R71A Mutant with Dna (Template A) 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 R71A Mutant with Dna (Template A) and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:32.8 occ:0.45 O1G A:TTP501 2.2 43.8 0.5 O1A A:TTP501 2.5 44.4 0.5 O3' B:DC18 2.8 42.5 1.0 OD1 A:ASP34 2.8 31.3 1.0 OD2 A:ASP126 2.9 37.5 1.0 OE2 A:GLU127 3.0 27.5 1.0 O A:HOH602 3.1 36.8 1.0 HG3 A:GLU127 3.3 34.3 1.0 OD1 A:ASP126 3.4 33.9 1.0 CG A:ASP126 3.4 30.4 1.0 OD2 A:ASP34 3.5 32.8 1.0 CG A:ASP34 3.5 29.5 1.0 PG A:TTP501 3.5 55.0 0.5 O3G A:TTP501 3.8 50.5 0.5 PA A:TTP501 3.8 54.1 0.5 CD A:GLU127 3.9 24.3 1.0 CG A:GLU127 3.9 28.4 1.0 O A:HOH604 4.0 35.9 1.0 HG2 A:GLU127 4.1 34.3 1.0 O3A A:TTP501 4.1 57.8 0.5 C3' B:DC18 4.2 37.1 1.0 O2G A:TTP501 4.4 41.3 0.5 O A:LEU35 4.5 35.1 1.0 HB2 A:ASP126 4.5 31.2 1.0 O5' A:TTP501 4.6 52.1 0.5 O3B A:TTP501 4.6 42.1 0.5 CB A:ASP126 4.6 25.9 1.0 C4' B:DC18 4.8 36.6 1.0 O A:ASP126 4.9 28.8 1.0 O2A A:TTP501 4.9 46.4 0.5 CB A:ASP34 4.9 26.6 1.0 C2' B:DC18 4.9 39.5 1.0 HA A:ASP34 5.0 34.1 1.0 H6 A:TTP501 5.0 61.1 0.5

Calcium binding site 2 out of 2 in the Ternary Substrate Complex of Dna Polymerase Iota R71A Mutant with Dna (Template A) 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 R71A Mutant with Dna (Template A) and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:65.6 occ:0.41 HH A:TYR68 1.9 78.1 1.0 OH A:TYR68 2.1 65.0 1.0 O3B A:TTP501 2.1 42.1 0.5 O2B A:TTP501 2.2 46.8 0.5 HZ3 A:LYS214 2.3 59.6 1.0 PB A:TTP501 2.5 45.8 0.5 HE2 A:LYS214 2.5 65.8 1.0 NZ A:LYS214 2.8 49.6 1.0 HZ1 A:LYS214 2.8 59.6 1.0 PG A:TTP501 2.9 55.0 0.5 O3G A:TTP501 3.1 50.5 0.5 CE A:LYS214 3.1 54.7 1.0 O2G A:TTP501 3.2 41.3 0.5 O1B A:TTP501 3.2 48.1 0.5 HG3 A:LYS214 3.2 70.6 1.0 CZ A:TYR68 3.3 56.1 1.0 HA A:ASP36 3.6 39.0 1.0 HZ2 A:LYS214 3.7 59.6 1.0 H A:CYS37 3.7 40.6 1.0 HE3 A:LYS214 3.8 65.8 1.0 O3A A:TTP501 3.9 57.8 0.5 CG A:LYS214 3.9 58.8 1.0 HE1 A:TYR68 4.0 61.5 1.0 HG2 A:LYS214 4.0 70.6 1.0 HE2 A:TYR68 4.1 69.9 1.0 CE1 A:TYR68 4.1 51.1 1.0 CE2 A:TYR68 4.1 58.1 1.0 CD A:LYS214 4.2 59.8 1.0 HB3 A:ASP36 4.2 37.0 1.0 O1G A:TTP501 4.3 43.8 0.5 OD1 A:ASP36 4.3 41.0 1.0 O A:LYS214 4.4 67.8 1.0 CA A:ASP36 4.5 32.4 1.0 N A:CYS37 4.5 33.7 1.0 HD2 A:LYS214 4.7 71.9 1.0 CB A:ASP36 4.7 30.7 1.0 HD3 A:LYS214 4.8 71.9 1.0 HZ1 A:LYS77 4.9 68.8 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