Calcium in PDB 9dqt: Binary Substrate Complex of Dna Polymerase Iota with Dna (Template A)

All present enzymatic activity of Binary Substrate Complex of Dna Polymerase Iota with Dna (Template A):
2.7.7.7;

The structure of Binary Substrate Complex of Dna Polymerase Iota with Dna (Template A), PDB code: 9dqt 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)	48.82 / 3.19
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.639, 97.639, 188.91, 90, 90, 120
R / Rfree (%)	31.7 / 36.4

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

Calcium binding site 1 out of 2 in the Binary Substrate Complex of Dna Polymerase Iota with Dna (Template A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Binary Substrate Complex of Dna Polymerase Iota with Dna (Template A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:103.0 occ:1.00 HH11 A:ARG71 2.2 142.1 1.0 HH22 A:ARG71 2.3 159.6 1.0 H A:CYS37 2.8 129.2 1.0 NH1 A:ARG71 2.8 118.5 1.0 NH2 A:ARG71 2.9 133.0 1.0 CZ A:ARG71 3.2 121.7 1.0 HH12 A:ARG71 3.5 142.1 1.0 HH21 A:ARG71 3.6 159.6 1.0 N A:CYS37 3.6 107.7 1.0 HA A:CYS37 3.7 126.5 1.0 HA A:ASP36 4.0 100.8 1.0 CA A:CYS37 4.1 105.5 1.0 HB3 A:CYS37 4.2 156.6 1.0 OH A:TYR68 4.2 125.3 1.0 HH A:TYR68 4.4 150.4 1.0 NE A:ARG71 4.5 138.1 1.0 HE2 A:TYR68 4.5 145.1 1.0 C A:ASP36 4.7 99.5 1.0 CB A:CYS37 4.7 130.5 1.0 CA A:ASP36 4.7 84.0 1.0 OD1 A:ASP36 4.8 91.1 1.0 CZ A:TYR68 4.8 129.8 1.0 CE2 A:TYR68 4.9 121.0 1.0 HE A:ARG71 4.9 165.7 1.0

Calcium binding site 2 out of 2 in the Binary Substrate Complex of Dna Polymerase Iota with Dna (Template A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Binary Substrate Complex of Dna Polymerase Iota with Dna (Template A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:104.8 occ:1.00 O A:LYS237 2.6 108.3 1.0 OP1 B:DC17 2.7 99.5 1.0 O A:ILE239 2.8 70.2 1.0 HZ3 A:LYS237 2.9 159.5 1.0 HZ2 A:LYS237 3.0 159.5 1.0 NZ A:LYS237 3.4 132.9 1.0 O A:ILE242 3.4 90.1 1.0 HA A:PRO240 3.4 124.9 1.0 H A:GLY241 3.4 113.0 1.0 C A:ILE239 3.6 95.8 1.0 HZ1 A:LYS237 3.6 159.5 1.0 C A:LYS237 3.7 101.8 1.0 HA A:GLU238 3.9 123.0 1.0 P B:DC17 4.0 100.7 1.0 C A:GLU238 4.0 79.5 1.0 HG3 A:LYS237 4.0 133.0 1.0 N A:GLY241 4.1 94.2 1.0 CA A:PRO240 4.1 104.1 1.0 N A:PRO240 4.2 101.1 1.0 N A:ILE239 4.2 69.3 1.0 O A:GLU238 4.2 85.3 1.0 H A:ILE242 4.2 101.0 1.0 CA A:GLU238 4.3 102.5 1.0 O5' B:DC17 4.3 64.9 1.0 C A:ILE242 4.4 87.5 1.0 HA2 A:GLY243 4.4 96.8 1.0 H A:ILE239 4.5 83.2 1.0 N A:GLU238 4.5 111.2 1.0 HA A:LYS237 4.5 108.1 1.0 CA A:ILE239 4.6 96.1 1.0 N A:ILE242 4.6 84.2 1.0 C A:PRO240 4.6 93.3 1.0 CE A:LYS237 4.7 129.5 1.0 CA A:LYS237 4.8 90.1 1.0 OP2 B:DC17 4.8 67.6 1.0 HD2 A:LYS237 4.8 146.5 1.0 CG A:LYS237 4.9 110.8 1.0 HB A:ILE242 4.9 92.8 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