Magnesium in PDB 9dqu: Product Complex of Dna Polymerase Iota with Pyrophosphate

All present enzymatic activity of Product Complex of Dna Polymerase Iota with Pyrophosphate:
2.7.7.7;

The structure of Product Complex of Dna Polymerase Iota with Pyrophosphate, PDB code: 9dqu 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)	43.27 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.488, 97.488, 201.55, 90, 90, 120
R / Rfree (%)	23.7 / 27.8

The binding sites of Magnesium atom in the Product Complex of Dna Polymerase Iota with Pyrophosphate (pdb code 9dqu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Product Complex of Dna Polymerase Iota with Pyrophosphate, PDB code: 9dqu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Product Complex of Dna Polymerase Iota with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Product Complex of Dna Polymerase Iota with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.5 occ:1.00 OP1 B:DT19 2.2 36.7 1.0 OD1 A:ASP34 2.3 31.4 1.0 O A:HOH671 2.6 39.2 1.0 OE2 A:GLU127 2.6 33.6 1.0 O3' B:DC18 2.7 32.7 1.0 MG A:MG503 2.7 29.9 1.0 OD1 A:ASP126 2.8 30.1 1.0 HG3 A:GLU127 2.9 37.8 1.0 OD2 A:ASP126 2.9 36.3 1.0 P B:DT19 2.9 45.3 1.0 CG A:ASP34 3.0 32.8 1.0 OD2 A:ASP34 3.1 46.8 1.0 CG A:ASP126 3.2 32.0 1.0 CD A:GLU127 3.4 30.7 1.0 CG A:GLU127 3.5 31.5 1.0 HG2 A:GLU127 3.7 37.8 1.0 OP2 B:DT19 4.0 40.4 1.0 C3' B:DC18 4.0 33.7 1.0 O6 A:POP501 4.1 39.9 0.8 O5' B:DT19 4.1 41.0 1.0 C5' B:DT19 4.2 36.4 1.0 C4' B:DC18 4.4 36.4 1.0 CB A:ASP34 4.4 32.8 1.0 O3 A:POP501 4.4 44.8 0.8 HA A:ASP34 4.4 36.4 1.0 O1 A:POP501 4.4 29.5 0.8 O A:HOH611 4.5 26.9 1.0 OE1 A:GLU127 4.6 34.3 1.0 HB2 A:ASP34 4.6 39.3 1.0 C5' B:DC18 4.6 32.3 1.0 O A:LEU35 4.7 31.5 1.0 HZ1 A:LYS214 4.7 77.5 1.0 CB A:ASP126 4.7 34.1 1.0 O A:ASP126 4.8 31.2 1.0 H A:LEU35 4.8 32.9 1.0 CA A:ASP34 4.9 30.4 1.0 CB A:GLU127 4.9 28.3 1.0 C2' B:DC18 5.0 31.2 1.0 C A:ASP126 5.0 26.6 1.0

Magnesium binding site 2 out of 3 in the Product Complex of Dna Polymerase Iota with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Product Complex of Dna Polymerase Iota with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:29.9 occ:1.00 O6 A:POP501 2.3 39.9 0.8 OD2 A:ASP126 2.3 36.3 1.0 O A:LEU35 2.4 31.5 1.0 O1 A:POP501 2.4 29.5 0.8 OD1 A:ASP34 2.4 31.4 1.0 OP1 B:DT19 2.5 36.7 1.0 MG A:MG502 2.7 38.5 1.0 P1 A:POP501 3.3 40.0 0.8 CG A:ASP34 3.4 32.8 1.0 O3 A:POP501 3.4 44.8 0.8 CG A:ASP126 3.5 32.0 1.0 P2 A:POP501 3.5 47.3 0.8 C A:LEU35 3.6 26.8 1.0 OD2 A:ASP34 3.7 46.8 1.0 O A:POP501 3.7 48.3 0.8 P B:DT19 3.9 45.3 1.0 HZ1 A:LYS214 4.0 77.5 1.0 OD1 A:ASP126 4.0 30.1 1.0 H A:LEU35 4.0 32.9 1.0 N A:LEU35 4.1 27.4 1.0 O4 A:POP501 4.1 42.5 0.8 H A:PHE38 4.2 34.8 1.0 HA A:ASP36 4.2 38.9 1.0 H A:CYS37 4.2 38.7 1.0 C5' B:DT19 4.4 36.4 1.0 HB2 A:PHE38 4.4 33.5 1.0 O A:HOH671 4.4 39.2 1.0 CA A:LEU35 4.4 31.7 1.0 C A:ASP34 4.4 27.4 1.0 HB2 A:LEU35 4.4 33.5 1.0 N A:CYS37 4.5 32.3 1.0 O5' B:DT19 4.6 41.0 1.0 N A:ASP36 4.6 29.8 1.0 O3' B:DC18 4.6 32.7 1.0 HB2 A:ASP126 4.6 40.9 1.0 CB A:ASP34 4.6 32.8 1.0 O2 A:POP501 4.7 36.8 0.8 O5 A:POP501 4.7 47.5 0.8 CB A:ASP126 4.7 34.1 1.0 HA A:ASP34 4.7 36.4 1.0 CA A:ASP36 4.7 32.4 1.0 NZ A:LYS214 4.8 64.6 1.0 C A:ASP36 4.8 31.5 1.0 HG3 A:GLU127 4.8 37.8 1.0 O A:ASP34 4.8 34.0 1.0 CA A:ASP34 4.9 30.4 1.0 HZ2 A:LYS214 4.9 77.5 1.0 N A:PHE38 4.9 29.0 1.0 HA A:CYS37 4.9 40.9 1.0 HB3 A:ASP34 5.0 39.3 1.0 HE3 A:LYS214 5.0 76.1 1.0

Magnesium binding site 3 out of 3 in the Product Complex of Dna Polymerase Iota with Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Product Complex of Dna Polymerase Iota with Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:37.9 occ:1.00 O A:ILE242 2.2 35.0 1.0 O A:LYS237 2.3 31.7 1.0 OP1 B:DC17 2.4 36.5 1.0 O A:HOH686 2.5 34.9 1.0 O A:ILE239 2.6 27.2 1.0 O A:HOH610 2.7 34.8 1.0 HG2 A:LYS237 3.2 56.5 1.0 C A:ILE242 3.3 34.8 1.0 H A:ILE242 3.3 37.9 1.0 HA A:PRO240 3.4 43.1 1.0 C A:LYS237 3.4 35.2 1.0 HA2 A:GLY243 3.5 50.8 1.0 C A:ILE239 3.5 33.5 1.0 P B:DC17 3.5 30.3 1.0 HA A:LYS237 3.7 45.0 1.0 OP2 B:DC17 3.8 33.5 1.0 H A:GLY241 3.8 37.9 1.0 HG3 A:LYS237 3.8 56.5 1.0 N A:ILE242 3.9 31.6 1.0 CG A:LYS237 3.9 47.1 1.0 HZ3 A:LYS237 3.9 54.8 1.0 HB A:ILE242 4.0 41.8 1.0 CA A:LYS237 4.1 37.5 1.0 CA A:PRO240 4.1 36.0 1.0 CA A:ILE242 4.1 33.9 1.0 N A:PRO240 4.1 35.2 1.0 N A:ILE239 4.1 27.9 1.0 N A:GLY243 4.1 40.8 1.0 CA A:GLY243 4.2 42.3 1.0 H A:ILE239 4.2 33.5 1.0 C A:GLU238 4.3 30.8 1.0 N A:GLY241 4.3 31.6 1.0 HA A:GLU238 4.3 41.6 1.0 N A:GLU238 4.4 36.6 1.0 CA A:ILE239 4.5 34.8 1.0 HE2 A:LYS237 4.5 58.7 1.0 CA A:GLU238 4.6 34.7 1.0 CB A:ILE242 4.6 34.8 1.0 O3' B:DC16 4.6 37.8 1.0 CB A:LYS237 4.6 40.3 1.0 C A:PRO240 4.6 32.6 1.0 O5' B:DC17 4.6 30.7 1.0 O A:GLU238 4.7 34.6 1.0 HA3 A:GLY243 4.7 50.8 1.0 NZ A:LYS237 4.7 45.7 1.0 HG22 A:ILE242 4.8 45.9 1.0 C A:GLY241 4.9 33.4 1.0 H A:GLY243 5.0 48.9 1.0 HA A:ILE242 5.0 40.7 1.0 CE A:LYS237 5.0 48.9 1.0 HB A:ILE239 5.0 37.8 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