Magnesium in PDB 9dr7: Product Complex of Dna Polymerase Iota with 2 Monophosphates

All present enzymatic activity of Product Complex of Dna Polymerase Iota with 2 Monophosphates:
2.7.7.7;

The structure of Product Complex of Dna Polymerase Iota with 2 Monophosphates, PDB code: 9dr7 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)	49.09 / 2.45
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.19, 98.19, 202.34, 90, 90, 120
R / Rfree (%)	25.4 / 31.2

The binding sites of Magnesium atom in the Product Complex of Dna Polymerase Iota with 2 Monophosphates (pdb code 9dr7). 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 2 Monophosphates, PDB code: 9dr7:
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 2 Monophosphates


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 2 Monophosphates within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.5 occ:1.00 MG A:MG503 2.4 38.4 1.0 OD1 A:ASP34 2.4 41.0 1.0 OD2 A:ASP126 2.4 40.1 1.0 O A:LEU35 2.5 41.1 1.0 O3 A:PO4501 2.5 48.4 1.0 OP1 B:DT19 2.5 42.6 1.0 CG A:ASP34 3.3 39.4 1.0 O1 B:PO4101 3.3 46.9 0.5 O2 B:PO4101 3.5 51.3 0.5 CG A:ASP126 3.6 42.4 1.0 OD2 A:ASP34 3.6 42.2 1.0 C A:LEU35 3.7 34.0 1.0 P A:PO4501 3.9 64.1 1.0 P B:DT19 4.0 48.8 1.0 HB2 A:ASP126 4.0 49.3 1.0 P B:PO4101 4.0 47.0 0.5 H A:LEU35 4.1 42.5 1.0 N A:LEU35 4.2 35.2 1.0 HA A:ASP36 4.3 47.6 1.0 H A:PHE38 4.3 40.5 1.0 CB A:ASP126 4.4 40.9 1.0 OD1 A:ASP126 4.4 40.8 1.0 O2 A:PO4501 4.4 53.7 1.0 HB2 A:PHE38 4.4 42.0 1.0 C5' B:DT19 4.4 39.2 1.0 HB2 A:LEU35 4.5 43.1 1.0 O3' B:DC18 4.5 37.2 1.0 CA A:LEU35 4.5 36.6 1.0 H A:CYS37 4.5 43.6 1.0 C A:ASP34 4.5 37.7 1.0 O5' B:DT19 4.6 45.4 1.0 O4 A:PO4501 4.6 51.9 1.0 CB A:ASP34 4.6 37.2 1.0 N A:ASP36 4.7 35.7 1.0 N A:CYS37 4.7 36.1 1.0 HA A:ASP34 4.7 45.1 1.0 HB3 A:ASP126 4.7 49.3 1.0 HG3 A:GLU127 4.8 43.6 1.0 CA A:ASP36 4.8 39.4 1.0 HZ2 A:LYS77 4.8 73.5 1.0 O1 A:PO4501 4.9 63.5 1.0 CA A:ASP34 4.9 37.4 1.0 C A:ASP36 4.9 37.1 1.0 HA A:CYS37 5.0 51.8 1.0

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


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 2 Monophosphates within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:38.4 occ:1.00 OD1 A:ASP34 2.3 41.0 1.0 MG A:MG502 2.4 51.5 1.0 OP1 B:DT19 2.4 42.6 1.0 OD2 A:ASP126 2.5 40.1 1.0 OE2 A:GLU127 2.8 36.1 1.0 CG A:ASP34 2.9 39.4 1.0 OD2 A:ASP34 2.9 42.2 1.0 HG3 A:GLU127 3.0 43.6 1.0 O3' B:DC18 3.1 37.2 1.0 CG A:ASP126 3.2 42.4 1.0 OD1 A:ASP126 3.3 40.8 1.0 P B:DT19 3.3 48.8 1.0 HG2 A:GLU127 3.4 43.6 1.0 CG A:GLU127 3.5 36.1 1.0 CD A:GLU127 3.5 32.0 1.0 O3 A:PO4501 4.1 48.4 1.0 CB A:ASP34 4.2 37.2 1.0 OP2 B:DT19 4.3 47.7 1.0 C3' B:DC18 4.4 39.1 1.0 HA A:ASP34 4.4 45.1 1.0 O5' B:DT19 4.5 45.4 1.0 HB2 A:ASP34 4.5 44.9 1.0 O A:LEU35 4.5 41.1 1.0 CB A:ASP126 4.5 40.9 1.0 HB2 A:ASP126 4.5 49.3 1.0 O2 B:PO4101 4.5 51.3 0.5 C5' B:DT19 4.5 39.2 1.0 C4' B:DC18 4.6 40.7 1.0 OE1 A:GLU127 4.7 36.5 1.0 H A:LEU35 4.8 42.5 1.0 CA A:ASP34 4.8 37.4 1.0 O A:HOH604 4.8 33.7 1.0 HB3 A:ASP34 4.9 44.9 1.0 CB A:GLU127 4.9 31.4 1.0 O1 B:PO4101 4.9 46.9 0.5

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


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 2 Monophosphates within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:44.0 occ:1.00 O A:LYS237 2.2 42.0 1.0 OP1 B:DC17 2.4 44.4 1.0 O A:ILE239 2.5 34.0 1.0 O A:ILE242 2.6 44.0 1.0 HA A:PRO240 3.0 43.9 1.0 C A:ILE239 3.2 37.7 1.0 H A:ILE242 3.3 45.1 1.0 C A:LYS237 3.4 44.7 1.0 H A:GLY241 3.6 44.6 1.0 O B:HOH215 3.7 44.1 1.0 P B:DC17 3.7 35.7 1.0 C A:ILE242 3.7 46.0 1.0 N A:PRO240 3.7 40.5 1.0 HG3 A:LYS237 3.7 59.6 1.0 CA A:PRO240 3.7 36.3 1.0 N A:ILE239 3.8 34.1 1.0 H A:ILE239 4.0 41.2 1.0 C A:GLU238 4.0 35.2 1.0 HA A:LYS237 4.0 50.4 1.0 N A:ILE242 4.0 37.4 1.0 HA A:GLU238 4.0 44.6 1.0 HB A:ILE242 4.0 53.9 1.0 OP2 B:DC17 4.1 34.5 1.0 HD2 A:LYS237 4.1 63.3 1.0 N A:GLY241 4.1 36.9 1.0 CA A:ILE239 4.2 39.8 1.0 HA2 A:GLY243 4.2 59.1 1.0 HZ3 A:LYS237 4.2 53.0 1.0 N A:GLU238 4.3 40.8 1.0 CA A:GLU238 4.3 37.0 1.0 CA A:LYS237 4.3 41.8 1.0 CA A:ILE242 4.4 41.2 1.0 O A:GLU238 4.4 35.6 1.0 C A:PRO240 4.4 35.5 1.0 CG A:LYS237 4.6 49.4 1.0 O5' B:DC17 4.6 32.6 1.0 N A:GLY243 4.7 53.3 1.0 CB A:ILE242 4.7 44.7 1.0 O3' B:DC16 4.7 37.8 1.0 CD A:LYS237 4.8 52.5 1.0 HA A:ILE239 4.8 48.0 1.0 HD3 A:PRO240 4.9 47.0 1.0 CD A:PRO240 4.9 39.0 1.0 HB A:ILE239 4.9 40.9 1.0 CA A:GLY243 4.9 49.0 1.0 O A:ILE236 5.0 44.4 1.0 CB A:PRO240 5.0 35.8 1.0 NZ A:LYS237 5.0 44.0 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