Magnesium in PDB 2w9b: Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna

All present enzymatic activity of Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna:
2.7.7.7;

The structure of Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna, PDB code: 2w9b was solved by R.L.Eoff, H.Zhang, I.D.Kosekov, C.J.Rizzo, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.75 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.794, 101.776, 97.268, 90.00, 91.95, 90.00
R / Rfree (%)	23.9 / 25.1

The binding sites of Magnesium atom in the Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna (pdb code 2w9b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna, PDB code: 2w9b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1342 b:42.9 occ:1.00 OD2 A:ASP105 1.8 36.7 1.0 O A:PHE8 2.8 21.5 1.0 OD2 A:ASP7 2.9 33.5 1.0 CG A:ASP105 2.9 27.2 1.0 O A:HOH2022 3.0 29.6 1.0 O C:HOH2012 3.6 30.8 1.0 CB A:ASP105 3.7 21.6 1.0 OD1 A:ASP105 3.9 30.5 1.0 C A:PHE8 3.9 21.5 1.0 CG A:ASP7 3.9 31.4 1.0 OE2 A:GLU106 4.0 23.7 1.0 N A:PHE11 4.0 21.5 1.0 N A:TYR10 4.1 23.2 1.0 N A:PHE8 4.1 22.7 1.0 CA A:TYR10 4.4 22.7 1.0 CB A:PHE8 4.5 21.8 1.0 CA A:PHE8 4.5 21.5 1.0 OD1 A:ASP7 4.6 39.7 1.0 O A:ASP105 4.7 23.9 1.0 C A:ASP9 4.7 24.0 1.0 CB A:PHE11 4.7 21.5 1.0 C A:TYR10 4.7 21.5 1.0 CA A:ASP9 4.8 22.6 1.0 N A:ASP9 4.9 21.7 1.0 CA A:PHE11 4.9 21.5 1.0 CB A:ASP7 4.9 23.1 1.0 CA A:ASP105 5.0 23.2 1.0

Magnesium binding site 2 out of 4 in the Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1343 b:53.6 occ:1.00 O A:HOH2058 2.3 22.2 1.0 O A:ILE186 2.5 32.7 1.0 O A:ALA181 2.8 29.9 1.0 OP2 C:DC13 3.4 34.0 1.0 C A:ILE186 3.7 33.4 1.0 CA A:GLY187 4.0 32.4 1.0 C A:ALA181 4.0 30.6 1.0 N A:GLY187 4.3 32.5 1.0 P C:DC13 4.6 29.8 1.0 C A:GLY187 4.6 32.1 1.0 CA A:ASP182 4.7 30.7 1.0 OP1 C:DC13 4.8 27.7 1.0 N A:VAL183 4.8 28.6 1.0 N A:ASP182 4.8 30.8 1.0 O A:VAL183 4.9 34.5 1.0 CA A:ILE186 4.9 32.0 1.0

Magnesium binding site 3 out of 4 in the Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1342 b:47.3 occ:1.00 OD2 B:ASP7 2.3 26.9 1.0 O D:HOH2016 2.7 20.3 1.0 O D:HOH2018 2.9 15.5 1.0 O B:HOH2011 3.0 16.3 1.0 OD1 B:ASP105 3.1 26.2 1.0 O B:PHE8 3.2 21.5 1.0 CG B:ASP7 3.3 21.5 1.0 CG B:ASP105 3.3 25.4 1.0 OD1 B:ASP7 3.5 24.7 1.0 OD2 B:ASP105 3.7 38.9 1.0 O B:HOH2002 4.0 26.1 1.0 NZ B:LYS159 4.0 39.3 1.0 CB B:ASP105 4.1 21.9 1.0 O B:ASP105 4.1 21.5 1.0 OE2 B:GLU106 4.3 30.6 1.0 C B:PHE8 4.4 21.5 1.0 C5' D:DOC14 4.5 40.0 0.8 OP1 D:DOC14 4.5 32.9 0.8 N B:TYR10 4.5 21.5 1.0 O B:HOH2001 4.6 20.3 1.0 O B:HOH2036 4.7 19.4 1.0 CB B:ASP7 4.7 21.5 1.0 N B:PHE8 4.8 21.5 1.0 N B:PHE11 4.8 21.5 1.0 O B:HOH2028 4.9 57.6 1.0 C B:ASP9 4.9 21.5 1.0 C B:ASP7 4.9 21.5 1.0 CE B:LYS159 5.0 41.3 1.0 CB B:PHE11 5.0 21.5 1.0

Magnesium binding site 4 out of 4 in the Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Binary Complex of DPO4 Bound to N2,N2-Dimethyl- Deoxyguanosine Modified Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1343 b:42.8 occ:1.00 O B:ILE186 2.6 22.3 1.0 O B:ALA181 2.7 32.8 1.0 OP2 D:DC13 2.9 27.9 1.0 O B:HOH2039 3.1 14.4 1.0 C B:ALA181 3.8 32.6 1.0 C B:ILE186 3.8 23.2 1.0 O B:VAL183 3.9 24.4 1.0 P D:DC13 4.1 30.2 1.0 CA B:ASP182 4.3 27.6 1.0 N B:ASP182 4.4 29.1 1.0 OP1 D:DC13 4.5 21.6 1.0 C B:ASP182 4.5 26.4 1.0 CA B:GLY187 4.6 28.1 1.0 CG2 B:ILE186 4.6 25.2 1.0 CB B:ILE186 4.6 24.8 1.0 N B:GLY187 4.6 25.4 1.0 N B:ILE186 4.7 23.2 1.0 N B:VAL183 4.7 24.2 1.0 C B:VAL183 4.7 21.7 1.0 CA B:ILE186 4.7 22.2 1.0 CA B:ALA181 4.9 34.6 1.0 O D:HOH2015 5.0 51.7 1.0

H.Zhang, R.L.Eoff, I.D.Kosekov, C.J.Rizzo, M.Egli, F.P.Guengerich. Structure-Function Relationships in Miscoding By Sulfolobus Solfataricus Dna Polymerase DPO4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. J.Biol.Chem. V. 284 17687 2009.
ISSN: ISSN 0021-9258
PubMed: 19542237
DOI: 10.1074/JBC.M109014274