Magnesium in PDB 2w8l: Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation

All present enzymatic activity of Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation:
2.7.7.7;

The structure of Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation, PDB code: 2w8l was solved by R.L.Eoff, H.Zhang, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.25 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.919, 103.832, 52.493, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 28.2

The binding sites of Magnesium atom in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation (pdb code 2w8l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation, PDB code: 2w8l:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1344 b:39.9 occ:1.00 O A:ALA181 2.3 83.4 1.0 O A:HOH2016 2.5 32.6 1.0 O P:HOH2010 2.5 51.5 1.0 O A:ILE186 2.6 73.3 1.0 C A:ALA181 3.5 82.9 1.0 C A:ILE186 3.5 72.5 1.0 CA A:GLY187 4.1 76.0 1.0 N A:GLY187 4.2 74.0 1.0 OP2 P:DC13 4.2 70.3 1.0 CA A:ALA181 4.2 83.7 1.0 OP1 P:DC13 4.4 67.0 1.0 O A:VAL183 4.5 74.5 1.0 C A:GLY187 4.5 76.5 1.0 CA A:ILE186 4.5 71.6 1.0 CB A:ALA181 4.5 83.2 1.0 N A:ASP182 4.5 82.2 1.0 O A:GLY187 4.6 76.9 1.0 CB A:ILE186 4.6 70.3 1.0 CA A:ASP182 4.7 80.5 1.0 N A:ILE186 4.8 70.8 1.0 P P:DC13 4.9 69.3 1.0

Magnesium binding site 2 out of 3 in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1345 b:53.6 occ:1.00 O P:HOH2011 2.3 62.9 1.0 O2A A:DGT1343 2.5 74.5 1.0 OD1 A:ASP105 2.6 66.5 1.0 OD2 A:ASP7 2.8 58.2 1.0 OE1 A:GLU106 2.8 75.4 1.0 O A:HOH2008 2.9 64.7 1.0 OD2 A:ASP105 3.0 63.7 1.0 CG A:ASP105 3.2 64.4 1.0 OD1 A:ASP7 3.3 63.0 1.0 CG A:ASP7 3.4 57.6 1.0 O5' P:DOC14 3.5 91.0 0.6 PA A:DGT1343 3.5 75.7 1.0 MG A:MG1346 3.7 40.9 1.0 O1A A:DGT1343 3.8 75.4 1.0 CD A:GLU106 3.9 75.5 1.0 C4' P:DOC14 4.0 91.5 0.0 O5' A:DGT1343 4.1 75.3 1.0 C5' P:DOC14 4.3 96.3 0.9 CG A:GLU106 4.3 71.3 1.0 C5' A:DGT1343 4.4 75.6 1.0 C3' P:DOC14 4.4 92.4 1.0 CB A:GLU106 4.4 69.9 1.0 O A:ASP105 4.4 65.7 1.0 OG A:SER103 4.4 78.9 1.0 CB A:ASP105 4.7 64.0 1.0 C A:ASP105 4.7 66.3 1.0 O3G A:DGT1343 4.8 77.3 1.0 CB A:ASP7 4.9 56.4 1.0 P P:DOC14 4.9 93.0 0.6 O3A A:DGT1343 5.0 76.6 1.0 OE2 A:GLU106 5.0 78.9 1.0

Magnesium binding site 3 out of 3 in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Anti Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1346 b:40.9 occ:1.00 O A:PHE8 2.3 54.5 1.0 O2A A:DGT1343 2.4 74.5 1.0 OD2 A:ASP105 2.6 63.7 1.0 O3G A:DGT1343 2.6 77.3 1.0 O1B A:DGT1343 2.6 78.7 1.0 OD2 A:ASP7 2.7 58.2 1.0 CG A:ASP7 3.1 57.6 1.0 NZ A:LYS159 3.1 90.2 1.0 OD1 A:ASP7 3.2 63.0 1.0 C A:PHE8 3.4 53.7 1.0 PG A:DGT1343 3.6 76.8 1.0 MG A:MG1345 3.7 53.6 1.0 PA A:DGT1343 3.7 75.7 1.0 CG A:ASP105 3.7 64.4 1.0 O1G A:DGT1343 3.8 77.4 1.0 PB A:DGT1343 3.8 76.6 1.0 O3A A:DGT1343 4.0 76.6 1.0 N A:PHE8 4.1 52.6 1.0 CE A:LYS159 4.2 88.2 0.5 C A:ASP7 4.2 54.9 1.0 CA A:ASP9 4.2 58.9 1.0 CB A:ASP7 4.2 56.4 1.0 N A:ASP9 4.2 55.6 1.0 O3B A:DGT1343 4.2 77.6 1.0 N A:TYR10 4.3 60.0 1.0 CA A:PHE8 4.3 52.0 1.0 O A:ASP7 4.4 58.1 1.0 OD1 A:ASP105 4.5 66.5 1.0 C A:ASP9 4.5 59.2 1.0 O A:ASP105 4.7 65.7 1.0 CA A:ASP7 4.7 55.9 1.0 C5' A:DGT1343 4.7 75.6 1.0 O5' A:DGT1343 4.7 75.3 1.0 CB A:ASP105 4.7 64.0 1.0 O1A A:DGT1343 4.9 75.4 1.0 N A:PHE11 5.0 57.0 1.0

H.Zhang, R.L.Eoff, I.D.Kozekov, C.J.Rizzo, M.Egli, F.P.Guengerich. Versatility of Y-Family Sulfolobus Solfataricus Dna Polymerase DPO4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts. J.Biol.Chem. V. 284 3563 2009.
ISSN: ISSN 0021-9258
PubMed: 19059910
DOI: 10.1074/JBC.M807778200