Magnesium in PDB 2w8k: Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Syn Orientation

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

The structure of Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Syn Orientation, PDB code: 2w8k 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)	19.97 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.040, 103.910, 52.320, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.2

The binding sites of Magnesium atom in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Syn Orientation (pdb code 2w8k). 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 Syn Orientation, PDB code: 2w8k:
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 Syn 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 Syn Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1343 b:69.9 occ:1.00 OD2 A:ASP7 2.7 72.5 1.0 C5' P:DOC14 2.8 0.7 1.0 O5' P:DOC14 3.0 0.6 1.0 O2A A:DGT1342 3.1 0.6 1.0 OE1 A:GLU106 3.3 85.3 1.0 OE2 A:GLU106 3.5 87.5 1.0 OP1 P:DOC14 3.6 0.8 1.0 CD A:GLU106 3.7 85.3 1.0 OD1 A:ASP105 3.7 86.5 1.0 C4' P:DOC14 3.8 0.6 1.0 O1A A:DGT1342 3.8 0.2 1.0 P P:DOC14 3.9 0.8 1.0 OD2 A:ASP105 3.9 86.8 1.0 CG A:ASP7 4.0 72.7 1.0 C3' P:DOC14 4.0 0.3 1.0 PA A:DGT1342 4.0 0.6 1.0 CG A:ASP105 4.1 85.6 1.0 MG A:MG1344 4.6 42.6 1.0 O3' P:DC13 4.7 0.5 1.0 OD1 A:ASP7 4.7 76.2 1.0 O5' A:DGT1342 4.9 0.0 1.0 CG A:GLU106 4.9 83.0 1.0 CB A:ASP7 5.0 71.1 1.0 CZ A:PHE5 5.0 68.5 1.0

Magnesium binding site 2 out of 3 in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Syn 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 Syn Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1344 b:42.6 occ:1.00 OD1 A:ASP7 2.2 76.2 1.0 O2A A:DGT1342 2.2 0.6 1.0 O A:PHE8 2.3 65.9 1.0 O1B A:DGT1342 2.4 0.7 1.0 OD1 A:ASP105 2.9 86.5 1.0 CG A:ASP7 2.9 72.7 1.0 OD2 A:ASP7 3.0 72.5 1.0 CG A:ASP105 3.3 85.6 1.0 CB A:ASP105 3.3 83.6 1.0 PA A:DGT1342 3.3 0.6 1.0 C A:PHE8 3.4 66.8 1.0 O1G A:DGT1342 3.4 0.8 1.0 PB A:DGT1342 3.5 0.1 1.0 N A:PHE8 3.5 67.9 1.0 O3A A:DGT1342 3.7 0.9 1.0 C5' A:DGT1342 3.9 0.5 1.0 CA A:PHE8 4.0 66.3 1.0 O3B A:DGT1342 4.0 0.9 1.0 O A:ASP105 4.0 80.0 1.0 O5' A:DGT1342 4.1 0.0 1.0 C A:ASP7 4.2 69.6 1.0 OD2 A:ASP105 4.2 86.8 1.0 CB A:ASP7 4.3 71.1 1.0 PG A:DGT1342 4.4 0.4 1.0 N A:ASP9 4.4 68.5 1.0 CB A:PHE8 4.5 64.2 1.0 CB A:PHE11 4.5 65.8 1.0 CA A:ASP7 4.6 69.7 1.0 MG A:MG1343 4.6 69.9 1.0 CA A:ASP105 4.6 82.3 1.0 N A:PHE11 4.7 70.5 1.0 O1A A:DGT1342 4.7 0.2 1.0 C A:ASP105 4.7 80.9 1.0 CA A:ASP9 4.7 70.9 1.0 N A:TYR10 4.7 73.1 1.0 C A:ASP9 4.8 72.2 1.0 O2B A:DGT1342 4.9 0.7 1.0 O3G A:DGT1342 5.0 0.0 1.0

Magnesium binding site 3 out of 3 in the Y-Family Dna Polymerase DPO4 Bypassing N2-Naphthyl-Guanine Adduct in Syn 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 Syn Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1345 b:46.3 occ:1.00 O A:HOH2038 2.4 44.3 1.0 O A:ALA181 2.5 87.0 1.0 O A:HOH2040 2.7 43.6 1.0 O A:ILE186 2.9 78.2 1.0 O A:VAL183 3.1 77.3 1.0 C A:ILE186 3.3 78.6 1.0 C A:ALA181 3.5 87.7 1.0 OP2 P:DC13 3.6 84.2 1.0 O P:HOH2004 3.8 70.6 1.0 N A:GLY187 4.0 79.8 1.0 CA A:ILE186 4.0 77.8 1.0 OP1 P:DC13 4.0 85.3 1.0 CB A:ILE186 4.0 77.7 1.0 N A:ILE186 4.1 76.6 1.0 N A:VAL183 4.1 81.5 1.0 C A:VAL183 4.2 78.0 1.0 CA A:ALA181 4.2 88.3 1.0 P P:DC13 4.3 85.4 1.0 CA A:GLY187 4.3 80.3 1.0 N A:ASP182 4.4 86.5 1.0 CG2 A:ILE186 4.5 78.3 1.0 CA A:ASP182 4.6 85.0 1.0 C A:ASP182 4.7 83.7 1.0 CB A:ALA181 4.8 88.7 1.0 CA A:VAL183 4.9 78.7 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