Magnesium in PDB 6vg6: Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*

All present enzymatic activity of Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*:
2.7.7.7;

The structure of Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*, PDB code: 6vg6 was solved by H.Jung, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.15 / 3.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.975, 97.761, 101.815, 90, 90, 90
R / Rfree (%)	25.4 / 30.2

The binding sites of Magnesium atom in the Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp* (pdb code 6vg6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*, PDB code: 6vg6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp* within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg102 b:71.7 occ:1.00 OE1 A:GLU106 2.0 59.5 1.0 O1A P:XG4101 2.1 68.6 1.0 OD1 A:ASP105 2.4 58.0 1.0 O5' P:DC13 2.5 99.1 1.0 OD2 A:ASP105 3.0 54.9 1.0 CG A:ASP105 3.1 52.6 1.0 CD A:GLU106 3.1 55.8 1.0 PA P:XG4101 3.1 83.4 1.0 C5' P:DC13 3.3 90.2 1.0 OD2 A:ASP7 3.4 66.5 1.0 OP1 P:DC13 3.5 87.4 1.0 P P:DC13 3.5 129.7 1.0 O2A P:XG4101 3.5 95.4 1.0 C3' P:DC13 3.6 89.7 1.0 O5' P:XG4101 3.6 77.5 1.0 C5' P:XG4101 3.9 75.7 1.0 OG A:SER103 3.9 48.6 1.0 OE2 A:GLU106 3.9 60.3 1.0 CG A:GLU106 3.9 49.8 1.0 C4' P:DC13 4.0 94.8 1.0 OP2 P:DC13 4.2 111.0 1.0 CG A:ASP7 4.3 57.2 1.0 C2' P:DC13 4.4 94.4 1.0 MG A:MG402 4.4 47.3 1.0 O3' P:DC13 4.5 79.5 1.0 CB A:ASP105 4.5 40.4 1.0 O1B P:XG4101 4.6 69.6 1.0 N3A P:XG4101 4.6 86.6 1.0 OD1 A:ASP7 4.7 59.9 1.0 CB A:GLU106 4.7 49.0 1.0 O3' P:DT12 4.8 90.5 1.0 O A:ASP105 4.9 48.4 1.0 C A:ASP105 5.0 41.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp* within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:47.3 occ:1.00 O A:PHE8 1.8 59.0 1.0 O1B P:XG4101 1.9 69.6 1.0 OD2 A:ASP105 1.9 54.9 1.0 OD1 A:ASP7 2.0 59.9 1.0 CG A:ASP7 2.9 57.2 1.0 C A:PHE8 3.0 48.0 1.0 CG A:ASP105 3.1 52.6 1.0 O1A P:XG4101 3.3 68.6 1.0 PB P:XG4101 3.3 78.5 1.0 N A:PHE8 3.4 46.7 1.0 OD2 A:ASP7 3.4 66.5 1.0 O2G P:XG4101 3.5 82.5 1.0 C A:ASP7 3.6 56.9 1.0 CA A:PHE8 3.7 43.8 1.0 CB A:ASP105 3.7 40.4 1.0 N A:ASP9 4.0 51.0 1.0 CB A:ASP7 4.0 50.8 1.0 O3B P:XG4101 4.1 79.5 1.0 OD1 A:ASP105 4.1 58.0 1.0 O A:ASP7 4.1 59.7 1.0 CA A:ASP7 4.1 50.3 1.0 O A:ASP105 4.2 48.4 1.0 PA P:XG4101 4.2 83.4 1.0 NZ A:LYS159 4.2 79.6 1.0 CB A:PHE8 4.2 41.3 1.0 N3A P:XG4101 4.3 86.6 1.0 CA A:ASP9 4.3 59.0 1.0 O2B P:XG4101 4.3 64.3 1.0 N A:TYR10 4.4 57.5 1.0 MG P:MG102 4.4 71.7 1.0 PG P:XG4101 4.5 105.8 1.0 C5' P:XG4101 4.5 75.7 1.0 C A:ASP9 4.6 55.5 1.0 N A:PHE11 4.7 47.8 1.0 CB A:PHE11 4.8 45.4 1.0 O5' P:XG4101 4.9 77.5 1.0 CA A:ASP105 4.9 37.1 1.0 C A:ASP105 4.9 41.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp* within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:67.9 occ:1.00 O1A D:XG4402 2.1 69.9 1.0 OE2 D:GLU106 2.1 66.9 1.0 OD1 D:ASP105 2.3 51.8 1.0 OD2 D:ASP7 2.9 61.3 1.0 CD D:GLU106 2.9 59.6 1.0 CG D:ASP105 3.1 54.1 1.0 C3' B:DC13 3.1 84.3 1.0 CG D:GLU106 3.2 56.8 1.0 O5' B:DC13 3.3 98.2 1.0 PA D:XG4402 3.3 88.5 1.0 OD2 D:ASP105 3.3 59.2 1.0 MG D:MG404 3.5 42.4 1.0 O3' B:DC13 3.6 81.2 1.0 CG D:ASP7 3.6 55.0 1.0 O2A D:XG4402 3.7 88.8 1.0 O D:ASP105 3.8 50.3 1.0 C5' B:DC13 3.8 92.1 1.0 OD1 D:ASP7 3.9 55.4 1.0 OE1 D:GLU106 4.0 54.2 1.0 C4' B:DC13 4.0 91.0 1.0 C2' B:DC13 4.0 88.6 1.0 O5' D:XG4402 4.1 75.6 1.0 C D:ASP105 4.2 46.1 1.0 C5' D:XG4402 4.2 69.9 1.0 CB D:GLU106 4.2 49.2 1.0 OG D:SER103 4.2 47.6 1.0 CB D:ASP105 4.4 50.5 1.0 P B:DC13 4.5 115.1 1.0 O1B D:XG4402 4.5 65.0 1.0 OP1 B:DC13 4.6 96.6 1.0 N3A D:XG4402 4.6 90.3 1.0 N D:GLU106 4.7 44.9 1.0 CA D:ASP105 4.8 44.3 1.0 CB D:ASP7 4.8 50.4 1.0 OP2 B:DC13 4.9 102.9 1.0 CA D:GLU106 4.9 45.3 1.0 N D:ASP105 5.0 44.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp*


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dgtp* within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:42.4 occ:1.00 OD2 D:ASP105 1.9 59.2 1.0 OD1 D:ASP7 2.0 55.4 1.0 O D:PHE8 2.1 51.5 1.0 O1B D:XG4402 2.4 65.0 1.0 CG D:ASP105 2.7 54.1 1.0 CG D:ASP7 2.9 55.0 1.0 O1A D:XG4402 2.9 69.9 1.0 C D:PHE8 3.1 46.2 1.0 N D:PHE8 3.3 49.5 1.0 OD1 D:ASP105 3.4 51.8 1.0 OD2 D:ASP7 3.4 61.3 1.0 MG D:MG403 3.5 67.9 1.0 CB D:ASP105 3.6 50.5 1.0 C D:ASP7 3.6 54.5 1.0 O D:ASP105 3.6 50.3 1.0 CA D:PHE8 3.7 42.1 1.0 PB D:XG4402 3.8 77.6 1.0 O2G D:XG4402 3.9 82.2 1.0 CB D:ASP7 4.0 50.4 1.0 CA D:ASP7 4.1 48.9 1.0 PA D:XG4402 4.1 88.5 1.0 CB D:PHE8 4.1 41.0 1.0 O D:ASP7 4.2 53.8 1.0 N D:ASP9 4.3 52.5 1.0 N3A D:XG4402 4.4 90.3 1.0 C D:ASP105 4.5 46.1 1.0 C5' D:XG4402 4.6 69.9 1.0 CA D:ASP9 4.7 59.0 1.0 N D:TYR10 4.7 52.2 1.0 CA D:ASP105 4.7 44.3 1.0 NZ D:LYS159 4.7 61.8 1.0 N D:PHE11 4.7 50.2 1.0 CB D:PHE11 4.7 45.6 1.0 O2B D:XG4402 4.8 68.8 1.0 O3B D:XG4402 4.8 85.5 1.0 O5' D:XG4402 4.8 75.6 1.0 C D:ASP9 4.9 52.1 1.0 PG D:XG4402 5.0 105.6 1.0

H.Jung, S.Lee. Promutagenic Bypass of 7,8-Dihydro-8-Oxoadenine By Translesion Synthesis Dna Polymerase DPO4. Biochem.J. V. 477 2859 2020.
ISSN: ESSN 1470-8728
PubMed: 32686822
DOI: 10.1042/BCJ20200449