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

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

The structure of Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dttp*, PDB code: 6vgm 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)	42.23 / 2.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.835, 97.459, 101.237, 90, 90.05, 90
R / Rfree (%)	23 / 28

The binding sites of Magnesium atom in the Crystal Structure of DPO4 with 8-Oxoadenine (Oxoa) and Dttp* (pdb code 6vgm). 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 Dttp*, PDB code: 6vgm:
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 Dttp*


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 Dttp* within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:47.2 occ:1.00 O2B A:1FZ401 1.9 49.8 1.0 O A:PHE8 2.0 55.1 1.0 OD2 A:ASP105 2.1 56.0 1.0 O1G A:1FZ401 2.1 57.6 1.0 OD1 A:ASP7 2.2 57.3 1.0 O1A A:1FZ401 2.4 58.8 1.0 CG A:ASP7 3.0 54.6 1.0 PB A:1FZ401 3.0 42.9 1.0 PA A:1FZ401 3.0 49.9 1.0 OD2 A:ASP7 3.2 58.0 1.0 O5' A:1FZ401 3.2 46.7 1.0 C A:PHE8 3.2 56.1 1.0 CG A:ASP105 3.3 55.6 1.0 PG A:1FZ401 3.4 51.1 1.0 N3A A:1FZ401 3.5 57.5 1.0 O3B A:1FZ401 3.6 52.7 1.0 N A:PHE8 3.8 64.8 1.0 MG A:MG403 3.9 49.8 1.0 OD1 A:ASP105 4.0 55.4 1.0 CA A:PHE8 4.0 59.3 1.0 NZ A:LYS159 4.1 62.8 1.0 C A:ASP7 4.2 65.2 1.0 O3G A:1FZ401 4.2 62.9 1.0 N A:ASP9 4.2 61.9 1.0 CB A:ASP105 4.3 54.3 1.0 CB A:ASP7 4.3 52.9 1.0 CA A:ASP9 4.4 65.7 1.0 O1B A:1FZ401 4.4 44.2 1.0 N A:TYR10 4.5 46.4 1.0 CE A:LYS159 4.5 59.1 1.0 O A:ASP7 4.5 61.1 1.0 O2G A:1FZ401 4.6 53.4 1.0 O2A A:1FZ401 4.6 49.2 1.0 C5' A:1FZ401 4.6 44.2 1.0 CB A:PHE8 4.6 56.9 1.0 N A:PHE11 4.7 58.0 1.0 C A:ASP9 4.7 54.9 1.0 CA A:ASP7 4.7 59.0 1.0 CB A:PHE11 4.8 58.8 1.0 O A:ASP105 4.9 51.7 1.0

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


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 Dttp* within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:49.8 occ:1.00 O1A A:1FZ401 2.2 58.8 1.0 OD2 A:ASP7 2.2 58.0 1.0 OE2 A:GLU106 2.4 77.7 1.0 CD A:GLU106 2.8 72.7 1.0 OD1 A:ASP105 2.9 55.4 1.0 PA A:1FZ401 3.0 49.9 1.0 C3' P:DC13 3.2 54.2 1.0 O2A A:1FZ401 3.2 49.2 1.0 CG A:ASP7 3.3 54.6 1.0 CG A:GLU106 3.4 63.1 1.0 OD2 A:ASP105 3.4 56.0 1.0 OE1 A:GLU106 3.4 78.0 1.0 O5' A:1FZ401 3.4 46.7 1.0 CG A:ASP105 3.5 55.6 1.0 O5' P:DC13 3.6 80.4 1.0 O3' P:DC13 3.7 56.7 1.0 OD1 A:ASP7 3.8 57.3 1.0 MG A:MG402 3.9 47.2 1.0 C5' P:DC13 3.9 61.0 1.0 C4' P:DC13 4.1 56.7 1.0 C5' A:1FZ401 4.2 44.2 1.0 C2' P:DC13 4.2 58.9 1.0 OP1 P:DC13 4.5 82.0 1.0 CB A:ASP7 4.5 52.9 1.0 N3A A:1FZ401 4.6 57.5 1.0 OG A:SER103 4.6 60.1 1.0 O1G A:1FZ401 4.7 57.6 1.0 P P:DC13 4.7 91.5 1.0 CB A:GLU106 4.8 56.0 1.0

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


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 Dttp* within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:48.9 occ:1.00 OE1 D:GLU106 2.0 73.0 1.0 O3' B:DC13 2.1 59.7 1.0 O1A D:1FZ401 2.1 46.4 1.0 OD1 D:ASP7 2.7 52.6 1.0 OD1 D:ASP105 2.7 54.2 1.0 CD D:GLU106 2.8 69.5 1.0 OD2 D:ASP7 2.9 62.4 1.0 CG D:GLU106 2.9 63.3 1.0 CG D:ASP7 3.1 56.2 1.0 OD2 D:ASP105 3.1 53.5 1.0 PA D:1FZ401 3.1 43.4 1.0 CG D:ASP105 3.3 53.8 1.0 C3' B:DC13 3.3 55.0 1.0 O2A D:1FZ401 3.5 52.0 1.0 MG D:MG402 3.6 44.3 1.0 O5' D:1FZ401 3.8 44.6 1.0 O5' B:DC13 4.0 76.4 1.0 OE2 D:GLU106 4.0 72.5 1.0 C4' B:DC13 4.1 52.0 1.0 C5' D:1FZ401 4.2 43.6 1.0 C5' B:DC13 4.3 61.6 1.0 CB D:GLU106 4.4 57.1 1.0 CB D:ASP7 4.5 54.9 1.0 C2' B:DC13 4.5 50.5 1.0 O1G D:1FZ401 4.5 57.8 1.0 OG D:SER103 4.6 57.7 1.0 N3A D:1FZ401 4.6 58.7 1.0 O D:ASP105 4.7 46.6 1.0 CB D:ASP105 4.7 56.0 1.0 O2B D:1FZ401 4.8 46.1 1.0 C D:ASP105 4.9 52.1 1.0

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


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 Dttp* within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:44.3 occ:1.00 O D:PHE8 2.0 55.5 1.0 O2B D:1FZ401 2.1 46.1 1.0 O1G D:1FZ401 2.1 57.8 1.0 OD2 D:ASP105 2.2 53.5 1.0 O1A D:1FZ401 2.3 46.4 1.0 OD1 D:ASP7 2.7 52.6 1.0 OD2 D:ASP7 2.9 62.4 1.0 CG D:ASP7 3.0 56.2 1.0 PB D:1FZ401 3.1 40.0 1.0 C D:PHE8 3.2 57.6 1.0 PA D:1FZ401 3.4 43.4 1.0 PG D:1FZ401 3.4 51.6 1.0 CG D:ASP105 3.5 53.8 1.0 NZ D:LYS159 3.5 54.6 1.0 MG B:MG101 3.6 48.9 1.0 O3B D:1FZ401 3.7 55.1 1.0 N3A D:1FZ401 3.7 58.7 1.0 N D:PHE8 3.8 57.8 1.0 CA D:PHE8 4.0 54.8 1.0 C D:ASP7 4.1 60.3 1.0 C5' D:1FZ401 4.2 43.6 1.0 CB D:ASP7 4.2 54.9 1.0 OD1 D:ASP105 4.2 54.2 1.0 N D:ASP9 4.2 59.2 1.0 O3G D:1FZ401 4.2 60.9 1.0 O5' D:1FZ401 4.3 44.6 1.0 CE D:LYS159 4.4 60.8 1.0 N D:TYR10 4.4 46.5 1.0 CA D:ASP9 4.4 66.4 1.0 CB D:ASP105 4.5 56.0 1.0 O2G D:1FZ401 4.5 56.9 1.0 CB D:PHE8 4.6 52.5 1.0 O1B D:1FZ401 4.6 43.8 1.0 O D:ASP7 4.6 62.6 1.0 CA D:ASP7 4.6 57.9 1.0 C D:ASP9 4.6 55.1 1.0 O2A D:1FZ401 4.7 52.0 1.0 N D:PHE11 4.8 59.4 1.0 O D:ASP105 4.9 46.6 1.0 CB D:PHE11 5.0 51.9 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