Magnesium in PDB 6vkp: Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg

All present enzymatic activity of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg:
2.7.7.7;

The structure of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg, PDB code: 6vkp 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)	49.55 / 2.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.098, 103.69, 99.105, 90, 89.94, 90
R / Rfree (%)	21 / 26

The binding sites of Magnesium atom in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg (pdb code 6vkp). 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 Extension Past 8-Oxoadenine (Oxoa) and Dg, PDB code: 6vkp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:37.3 occ:1.00 OD1 A:ASP105 2.0 44.3 1.0 O P:HOH103 2.1 42.9 1.0 O A:HOH507 2.2 42.9 1.0 OD2 A:ASP7 2.2 46.8 1.0 OE2 A:GLU106 2.5 63.8 1.0 O1A A:DZ4403 2.5 36.0 1.0 CG A:GLU106 2.7 50.7 1.0 CD A:GLU106 3.0 50.9 1.0 CG A:ASP105 3.0 38.3 1.0 CG A:ASP7 3.3 49.1 1.0 OG A:SER103 3.4 39.4 1.0 PA A:DZ4403 3.4 30.7 1.0 OD2 A:ASP105 3.4 41.2 1.0 O2A A:DZ4403 3.7 35.3 1.0 OP2 P:DG13 3.7 62.8 1.0 O5' A:DZ4403 3.8 34.0 1.0 OD1 A:ASP7 3.9 46.8 1.0 MG A:MG402 3.9 36.1 1.0 OE1 A:GLU106 4.2 58.9 1.0 C5' A:DZ4403 4.2 23.4 1.0 CB A:GLU106 4.2 48.0 1.0 O A:HOH510 4.4 42.9 1.0 CB A:ASP105 4.4 36.5 1.0 CB A:SER103 4.4 39.4 1.0 C A:ASP105 4.5 42.0 1.0 CB A:ASP7 4.5 46.6 1.0 O A:ASP105 4.6 37.8 1.0 N A:GLU106 4.6 41.5 1.0 CA A:ASP105 4.8 42.3 1.0 O2G A:DZ4403 4.8 44.6 1.0 CA A:GLU106 4.9 39.2 1.0 O P:HOH101 4.9 42.9 1.0 N A:ASP105 4.9 41.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:36.1 occ:1.00 O2G A:DZ4403 2.0 44.6 1.0 OD1 A:ASP7 2.1 46.8 1.0 O1A A:DZ4403 2.1 36.0 1.0 O A:PHE8 2.1 43.1 1.0 OD2 A:ASP105 2.2 41.2 1.0 O2B A:DZ4403 2.2 36.1 1.0 CG A:ASP7 3.0 49.1 1.0 PG A:DZ4403 3.2 42.5 1.0 PB A:DZ4403 3.2 37.2 1.0 CG A:ASP105 3.3 38.3 1.0 PA A:DZ4403 3.3 30.7 1.0 C A:PHE8 3.4 41.0 1.0 OD2 A:ASP7 3.4 46.8 1.0 O3B A:DZ4403 3.5 38.8 1.0 N3A A:DZ4403 3.6 31.7 1.0 O1G A:DZ4403 3.6 42.3 1.0 OD1 A:ASP105 3.7 44.3 1.0 O A:HOH510 3.7 42.9 1.0 NZ A:LYS159 3.9 66.8 1.0 MG A:MG401 3.9 37.3 1.0 N A:PHE8 3.9 45.5 1.0 C5' A:DZ4403 4.0 23.4 1.0 O5' A:DZ4403 4.1 34.0 1.0 CA A:PHE8 4.2 40.0 1.0 C A:ASP7 4.2 43.9 1.0 CE A:LYS159 4.3 50.7 1.0 N A:ASP9 4.3 44.1 1.0 O A:HOH507 4.4 42.9 1.0 CB A:ASP7 4.4 46.6 1.0 N A:TYR10 4.4 34.8 1.0 CA A:ASP9 4.4 44.7 1.0 O2A A:DZ4403 4.5 35.3 1.0 O3G A:DZ4403 4.5 43.4 1.0 O A:ASP7 4.5 42.0 1.0 O1B A:DZ4403 4.5 34.3 1.0 CB A:ASP105 4.6 36.5 1.0 C A:ASP9 4.6 38.3 1.0 N A:PHE11 4.8 33.0 1.0 CA A:ASP7 4.8 42.5 1.0 CB A:PHE8 4.8 40.5 1.0 CB A:PHE11 4.9 33.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:39.8 occ:1.00 OD1 D:ASP105 2.1 56.4 1.0 O B:HOH105 2.2 46.7 1.0 OE2 D:GLU106 2.2 62.5 1.0 OD2 D:ASP7 2.2 46.0 1.0 O1A D:DZ4403 2.4 35.7 1.0 O D:HOH505 2.7 42.9 1.0 CG D:ASP105 2.9 42.8 1.0 CD D:GLU106 3.0 51.4 1.0 OD2 D:ASP105 3.1 42.1 1.0 CG D:GLU106 3.1 50.9 1.0 PA D:DZ4403 3.2 39.0 1.0 CG D:ASP7 3.3 49.0 1.0 O2A D:DZ4403 3.4 38.9 1.0 O5' D:DZ4403 3.6 34.0 1.0 OP2 B:DG13 3.7 65.3 1.0 OG D:SER103 3.7 43.5 1.0 OD1 D:ASP7 3.7 46.7 1.0 MG D:MG402 3.8 37.0 1.0 O D:HOH504 3.8 42.9 1.0 C5' D:DZ4403 3.9 24.0 1.0 OE1 D:GLU106 4.2 58.8 1.0 CB D:ASP105 4.4 37.5 1.0 CB D:GLU106 4.5 49.5 1.0 O B:HOH102 4.6 45.4 1.0 CB D:ASP7 4.6 47.7 1.0 CB D:SER103 4.6 45.3 1.0 C D:ASP105 4.6 41.5 1.0 O1G D:DZ4403 4.6 42.0 1.0 O D:ASP105 4.8 41.5 1.0 N D:GLU106 4.8 45.9 1.0 N3A D:DZ4403 4.8 31.4 1.0 O2B D:DZ4403 4.9 36.2 1.0 CA D:ASP105 4.9 42.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Extension Past 8-Oxoadenine (Oxoa) and Dg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:37.0 occ:1.00 O D:PHE8 2.1 48.3 1.0 O1G D:DZ4403 2.1 42.0 1.0 OD1 D:ASP7 2.1 46.7 1.0 O1A D:DZ4403 2.1 35.7 1.0 O2B D:DZ4403 2.2 36.2 1.0 OD2 D:ASP105 2.3 42.1 1.0 CG D:ASP7 3.1 49.0 1.0 PG D:DZ4403 3.2 85.5 1.0 PB D:DZ4403 3.2 30.3 1.0 C D:PHE8 3.3 44.8 1.0 O D:HOH504 3.3 42.9 1.0 PA D:DZ4403 3.3 39.0 1.0 OD2 D:ASP7 3.4 46.0 1.0 O3G D:DZ4403 3.4 42.5 1.0 CG D:ASP105 3.5 42.8 1.0 O3B D:DZ4403 3.6 49.9 1.0 N3A D:DZ4403 3.7 31.4 1.0 MG D:MG401 3.8 39.8 1.0 N D:PHE8 3.9 42.9 1.0 C5' D:DZ4403 4.0 24.0 1.0 OD1 D:ASP105 4.1 56.4 1.0 CA D:PHE8 4.1 43.9 1.0 O5' D:DZ4403 4.2 34.0 1.0 NZ D:LYS159 4.2 70.4 1.0 CE D:LYS159 4.2 51.1 1.0 C D:ASP7 4.2 45.5 1.0 N D:ASP9 4.2 45.2 1.0 CA D:ASP9 4.3 48.7 1.0 CB D:ASP7 4.4 47.7 1.0 N D:TYR10 4.4 40.9 1.0 O2G D:DZ4403 4.5 41.5 1.0 O2A D:DZ4403 4.5 38.9 1.0 O D:HOH505 4.5 42.9 1.0 O D:ASP7 4.5 44.4 1.0 O1B D:DZ4403 4.6 39.5 1.0 CB D:ASP105 4.6 37.5 1.0 C D:ASP9 4.6 44.6 1.0 CB D:PHE8 4.8 40.7 1.0 CA D:ASP7 4.8 44.3 1.0 N D:PHE11 4.8 40.9 1.0 CB D:PHE11 4.9 35.8 1.0

H.Jung, S.Lee. Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg To Be Published.