Magnesium in PDB 6ipg: Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP

All present enzymatic activity of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP, PDB code: 6ipg was solved by Y.K.Chang, W.J.Wu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.884, 68.403, 110.481, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.1

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP (pdb code 6ipg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP, PDB code: 6ipg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.8 occ:0.70 OD2 A:ASP330 0.6 30.6 0.3 CG A:ASP330 1.9 30.4 0.3 O3 A:PO4504 2.0 32.7 0.7 OD1 A:ASP330 2.3 31.4 0.7 OP1 P:8OG5 2.3 23.5 1.0 O A:HOH602 2.4 28.8 0.7 OD2 A:ASP332 2.5 24.9 1.0 OD1 A:ASP330 2.6 33.1 0.3 CB A:ASP330 3.0 30.9 0.3 P A:PO4504 3.3 34.4 0.7 O1 A:PO4504 3.4 36.9 0.7 CG A:ASP332 3.4 21.2 1.0 CG A:ASP330 3.5 31.7 0.7 O A:HOH616 3.5 55.5 1.0 P P:8OG5 3.5 21.9 1.0 MG A:MG502 3.6 23.7 1.0 OD1 A:ASP332 3.7 22.4 1.0 O5' P:8OG5 3.7 20.8 1.0 C5' P:8OG5 3.9 19.8 1.0 O4 A:PO4504 4.1 37.8 0.7 O A:ASP330 4.2 28.0 0.7 OD2 A:ASP330 4.2 31.1 0.7 OP2 P:8OG5 4.3 22.4 1.0 CA A:GLY319 4.3 16.7 1.0 C A:ASP330 4.3 27.7 0.3 O A:ASP330 4.3 27.5 0.3 N A:GLY320 4.3 16.4 1.0 CA A:ASP330 4.3 29.7 0.3 C A:ASP330 4.3 26.9 0.7 O2 A:PO4504 4.4 28.5 0.7 O A:HOH879 4.4 47.1 1.0 O A:HOH644 4.4 22.9 1.0 CB A:ASP330 4.4 30.4 0.7 O P:HOH103 4.6 30.2 1.0 CB A:ASP332 4.6 18.4 1.0 O3' P:DA4 4.7 20.8 1.0 CA A:ASP330 4.8 28.7 0.7 N A:VAL331 4.9 26.6 1.0 C A:GLY319 4.9 16.4 1.0 N A:ASP332 4.9 17.9 1.0

Magnesium binding site 2 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mg-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.7 occ:1.00 OD2 A:ASP418 2.1 20.9 1.0 OP1 P:8OG5 2.1 23.5 1.0 OD1 A:ASP332 2.2 22.4 1.0 OD2 A:ASP330 2.2 31.1 0.7 OD1 A:ASP330 2.3 33.1 0.3 O P:HOH103 2.5 30.2 1.0 CG A:ASP330 2.6 31.7 0.7 OD1 A:ASP330 2.7 31.4 0.7 CG A:ASP418 3.1 18.9 1.0 P P:8OG5 3.1 21.9 1.0 CG A:ASP332 3.1 21.2 1.0 O3' P:DA4 3.2 20.8 1.0 CG A:ASP330 3.2 30.4 0.3 OD2 A:ASP332 3.3 24.9 1.0 MG A:MG501 3.6 30.8 0.7 OD2 A:ASP330 3.6 30.6 0.3 CB A:ASP418 3.8 17.8 1.0 OP2 P:8OG5 3.9 22.4 1.0 OD1 A:ASP418 3.9 19.8 1.0 CB A:ASP330 3.9 30.4 0.7 C5' P:DA4 4.1 20.1 1.0 C3' P:DA4 4.3 19.8 1.0 C4' P:DA4 4.3 19.6 1.0 NH2 A:ARG416 4.4 18.6 1.0 O5' P:8OG5 4.4 20.8 1.0 O A:VAL331 4.4 18.6 1.0 CB A:ASP330 4.4 30.9 0.3 O A:HOH879 4.4 47.1 1.0 CB A:ASP332 4.5 18.4 1.0 N A:ASP418 4.6 16.7 1.0 OP1 P:DA4 4.7 19.9 1.0 C5' P:8OG5 4.8 19.8 1.0 C A:VAL331 4.8 19.4 1.0 CZ3 A:TRP434 4.8 19.5 1.0 CA A:ASP418 4.8 17.0 1.0 CA A:ASP330 4.9 29.7 0.3 N A:VAL331 4.9 26.6 1.0 CA A:ASP332 5.0 17.8 1.0 O5' P:DA4 5.0 19.7 1.0

Y.K.Chang, Y.P.Huang, X.X.Liu, T.P.Ko, Y.Bessho, Y.Kawano, M.Maestre-Reyna, W.J.Wu, M.D.Tsai. Human Dna Polymerase Mu Can Use A Noncanonical Mechanism For Multiple MN2+-Mediated Functions. J.Am.Chem.Soc. V. 141 8489 2019.
ISSN: ESSN 1520-5126
PubMed: 31067051
DOI: 10.1021/JACS.9B01741