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

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

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mg-8OXODGMP, PDB code: 6ipe 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.889, 68.402, 110.512, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.4

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine 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 Adenine and Mg-8OXODGMP (pdb code 6ipe). 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 Adenine and Mg-8OXODGMP, PDB code: 6ipe:
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 Adenine 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 Adenine and Mg-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:25.3 occ:1.00 O4 A:PO4504 2.0 23.9 0.8 OD1 A:ASP330 2.2 23.2 1.0 O A:HOH718 2.3 21.5 1.0 OP1 P:8OG5 2.3 8.6 1.0 O A:HOH627 2.4 44.7 1.0 OD2 A:ASP332 2.4 12.8 1.0 P A:PO4504 3.3 26.4 0.8 CG A:ASP330 3.3 24.2 1.0 CG A:ASP332 3.4 10.9 1.0 O1 A:PO4504 3.5 26.9 0.8 O A:HOH616 3.6 31.6 1.0 MG A:MG502 3.6 9.9 1.0 P P:8OG5 3.6 8.7 1.0 OD1 A:ASP332 3.7 11.5 1.0 OD2 A:ASP330 3.8 26.4 1.0 O5' P:8OG5 4.0 7.7 1.0 O3 A:PO4504 4.1 27.1 0.8 N A:GLY320 4.2 6.8 1.0 O A:ASP330 4.2 17.2 1.0 C5' P:8OG5 4.3 7.7 1.0 CA A:GLY319 4.3 6.8 1.0 O A:HOH614 4.3 10.7 1.0 OP2 P:8OG5 4.3 8.7 1.0 O2 A:PO4504 4.4 21.2 0.8 C A:ASP330 4.5 17.0 1.0 ND1 A:HIS329 4.5 21.4 0.3 CE1 A:HIS329 4.6 21.2 0.3 CB A:ASP330 4.6 21.9 1.0 CB A:ASP332 4.6 9.8 1.0 O A:HOH641 4.7 48.8 1.0 O A:HOH642 4.7 19.4 1.0 C A:GLY319 4.8 6.7 1.0 O3' P:DA4 4.8 8.4 1.0 N A:VAL331 4.9 14.9 1.0 CA A:ASP330 4.9 19.6 1.0 N A:ASP332 4.9 9.5 1.0 N A:ASP330 4.9 19.6 1.0

Magnesium binding site 2 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine 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 Adenine and Mg-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:9.9 occ:1.00 OD2 A:ASP330 1.8 26.4 1.0 OD1 A:ASP332 2.0 11.5 1.0 OP1 P:8OG5 2.1 8.6 1.0 OD2 A:ASP418 2.2 10.4 1.0 O A:HOH642 2.7 19.4 1.0 CG A:ASP330 2.8 24.2 1.0 O3' P:DA4 3.0 8.4 1.0 CG A:ASP332 3.0 10.9 1.0 P P:8OG5 3.0 8.7 1.0 OD1 A:ASP330 3.1 23.2 1.0 CG A:ASP418 3.2 9.3 1.0 OD2 A:ASP332 3.3 12.8 1.0 MG A:MG501 3.6 25.3 1.0 CB A:ASP418 3.8 8.7 1.0 OP2 P:8OG5 3.9 8.7 1.0 OD1 A:ASP418 4.1 9.8 1.0 CB A:ASP330 4.1 21.9 1.0 C3' P:DA4 4.1 8.4 1.0 C5' P:DA4 4.2 8.5 1.0 C4' P:DA4 4.2 8.5 1.0 O5' P:8OG5 4.3 7.7 1.0 CB A:ASP332 4.4 9.8 1.0 O A:VAL331 4.4 9.9 1.0 NH2 A:ARG416 4.5 8.9 1.0 CZ3 A:TRP434 4.6 7.1 1.0 C5' P:8OG5 4.6 7.7 1.0 N A:ASP418 4.7 7.8 1.0 CE1 A:HIS329 4.7 21.2 0.3 C A:VAL331 4.8 11.2 1.0 CA A:ASP332 4.9 9.4 1.0 CA A:ASP418 4.9 8.2 1.0 O A:HOH627 4.9 44.7 1.0 N A:ASP332 5.0 9.5 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