Manganese in PDB 6ipd: Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP

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

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP, PDB code: 6ipd 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 (°)	59.680, 68.671, 109.576, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.8

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

Sodium

(Na)

2 atoms

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

Manganese binding site 1 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:6.6 occ:1.00 OD2 A:ASP330 2.1 10.1 1.0 OD2 A:ASP332 2.1 6.2 1.0 O5 A:OXD505 2.2 8.8 1.0 O A:HOH762 2.2 7.9 1.0 OP1 P:8OG5 2.2 7.7 1.0 O6 A:OXD505 2.3 11.2 1.0 CG A:ASP330 3.0 10.4 1.0 C1 A:OXD505 3.0 9.7 1.0 C2 A:OXD505 3.0 11.3 1.0 CG A:ASP332 3.1 6.3 1.0 OD1 A:ASP330 3.2 11.3 1.0 MN A:MN502 3.3 7.7 1.0 OD1 A:ASP332 3.4 6.2 1.0 P P:8OG5 3.4 7.9 1.0 O5' P:8OG5 3.8 7.3 1.0 C5' P:8OG5 4.1 7.4 1.0 O A:HOH876 4.1 9.1 1.0 O P:HOH102 4.1 17.3 1.0 O3 A:OXD505 4.2 9.2 1.0 OP2 P:8OG5 4.2 8.3 1.0 O4 A:OXD505 4.2 14.1 1.0 O A:ASP330 4.2 7.9 1.0 O P:HOH108 4.3 8.0 1.0 O A:HOH678 4.3 5.0 1.0 N A:GLY320 4.4 5.7 1.0 CB A:ASP330 4.4 10.1 1.0 CB A:ASP332 4.4 6.1 1.0 CA A:GLY319 4.4 5.8 1.0 O A:HOH764 4.5 12.7 1.0 C A:ASP330 4.6 8.2 1.0 O3' P:DA4 4.7 8.3 1.0 O A:HOH793 4.8 13.0 1.0 N A:ASP332 4.9 6.0 1.0 C A:GLY319 5.0 5.7 1.0

Manganese binding site 2 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:7.7 occ:1.00 OP1 P:8OG5 2.1 7.7 1.0 OD1 A:ASP332 2.1 6.2 1.0 OD2 A:ASP418 2.1 7.0 1.0 O P:HOH108 2.2 8.0 1.0 O A:HOH793 2.4 13.0 1.0 OD2 A:ASP330 2.4 10.1 1.0 CG A:ASP418 3.0 7.1 1.0 CG A:ASP332 3.1 6.3 1.0 P P:8OG5 3.2 7.9 1.0 CG A:ASP330 3.3 10.4 1.0 MN A:MN501 3.3 6.6 1.0 O3' P:DA4 3.4 8.3 1.0 OD2 A:ASP332 3.5 6.2 1.0 CB A:ASP418 3.8 7.1 1.0 OD1 A:ASP418 3.9 7.6 1.0 CB A:ASP330 3.9 10.1 1.0 OP2 P:8OG5 4.0 8.3 1.0 OD1 A:ASP330 4.2 11.3 1.0 C5' P:DA4 4.3 9.1 1.0 O P:HOH102 4.3 17.3 1.0 O A:VAL331 4.3 5.9 1.0 CB A:ASP332 4.4 6.1 1.0 NH2 A:ARG416 4.4 8.8 1.0 C3' P:DA4 4.5 8.8 1.0 O5' P:8OG5 4.5 7.3 1.0 O6 A:OXD505 4.5 11.2 1.0 C4' P:DA4 4.5 9.0 1.0 OP1 P:DA4 4.6 9.9 1.0 C A:VAL331 4.7 6.6 1.0 N A:ASP418 4.8 6.9 1.0 C5' P:8OG5 4.9 7.4 1.0 CA A:ASP332 4.9 6.2 1.0 CA A:ASP418 4.9 7.0 1.0 N A:ASP332 4.9 6.0 1.0 N A:VAL331 4.9 7.5 1.0 O A:HOH762 5.0 7.9 1.0 CZ3 A:TRP434 5.0 7.1 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