Manganese in PDB 6ipk: Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP

All present enzymatic activity of Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP:
2.7.7.7;

The structure of Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP, PDB code: 6ipk 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 / 2.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	122.827, 122.827, 49.859, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.6

The binding sites of Manganese atom in the Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP (pdb code 6ipk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP, PDB code: 6ipk:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:41.5 occ:1.00 OD1 A:ASP330 1.9 37.9 1.0 O1B A:8DG502 2.0 44.0 1.0 O1A A:8DG502 2.1 39.7 1.0 OD2 A:ASP332 2.1 37.4 1.0 O3G A:8DG502 2.3 52.0 1.0 O A:HOH603 2.3 38.5 1.0 CG A:ASP330 3.0 37.7 1.0 CG A:ASP332 3.1 37.8 1.0 PB A:8DG502 3.2 47.5 1.0 PA A:8DG502 3.3 45.1 1.0 OD2 A:ASP330 3.5 38.9 1.0 PG A:8DG502 3.5 50.1 1.0 OD1 A:ASP332 3.5 37.4 1.0 O3A A:8DG502 3.5 48.9 1.0 MN A:MN501 3.6 46.5 1.0 O3B A:8DG502 3.7 44.9 1.0 O A:ASP330 3.8 40.2 1.0 ND1 A:HIS329 4.1 47.4 1.0 O A:HOH626 4.1 35.3 1.0 C A:ASP330 4.1 39.4 1.0 O5' A:8DG502 4.2 47.9 1.0 CE1 A:HIS329 4.2 47.8 1.0 O A:HOH602 4.2 49.0 1.0 N A:GLY320 4.2 37.5 1.0 O1G A:8DG502 4.3 54.2 1.0 CB A:ASP330 4.3 38.0 1.0 CA A:GLY319 4.5 36.9 1.0 N A:ASP330 4.5 39.7 1.0 CB A:ASP332 4.5 38.4 1.0 O2A A:8DG502 4.5 44.2 1.0 O A:HOH629 4.5 43.4 1.0 O2B A:8DG502 4.5 44.6 1.0 CA A:ASP330 4.6 39.1 1.0 O2G A:8DG502 4.6 54.3 1.0 C5' A:8DG502 4.6 57.3 1.0 N A:ASP332 4.7 36.9 1.0 N A:VAL331 4.7 38.6 1.0 C A:GLY319 4.9 37.6 1.0 C A:VAL331 5.0 37.3 1.0 CA A:VAL331 5.0 38.5 1.0

Manganese binding site 2 out of 2 in the Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Binary Complex of Human Dna Polymerase Mu with MN8OXODGTP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:46.5 occ:1.00 OD2 A:ASP330 2.0 38.9 1.0 OD2 A:ASP418 2.0 41.4 1.0 OD1 A:ASP332 2.1 37.4 1.0 O A:HOH629 2.1 43.4 1.0 O1A A:8DG502 2.4 39.7 1.0 O A:HOH633 2.6 41.1 1.0 CG A:ASP330 3.0 37.7 1.0 CG A:ASP418 3.1 40.4 1.0 CG A:ASP332 3.1 37.8 1.0 OD1 A:ASP330 3.4 37.9 1.0 PA A:8DG502 3.5 45.1 1.0 OD2 A:ASP332 3.5 37.4 1.0 MN A:MN500 3.6 41.5 1.0 O2A A:8DG502 3.8 44.2 1.0 CB A:ASP418 3.9 39.2 1.0 OD1 A:ASP418 4.0 39.7 1.0 O5' A:8DG502 4.0 47.9 1.0 CE1 A:HIS329 4.1 47.8 1.0 O8 A:8DG502 4.2 57.5 1.0 CB A:ASP330 4.3 38.0 1.0 CB A:ASP332 4.4 38.4 1.0 NH2 A:ARG416 4.4 51.4 1.0 CZ3 A:TRP434 4.8 48.3 1.0 NE2 A:HIS329 4.8 48.3 1.0 O1B A:8DG502 4.9 44.0 1.0 O3A A:8DG502 4.9 48.9 1.0 ND1 A:HIS329 5.0 47.4 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