Manganese in PDB 6akh: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp:
2.7.7.7;

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp, PDB code: 6akh 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 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.838, 68.800, 109.680, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

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

Manganese binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:9.3 occ:1.00 OD2 A:ASP332 2.1 8.8 1.0 OD1 A:ASP330 2.1 10.6 1.0 O2B A:DUP505 2.2 8.9 1.0 O3G A:DUP505 2.2 12.6 1.0 O2A A:DUP505 2.2 9.8 1.0 O A:HOH764 2.3 9.5 1.0 CG A:ASP332 3.1 9.4 1.0 CG A:ASP330 3.2 11.4 1.0 PB A:DUP505 3.2 10.1 1.0 PA A:DUP505 3.4 10.2 1.0 PG A:DUP505 3.4 12.9 1.0 OD1 A:ASP332 3.5 9.9 1.0 OD2 A:ASP330 3.6 11.4 1.0 N3A A:DUP505 3.6 9.7 1.0 MN A:MN503 3.6 9.9 1.0 O3B A:DUP505 3.6 10.5 1.0 O A:ASP330 4.1 10.2 1.0 ND1 A:HIS329 4.1 21.2 1.0 C5' A:DUP505 4.2 9.3 1.0 O1G A:DUP505 4.2 13.2 1.0 O A:HOH675 4.2 14.9 1.0 O A:HOH730 4.3 10.6 1.0 N A:GLY320 4.3 9.2 1.0 O5' A:DUP505 4.3 9.4 1.0 C A:ASP330 4.3 11.1 1.0 CE1 A:HIS329 4.3 20.7 1.0 CB A:ASP330 4.5 11.2 1.0 CB A:ASP332 4.5 9.5 1.0 CA A:GLY319 4.5 9.8 1.0 O1A A:DUP505 4.5 10.5 1.0 N A:ASP330 4.6 12.0 1.0 O2G A:DUP505 4.6 13.8 1.0 O1B A:DUP505 4.6 9.6 1.0 CA A:ASP330 4.7 11.7 1.0 N A:ASP332 4.7 9.9 1.0 O P:HOH102 4.8 13.0 1.0 N A:VAL331 4.9 10.8 1.0 C A:GLY319 5.0 9.6 1.0 C A:VAL331 5.0 10.8 1.0

Manganese binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Mn-Dumpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:9.9 occ:1.00 OD2 A:ASP330 2.1 11.4 1.0 OD1 A:ASP332 2.1 9.9 1.0 OD2 A:ASP418 2.1 12.0 1.0 O P:HOH102 2.2 13.0 1.0 O2A A:DUP505 2.2 9.8 1.0 O3' P:DA4 2.3 12.3 1.0 CG A:ASP330 3.1 11.4 1.0 CG A:ASP332 3.1 9.4 1.0 CG A:ASP418 3.2 12.5 1.0 PA A:DUP505 3.4 10.2 1.0 OD1 A:ASP330 3.4 10.6 1.0 C3' P:DA4 3.5 13.4 1.0 OD2 A:ASP332 3.5 8.8 1.0 MN A:MN502 3.6 9.3 1.0 O1A A:DUP505 3.7 10.5 1.0 O5' A:DUP505 3.8 9.4 1.0 CB A:ASP418 3.9 12.2 1.0 C4' P:DA4 4.0 13.9 1.0 C5' P:DA4 4.0 14.1 1.0 CE1 A:HIS329 4.1 20.7 1.0 C5' A:DUP505 4.1 9.3 1.0 OD1 A:ASP418 4.2 12.3 1.0 CB A:ASP330 4.5 11.2 1.0 CB A:ASP332 4.5 9.5 1.0 OP1 P:DA4 4.5 14.2 1.0 O5' P:DA4 4.6 14.9 1.0 CZ3 A:TRP434 4.6 14.5 1.0 NH2 A:ARG416 4.6 13.1 1.0 C2' P:DA4 4.8 13.8 1.0 O3G A:DUP505 4.8 12.6 1.0 ND1 A:HIS329 4.9 21.2 1.0 N3A A:DUP505 4.9 9.7 1.0 NE2 A:HIS329 4.9 23.2 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