Calcium in PDB 6ak8: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP:
2.7.7.7;

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP, PDB code: 6ak8 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)	50.00 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.750, 68.548, 110.165, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.1

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP (pdb code 6ak8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP, PDB code: 6ak8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:18.7 occ:1.00 OD1 A:ASP330 2.3 17.7 1.0 O3G A:8DG504 2.3 24.5 1.0 OD1 A:ASP332 2.4 20.8 1.0 O1B A:8DG504 2.4 16.6 1.0 O1A A:8DG504 2.4 19.1 1.0 O A:HOH764 2.5 20.2 1.0 O A:ASP330 2.5 19.8 1.0 CG A:ASP332 3.4 19.7 1.0 C A:ASP330 3.4 19.7 1.0 PB A:8DG504 3.5 21.0 1.0 CG A:ASP330 3.5 20.8 1.0 PG A:8DG504 3.6 24.2 1.0 OD2 A:ASP332 3.7 19.0 1.0 PA A:8DG504 3.7 20.3 1.0 O3B A:8DG504 3.8 23.5 1.0 CA A:CA502 3.9 18.1 1.0 O3A A:8DG504 3.9 21.1 1.0 N A:ASP330 4.0 20.8 1.0 CA A:ASP330 4.1 19.8 1.0 O A:HOH694 4.1 18.6 1.0 O1G A:8DG504 4.2 27.5 1.0 N A:VAL331 4.3 19.2 1.0 CB A:ASP330 4.4 20.3 1.0 O A:HOH604 4.4 24.1 1.0 OD2 A:ASP330 4.4 21.5 1.0 N A:GLY320 4.5 18.2 1.0 CA A:VAL331 4.6 19.4 1.0 C A:VAL331 4.7 20.2 1.0 CB A:ASP332 4.7 18.3 1.0 N A:ASP332 4.7 18.7 1.0 O5' A:8DG504 4.7 19.3 1.0 O2G A:8DG504 4.7 28.1 1.0 CA A:GLY319 4.7 18.2 1.0 O2A A:8DG504 4.7 19.3 1.0 ND1 A:HIS329 4.8 42.0 1.0 C5' A:8DG504 4.8 17.3 1.0 O2B A:8DG504 4.8 21.8 1.0 CE1 A:HIS329 4.9 41.3 1.0

Calcium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Adenine and Incoming Ca-8OXODGTP within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.1 occ:1.00 OD2 A:ASP418 2.2 17.9 1.0 OD2 A:ASP332 2.3 19.0 1.0 OD2 A:ASP330 2.3 21.5 1.0 O1A A:8DG504 2.5 19.1 1.0 O P:HOH107 2.6 19.4 1.0 OD1 A:ASP330 2.6 17.7 1.0 O3' P:DA4 2.6 18.8 1.0 CG A:ASP330 2.9 20.8 1.0 CG A:ASP418 3.4 19.6 1.0 CG A:ASP332 3.4 19.7 1.0 PA A:8DG504 3.5 20.3 1.0 C3' P:DA4 3.8 18.4 1.0 O5' A:8DG504 3.8 19.3 1.0 OD1 A:ASP332 3.8 20.8 1.0 CA A:CA501 3.9 18.7 1.0 O2A A:8DG504 3.9 19.3 1.0 C5' P:DA4 4.1 18.2 1.0 CB A:ASP418 4.1 18.6 1.0 C4' P:DA4 4.1 18.9 1.0 OD1 A:ASP418 4.2 19.6 1.0 C5' A:8DG504 4.2 17.3 1.0 CB A:ASP330 4.4 20.3 1.0 CZ3 A:TRP434 4.6 20.4 1.0 NH2 A:ARG416 4.6 19.3 1.0 CE1 A:HIS329 4.6 41.3 1.0 OP1 P:DA4 4.7 19.2 1.0 CB A:ASP332 4.7 18.3 1.0 O5' P:DA4 4.8 18.3 1.0 O A:VAL331 4.9 20.7 1.0 O3A A:8DG504 4.9 21.1 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