Calcium in PDB 6ak9: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine and Incoming Ca-8OXODGTP

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

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine and Incoming Ca-8OXODGTP, PDB code: 6ak9 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 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.907, 68.742, 110.211, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.4

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

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine and Incoming Ca-8OXODGTP (pdb code 6ak9). 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 Cytosine and Incoming Ca-8OXODGTP, PDB code: 6ak9:
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 Cytosine 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 Cytosine and Incoming Ca-8OXODGTP within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:12.3 occ:1.00 O1B A:8DG503 2.3 13.8 1.0 O2G A:8DG503 2.3 18.6 1.0 OD2 A:ASP332 2.3 12.1 1.0 OD1 A:ASP330 2.3 15.7 1.0 O1A A:8DG503 2.4 14.2 1.0 O A:HOH788 2.5 13.6 1.0 O A:ASP330 2.8 15.4 1.0 CG A:ASP332 3.3 12.3 1.0 PB A:8DG503 3.4 15.2 1.0 PG A:8DG503 3.5 18.6 1.0 CG A:ASP330 3.5 16.9 1.0 C A:ASP330 3.6 14.7 1.0 PA A:8DG503 3.6 15.2 1.0 OD1 A:ASP332 3.7 11.2 1.0 O3B A:8DG503 3.8 18.5 1.0 O3A A:8DG503 3.8 15.7 1.0 CA A:CA502 3.9 12.5 1.0 N A:ASP330 4.1 16.3 1.0 O A:HOH699 4.1 13.0 1.0 CA A:ASP330 4.2 16.0 1.0 O1G A:8DG503 4.2 20.8 1.0 OD2 A:ASP330 4.4 19.7 1.0 O A:HOH602 4.4 19.6 1.0 N A:GLY320 4.4 10.5 1.0 N A:VAL331 4.4 13.6 1.0 CB A:ASP330 4.5 16.0 1.0 O5' A:8DG503 4.6 15.4 1.0 C5' A:8DG503 4.6 15.4 1.0 ND1 A:HIS329 4.6 31.1 1.0 O3G A:8DG503 4.6 21.9 1.0 CB A:ASP332 4.7 11.5 1.0 CE1 A:HIS329 4.7 31.8 1.0 CA A:GLY319 4.7 10.9 1.0 CA A:VAL331 4.7 12.9 1.0 O2A A:8DG503 4.7 15.2 1.0 O2B A:8DG503 4.8 16.7 1.0 N A:ASP332 4.8 11.9 1.0 C A:VAL331 4.8 12.5 1.0

Calcium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with Templating Cytosine 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 Cytosine and Incoming Ca-8OXODGTP within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:12.5 occ:1.00 OD2 A:ASP418 2.3 14.0 1.0 OD1 A:ASP332 2.3 11.2 1.0 OD2 A:ASP330 2.3 19.7 1.0 O P:HOH107 2.4 16.0 1.0 O1A A:8DG503 2.5 14.2 1.0 O3' P:DA4 2.6 17.0 1.0 OD1 A:ASP330 2.7 15.7 1.0 CG A:ASP330 2.9 16.9 1.0 CG A:ASP332 3.4 12.3 1.0 CG A:ASP418 3.4 13.8 1.0 PA A:8DG503 3.5 15.2 1.0 O5' A:8DG503 3.7 15.4 1.0 C3' P:DA4 3.7 17.4 1.0 OD2 A:ASP332 3.8 12.1 1.0 CA A:CA501 3.9 12.3 1.0 O2A A:8DG503 4.0 15.2 1.0 C4' P:DA4 4.0 17.3 1.0 C5' P:DA4 4.0 17.1 1.0 C5' A:8DG503 4.0 15.4 1.0 CB A:ASP418 4.2 13.2 1.0 OD1 A:ASP418 4.3 14.0 1.0 CB A:ASP330 4.4 16.0 1.0 CE1 A:HIS329 4.5 31.8 1.0 OP1 P:DA4 4.6 16.3 1.0 NH2 A:ARG416 4.7 14.2 1.0 CB A:ASP332 4.7 11.5 1.0 CZ3 A:TRP434 4.7 16.0 1.0 O5' P:DA4 4.7 17.0 1.0 NE2 A:HIS329 4.8 32.4 1.0 O3A A:8DG503 4.9 15.7 1.0 C2' P:DA4 5.0 17.4 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