Calcium in PDB 7kss: Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN), PDB code: 7kss was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.84 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.023, 68.767, 110.27, 90, 90, 90
R / Rfree (%)	16 / 17.7

The structure of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) (pdb code 7kss). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN), PDB code: 7kss:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:14.9 occ:1.00 OD2 A:ASP418 2.3 19.9 1.0 OD2 A:ASP330 2.3 25.1 1.0 OD1 A:ASP332 2.3 15.8 1.0 O P:HOH107 2.3 21.6 1.0 O2A A:DGT511 2.4 15.4 1.0 O3' P:DA4 2.5 20.1 1.0 OD1 A:ASP330 2.5 15.5 1.0 CG A:ASP330 2.8 21.1 1.0 CG A:ASP332 3.4 15.6 1.0 CG A:ASP418 3.4 16.7 1.0 PA A:DGT511 3.5 16.2 1.0 C3' P:DA4 3.6 19.6 1.0 OD2 A:ASP332 3.7 15.2 1.0 CA A:CA502 3.8 14.4 1.0 O5' A:DGT511 3.8 16.2 1.0 O1A A:DGT511 4.0 17.9 1.0 C5' P:DA4 4.1 20.3 1.0 C5' A:DGT511 4.1 14.2 1.0 C4' P:DA4 4.1 18.9 1.0 CB A:ASP418 4.2 15.8 1.0 CB A:ASP330 4.3 17.8 1.0 OD1 A:ASP418 4.4 17.5 1.0 CE1 A:HIS329 4.4 46.5 1.0 OP1 P:DA4 4.5 23.2 1.0 CB A:ASP332 4.7 14.4 1.0 O5' P:DA4 4.7 21.0 1.0 NH2 A:ARG416 4.7 20.0 1.0 NE2 A:HIS329 4.8 46.7 1.0 CZ3 A:TRP434 4.8 23.7 1.0 O A:VAL331 4.9 16.7 1.0 C2' P:DA4 4.9 20.1 1.0 O3A A:DGT511 4.9 17.4 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:14.4 occ:1.00 O2G A:DGT511 2.3 17.2 1.0 OD1 A:ASP330 2.3 15.5 1.0 OD2 A:ASP332 2.4 15.2 1.0 O2B A:DGT511 2.4 15.0 1.0 O A:HOH760 2.5 17.4 1.0 O2A A:DGT511 2.5 15.4 1.0 O A:ASP330 2.6 17.5 1.0 CG A:ASP332 3.4 15.6 1.0 CG A:ASP330 3.4 21.1 1.0 PB A:DGT511 3.5 16.0 1.0 C A:ASP330 3.5 16.3 1.0 PG A:DGT511 3.5 20.1 1.0 PA A:DGT511 3.7 16.2 1.0 OD1 A:ASP332 3.7 15.8 1.0 CA A:CA501 3.8 14.9 1.0 O3A A:DGT511 3.8 17.4 1.0 O3B A:DGT511 3.8 21.4 1.0 N A:ASP330 4.0 17.6 1.0 CA A:ASP330 4.1 17.4 1.0 O A:HOH633 4.2 16.8 1.0 OD2 A:ASP330 4.3 25.1 1.0 N A:VAL331 4.3 14.4 1.0 CB A:ASP330 4.4 17.8 1.0 O3G A:DGT511 4.4 25.5 1.0 ND1 A:HIS329 4.5 45.7 1.0 C5' A:DGT511 4.5 14.2 1.0 N A:GLY320 4.5 13.0 1.0 O A:HOH634 4.5 21.1 1.0 CE1 A:HIS329 4.6 46.5 1.0 O1G A:DGT511 4.6 24.6 1.0 O5' A:DGT511 4.6 16.2 1.0 CA A:VAL331 4.7 14.8 1.0 CB A:ASP332 4.7 14.4 1.0 N A:ASP332 4.7 13.5 1.0 C A:VAL331 4.7 13.6 1.0 O1A A:DGT511 4.8 17.9 1.0 CA A:GLY319 4.8 13.1 1.0 O1B A:DGT511 4.8 17.0 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6