Calcium in PDB 7ksz: Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN), PDB code: 7ksz 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)	32.83 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.753, 68.778, 110.133, 90, 90, 90
R / Rfree (%)	15.7 / 17.5

The structure of Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN) (pdb code 7ksz). 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:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN), PDB code: 7ksz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN)


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:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:11.6 occ:1.00 OD1 A:ASP330 2.2 15.4 1.0 O1G A:DGT511 2.3 16.4 0.9 OD2 A:ASP332 2.3 12.1 1.0 O2B A:DGT511 2.3 12.1 1.0 O A:HOH731 2.5 16.2 1.0 O2A A:DGT511 2.5 13.9 1.0 O A:ASP330 2.7 15.0 1.0 CG A:ASP332 3.3 12.1 1.0 CG A:ASP330 3.4 15.2 1.0 PB A:DGT511 3.4 14.7 1.0 PG A:DGT511 3.5 14.0 0.7 C A:ASP330 3.6 13.9 1.0 OD1 A:ASP332 3.6 13.9 1.0 O3B A:DGT511 3.7 15.0 0.7 PA A:DGT511 3.7 17.6 0.9 CA A:CA508 3.8 12.3 1.0 O3A A:DGT511 3.9 13.4 0.8 N A:ASP330 4.1 13.3 1.0 O3G A:DGT511 4.2 20.1 0.9 O A:HOH643 4.2 11.2 1.0 CA A:ASP330 4.2 13.8 1.0 OD2 A:ASP330 4.2 24.0 1.0 N A:GLY320 4.4 8.9 1.0 CB A:ASP330 4.4 12.7 1.0 O A:HOH614 4.4 16.3 1.0 O5' A:DGT511 4.5 24.8 0.9 N A:VAL331 4.5 10.9 1.0 ND1 A:HIS329 4.7 17.1 0.7 CB A:ASP332 4.7 10.0 1.0 O2G A:DGT511 4.7 23.5 0.8 CA A:GLY319 4.7 9.4 1.0 CA A:VAL331 4.8 10.9 1.0 N A:ASP332 4.8 10.6 1.0 CE1 A:HIS329 4.8 22.9 0.7 O1B A:DGT511 4.8 17.9 1.0 C A:VAL331 4.9 10.4 1.0 O1A A:DGT511 5.0 21.5 0.9

Calcium binding site 2 out of 2 in the Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN)


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:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:12.3 occ:1.00 OD2 A:ASP418 2.3 15.4 1.0 OD1 A:ASP332 2.3 13.9 1.0 OD2 A:ASP330 2.3 24.0 1.0 O2A A:DGT511 2.3 13.9 1.0 O3' P:DA4 2.4 21.4 1.0 O P:HOH204 2.4 20.1 1.0 OD1 A:ASP330 2.6 15.4 1.0 CG A:ASP330 2.8 15.2 1.0 CG A:ASP332 3.4 12.1 1.0 CG A:ASP418 3.4 14.1 1.0 PA A:DGT511 3.5 17.6 0.9 C3' P:DA4 3.5 21.8 1.0 OD2 A:ASP332 3.8 12.1 1.0 C4' P:DA4 3.8 19.5 1.0 O1A A:DGT511 3.8 21.5 0.9 CA A:CA507 3.8 11.6 1.0 C5' P:DA4 3.8 28.2 1.0 O5' A:DGT511 4.2 24.8 0.9 CB A:ASP418 4.2 11.4 1.0 CB A:ASP330 4.3 12.7 1.0 OD1 A:ASP418 4.3 13.3 1.0 CE1 A:HIS329 4.6 22.9 0.7 O5' P:DA4 4.6 32.0 1.0 OP1 P:DA4 4.7 20.3 1.0 CB A:ASP332 4.7 10.0 1.0 C2' P:DA4 4.8 23.9 1.0 NH2 A:ARG416 4.8 13.2 1.0 O3A A:DGT511 4.9 13.4 0.8 CZ3 A:TRP434 4.9 21.1 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