Calcium in PDB 5txx: Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+

All present enzymatic activity of Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+:
2.7.7.7;

The structure of Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+, PDB code: 5txx 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)	29.77 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.538, 68.243, 110.200, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.5

The structure of Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+ also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+ (pdb code 5txx). 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 Pre-Catalytic Ground State Ternary Complex, CA2+, PDB code: 5txx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+


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 Pre-Catalytic Ground State Ternary Complex, CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:12.8 occ:1.00 O1G A:TTP501 2.3 19.0 1.0 OD2 A:ASP332 2.3 11.4 1.0 O1B A:TTP501 2.3 10.8 1.0 OD1 A:ASP330 2.3 13.8 1.0 O1A A:TTP501 2.5 11.6 1.0 O A:HOH693 2.5 14.3 1.0 O A:ASP330 2.6 13.6 1.0 CG A:ASP332 3.3 11.5 1.0 PB A:TTP501 3.4 15.4 1.0 PG A:TTP501 3.4 24.6 1.0 C A:ASP330 3.5 11.9 1.0 CG A:ASP330 3.5 21.6 1.0 OD1 A:ASP332 3.7 11.6 1.0 PA A:TTP501 3.7 15.8 1.0 CA A:CA503 3.8 13.2 1.0 O3B A:TTP501 3.8 26.1 1.0 O3A A:TTP501 3.8 15.2 1.0 O2G A:TTP501 3.9 28.6 1.0 N A:ASP330 4.0 15.7 1.0 O A:HOH615 4.1 12.5 1.0 CA A:ASP330 4.1 18.5 1.0 N A:VAL331 4.4 12.8 1.0 OD2 A:ASP330 4.4 27.2 1.0 N A:GLY320 4.4 11.7 1.0 CB A:ASP330 4.4 15.5 1.0 C5' A:TTP501 4.5 9.5 1.0 O5' A:TTP501 4.6 15.0 1.0 CB A:ASP332 4.6 8.8 1.0 O3G A:TTP501 4.7 32.1 1.0 CA A:VAL331 4.7 12.9 1.0 O2B A:TTP501 4.7 15.0 1.0 N A:ASP332 4.7 12.7 1.0 C A:VAL331 4.7 12.2 1.0 CA A:GLY319 4.7 13.0 1.0 O2A A:TTP501 4.8 13.9 1.0 CD2 A:HIS329 4.9 40.2 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Mu Pre-Catalytic Ground State Ternary Complex, CA2+


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 Pre-Catalytic Ground State Ternary Complex, CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:13.2 occ:1.00 OD2 A:ASP418 2.2 15.9 1.0 OD1 A:ASP332 2.3 11.6 1.0 OD2 A:ASP330 2.4 27.2 1.0 O P:HOH204 2.4 18.9 1.0 O1A A:TTP501 2.4 11.6 1.0 O3' P:DA4 2.5 12.9 1.0 OD1 A:ASP330 2.6 13.8 1.0 CG A:ASP330 2.8 21.6 1.0 CG A:ASP332 3.4 11.5 1.0 CG A:ASP418 3.4 16.8 1.0 PA A:TTP501 3.5 15.8 1.0 C3' P:DA4 3.6 14.9 1.0 OD2 A:ASP332 3.7 11.4 1.0 O5' A:TTP501 3.8 15.0 1.0 CA A:CA502 3.8 12.8 1.0 O2A A:TTP501 4.0 13.9 1.0 C5' P:DA4 4.0 18.7 1.0 C4' P:DA4 4.0 16.4 1.0 CB A:ASP418 4.1 13.9 1.0 C5' A:TTP501 4.1 9.5 1.0 OD1 A:ASP418 4.4 16.5 1.0 CB A:ASP330 4.4 15.5 1.0 NH2 A:ARG416 4.6 15.2 1.0 OP1 P:DA4 4.6 15.9 1.0 CB A:ASP332 4.7 8.8 1.0 O5' P:DA4 4.7 17.9 1.0 CZ3 A:TRP434 4.7 23.1 1.0 O A:VAL331 4.9 12.2 1.0 C2' P:DA4 4.9 15.3 1.0 O3A A:TTP501 4.9 15.2 1.0

J.A.Jamsen, W.A.Beard, L.C.Pedersen, D.D.Shock, A.F.Moon, J.M.Krahn, K.Bebenek, T.A.Kunkel, S.H.Wilson. Time-Lapse Crystallography Snapshots of A Double-Strand Break Repair Polymerase in Action. Nat Commun V. 8 253 2017.
ISSN: ESSN 2041-1723
PubMed: 28811466
DOI: 10.1038/S41467-017-00271-7