Calcium in PDB 7m4d: Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex, PDB code: 7m4d 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)	39.21 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.75, 59.917, 141.302, 90, 90, 90
R / Rfree (%)	21 / 25.4

The structure of Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex (pdb code 7m4d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex, PDB code: 7m4d:

Calcium binding site 1 out of 1 in the Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:63.7 occ:1.00 OD1 A:ASP427 2.1 75.4 1.0 O A:HOH701 2.3 87.7 1.0 O1A A:DCP604 2.3 48.2 1.0 OD2 A:ASP429 2.4 53.7 1.0 O1B A:DCP604 2.4 86.0 0.5 O1G A:DCP604 2.4 86.6 0.5 O1B A:DCP604 2.5 83.3 0.5 O A:HOH717 3.0 41.5 1.0 O A:ASP427 3.2 40.1 1.0 CG A:ASP427 3.3 69.7 1.0 CG A:ASP429 3.4 54.9 1.0 PB A:DCP604 3.5 81.2 0.5 NA A:NA602 3.5 59.1 1.0 PB A:DCP604 3.6 78.4 0.5 PA A:DCP604 3.6 57.1 1.0 C A:ASP427 3.7 41.0 1.0 PG A:DCP604 3.7 84.5 0.5 OD1 A:ASP429 3.8 50.8 1.0 O3A A:DCP604 3.9 76.4 0.7 O3B A:DCP604 4.0 89.8 0.5 OD2 A:ASP427 4.1 72.0 1.0 O3B A:DCP604 4.1 89.2 0.5 N A:ASP427 4.1 30.2 1.0 O1G A:DCP604 4.2 91.9 0.5 O A:HOH754 4.2 38.5 1.0 CA A:ASP427 4.3 39.1 1.0 CB A:ASP427 4.3 54.3 1.0 C5' A:DCP604 4.4 73.0 1.0 O2G A:DCP604 4.4 90.2 0.5 N A:VAL428 4.4 30.5 1.0 O5' A:DCP604 4.4 68.0 0.4 CA A:GLY416 4.5 26.2 1.0 N A:SER417 4.6 27.4 1.0 N A:ASP429 4.6 28.1 1.0 OG A:SER417 4.7 46.4 1.0 CA A:VAL428 4.7 27.5 1.0 O2A A:DCP604 4.7 63.1 1.0 CB A:ASP429 4.8 38.2 1.0 PG A:DCP604 4.8 90.7 0.5 C A:VAL428 4.8 31.5 1.0 O3G A:DCP604 4.8 94.8 0.5 O2B A:DCP604 4.8 81.6 0.5 O2B A:DCP604 4.9 74.8 0.5

J.A.Jamsen, D.D.Shock, S.H.Wilson. Watching Right and Wrong Nucleotide Insertion Captures Hidden Polymerase Fidelity Checkpoints. Nat Commun V. 13 3193 2022.
ISSN: ESSN 2041-1723
PubMed: 35680862
DOI: 10.1038/S41467-022-30141-W