Sodium 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:

Calcium

(Ca)

1 atom

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex, PDB code: 7m4d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na602 b:59.1 occ:1.00 OD1 A:ASP429 2.2 50.8 1.0 O1A A:DCP604 2.6 48.2 1.0 OD2 A:ASP427 2.7 72.0 1.0 OD1 A:ASP427 2.9 75.4 1.0 CG A:ASP427 3.0 69.7 1.0 CG A:ASP429 3.2 54.9 1.0 OD2 A:ASP490 3.2 44.0 1.0 OD2 A:ASP429 3.4 53.7 1.0 CA A:CA601 3.5 63.7 1.0 PA A:DCP604 3.6 57.1 1.0 O5' A:DCP604 3.8 68.0 0.4 O P:HOH101 3.9 43.3 0.7 CG A:ASP490 4.0 46.1 1.0 C5' A:DCP604 4.2 73.0 1.0 O2A A:DCP604 4.2 63.1 1.0 CB A:ASP427 4.3 54.3 1.0 OD1 A:ASP490 4.5 40.9 1.0 OP1 P:DC6 4.5 35.1 1.0 CB A:ASP429 4.6 38.2 1.0 C3' P:DC6 4.6 44.7 1.0 O3' P:DC6 4.6 63.1 1.0 NH2 A:ARG488 4.7 34.6 1.0 O5' P:DC6 4.7 42.4 1.0 CB A:ASP490 4.9 32.2 1.0 C5' P:DC6 4.9 38.1 1.0 O1G A:DCP604 5.0 86.6 0.5

Sodium binding site 2 out of 2 in the Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:25.9 occ:1.00 O A:HOH782 2.3 34.8 1.0 O A:SER339 2.3 28.2 1.0 O A:ALA344 2.4 30.1 1.0 O A:ILE341 2.4 28.4 1.0 OP1 P:DA5 2.5 32.6 1.0 O P:HOH110 2.5 32.0 1.0 C A:ILE341 3.4 24.2 1.0 C A:SER339 3.4 27.4 1.0 P P:DA5 3.5 32.0 1.0 C A:ALA344 3.5 28.4 1.0 OP2 P:DA5 3.7 24.9 1.0 N A:ALA344 3.8 23.6 1.0 O A:HOH817 3.9 61.3 1.0 N A:GLY343 4.0 26.2 1.0 CA A:TRP342 4.0 28.4 1.0 N A:TRP342 4.0 28.2 1.0 N A:ILE341 4.1 28.4 1.0 CA A:SER339 4.1 29.3 1.0 C A:ASN340 4.2 25.1 1.0 CA A:ALA344 4.3 30.1 1.0 N A:ASN340 4.3 31.5 1.0 CA A:ASN340 4.4 27.0 1.0 CA A:ILE341 4.4 27.3 1.0 C A:TRP342 4.4 30.9 1.0 O3' P:DT4 4.4 29.9 1.0 N A:GLY345 4.5 27.9 1.0 CB A:SER339 4.7 36.2 1.0 O5' P:DA5 4.7 24.1 1.0 CB A:ALA344 4.7 28.3 1.0 C A:GLY343 4.7 25.4 1.0 O A:ASN340 4.7 26.8 1.0 CA A:GLY345 4.8 33.2 1.0 O2 A:EDO605 4.8 50.0 1.0 CA A:GLY343 4.9 24.3 1.0 O A:PHE338 5.0 27.5 1.0

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