Sodium in PDB 7m4e: Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min, PDB code: 7m4e 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)	31.22 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.825, 62.088, 142.096, 90, 90, 90
R / Rfree (%)	20.9 / 23.3

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min (pdb code 7m4e). 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 MG2+ Reaction State Ternary Complex, 120 Min, PDB code: 7m4e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min


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 MG2+ Reaction State Ternary Complex, 120 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:34.0 occ:1.00 O A:ALA344 2.3 34.4 1.0 O P:HOH114 2.4 44.6 1.0 O A:SER339 2.4 36.1 1.0 O A:ILE341 2.4 36.5 1.0 OP1 P:DA5 2.5 35.7 1.0 O P:HOH105 2.7 47.2 1.0 C A:ILE341 3.3 36.4 1.0 C A:ALA344 3.4 35.1 1.0 C A:SER339 3.4 35.6 1.0 P P:DA5 3.5 35.4 1.0 OP2 P:DA5 3.7 35.6 1.0 O A:HOH754 3.7 54.9 1.0 N A:ALA344 3.7 37.0 1.0 CA A:TRP342 3.9 37.6 1.0 N A:TRP342 4.0 37.4 1.0 N A:GLY343 4.0 36.6 1.0 N A:ILE341 4.0 35.1 1.0 CA A:ALA344 4.1 35.9 1.0 CA A:SER339 4.1 35.1 1.0 C A:ASN340 4.3 36.9 1.0 C A:TRP342 4.3 37.0 1.0 N A:ASN340 4.3 36.0 1.0 CA A:ILE341 4.4 35.2 1.0 O3' P:DT4 4.4 36.5 1.0 N A:GLY345 4.4 36.3 1.0 CA A:ASN340 4.4 36.6 1.0 CB A:ALA344 4.6 36.2 1.0 O P:HOH117 4.6 61.6 1.0 CA A:GLY345 4.6 36.9 1.0 CB A:SER339 4.7 39.0 1.0 C A:GLY343 4.7 38.0 1.0 O5' P:DA5 4.7 36.0 1.0 O A:HOH759 4.8 58.7 1.0 O A:ASN340 4.8 39.0 1.0 O A:PHE338 4.9 34.0 1.0 CA A:GLY343 4.9 38.4 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min


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 MG2+ Reaction State Ternary Complex, 120 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:69.5 occ:1.00 O A:ILE305 2.5 73.9 1.0 OP1 D:DC3 2.8 68.5 1.0 O A:CYS300 2.9 97.6 1.0 O A:ILE302 3.0 82.0 1.0 OP2 D:DC3 3.3 68.5 1.0 P D:DC3 3.5 66.2 1.0 C A:ILE305 3.7 72.7 1.0 C A:ILE302 3.8 84.5 1.0 C A:CYS300 3.9 97.3 1.0 N A:ILE305 4.1 69.9 1.0 CA A:PRO303 4.3 88.6 1.0 CA A:CYS300 4.4 97.6 1.0 N A:PRO303 4.4 90.3 1.0 CA A:ILE305 4.4 72.5 1.0 N A:GLY304 4.5 68.4 1.0 N A:ILE302 4.5 84.9 1.0 O3' D:DC2 4.6 63.0 1.0 N A:GLY306 4.6 70.6 1.0 C A:SER301 4.7 90.4 1.0 C A:PRO303 4.7 79.7 1.0 CA A:GLY306 4.7 71.0 1.0 O5' D:DC3 4.8 64.2 1.0 O A:SER301 4.8 91.7 1.0 CA A:ILE302 4.8 82.0 1.0 O A:ALA299 4.9 81.0 1.0 CB A:ILE305 5.0 74.1 1.0 N A:SER301 5.0 96.5 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