Sodium in PDB 7m4h: Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min, PDB code: 7m4h 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)	41.57 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.814, 62.299, 142.057, 90, 90, 90
R / Rfree (%)	19.2 / 22.8

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min (pdb code 7m4h). 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 MN2+ Reaction State Ternary Complex, 225 Min, PDB code: 7m4h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 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 MN2+ Reaction State Ternary Complex, 225 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:24.3 occ:1.00 O A:ALA344 2.3 23.0 1.0 O A:SER339 2.3 23.0 1.0 OP1 P:DA5 2.4 25.3 1.0 O A:ILE341 2.5 24.5 1.0 O A:HOH703 2.5 32.0 1.0 O P:HOH115 2.7 28.7 1.0 C A:ILE341 3.4 22.9 1.0 C A:SER339 3.4 26.1 1.0 C A:ALA344 3.4 26.8 1.0 P P:DA5 3.5 25.8 1.0 OP2 P:DA5 3.7 21.8 1.0 O A:HOH784 3.7 42.5 1.0 N A:ALA344 3.8 23.8 1.0 CA A:TRP342 3.9 27.8 1.0 N A:TRP342 4.0 25.4 1.0 N A:GLY343 4.0 24.3 1.0 CA A:SER339 4.1 28.2 1.0 N A:ILE341 4.1 23.4 1.0 CA A:ALA344 4.1 29.8 1.0 C A:ASN340 4.3 23.2 1.0 C A:TRP342 4.3 27.0 1.0 N A:ASN340 4.3 26.3 1.0 O3' P:DT4 4.4 26.7 1.0 CA A:ILE341 4.4 23.3 1.0 N A:GLY345 4.4 27.2 1.0 CA A:ASN340 4.4 23.3 1.0 O1 A:EDO606 4.5 50.1 1.0 O P:HOH128 4.5 67.3 1.0 CB A:ALA344 4.6 30.3 1.0 CB A:SER339 4.7 38.5 1.0 O5' P:DA5 4.7 22.0 1.0 CA A:GLY345 4.7 31.0 1.0 C A:GLY343 4.7 25.2 1.0 O A:ASN340 4.9 26.7 1.0 CA A:GLY343 4.9 23.3 1.0 O A:PHE338 5.0 24.2 1.0 O A:HOH853 5.0 54.4 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 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 MN2+ Reaction State Ternary Complex, 225 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:48.2 occ:1.00 O D:HOH107 2.2 62.5 1.0 O A:ILE302 2.4 55.4 1.0 O A:ILE305 2.8 51.6 1.0 O A:CYS300 2.8 80.3 1.0 OP1 D:DC3 2.9 49.8 1.0 C A:ILE302 3.3 78.5 1.0 OP2 D:DC3 3.4 45.1 1.0 P D:DC3 3.6 48.4 1.0 CA A:PRO303 3.8 56.2 1.0 C A:ILE305 3.8 47.1 1.0 C A:CYS300 3.9 80.9 1.0 N A:PRO303 3.9 77.5 1.0 N A:ILE305 4.1 47.6 1.0 N A:GLY304 4.1 49.1 1.0 N A:ILE302 4.2 62.8 1.0 C A:PRO303 4.4 52.3 1.0 C A:SER301 4.4 58.7 1.0 CA A:ILE302 4.4 64.6 1.0 CA A:CYS300 4.5 81.3 1.0 CA A:ILE305 4.5 61.6 1.0 O A:SER301 4.6 66.1 1.0 O3' D:DC2 4.7 47.6 1.0 N A:GLY306 4.7 51.7 1.0 O5' D:DC3 4.8 47.9 1.0 N A:SER301 4.9 77.9 1.0 O A:ALA299 4.9 66.2 1.0 CA A:GLY306 4.9 48.8 1.0 CB A:ILE305 5.0 73.3 1.0 CB A:PRO303 5.0 64.5 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