Sodium in PDB 7m44: Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec:
2.7.7.7;

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec, PDB code: 7m44 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)	21.89 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.042, 62.356, 140.228, 90, 90, 90
R / Rfree (%)	19.5 / 22.6

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec (pdb code 7m44). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec, PDB code: 7m44:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec


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, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:21.7 occ:1.00 O A:ALA344 2.3 19.9 1.0 O A:SER339 2.3 21.4 0.3 OP1 P:DA5 2.4 20.9 1.0 O A:SER339 2.4 20.3 0.7 O A:HOH808 2.4 28.6 1.0 O A:ILE341 2.5 23.6 1.0 O P:HOH104 2.7 27.1 1.0 C A:ILE341 3.4 24.6 1.0 P P:DA5 3.4 22.4 1.0 C A:ALA344 3.4 20.7 1.0 C A:SER339 3.4 24.1 0.7 C A:SER339 3.4 23.3 0.3 OP2 P:DA5 3.6 21.4 1.0 N A:ALA344 3.8 20.5 1.0 O A:HOH802 3.8 44.3 1.0 N A:GLY343 3.9 21.6 1.0 CA A:TRP342 3.9 23.4 1.0 N A:TRP342 4.0 22.1 1.0 CA A:SER339 4.1 20.4 0.7 CA A:ALA344 4.1 23.2 1.0 N A:ILE341 4.1 20.3 1.0 CA A:SER339 4.3 22.0 0.3 O P:HOH127 4.3 26.6 0.5 C A:ASN340 4.3 21.9 1.0 C A:TRP342 4.3 23.6 1.0 O3' P:DT4 4.4 21.0 1.0 N A:ASN340 4.4 19.5 1.0 CA A:ILE341 4.4 18.9 1.0 N A:GLY345 4.4 19.9 1.0 CA A:ASN340 4.4 23.3 1.0 O P:HOH127 4.6 26.8 0.6 CB A:ALA344 4.6 21.6 1.0 O5' P:DA5 4.6 21.3 1.0 CB A:SER339 4.6 25.8 0.7 C A:GLY343 4.7 21.5 1.0 CA A:GLY345 4.7 21.2 1.0 O A:ASN340 4.8 23.7 1.0 CA A:GLY343 4.9 20.2 1.0 O1 A:EDO612 4.9 37.8 0.6 CB A:SER339 4.9 24.3 0.3

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec


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, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:79.8 occ:1.00 OE1 A:GLN366 2.9 51.2 1.0 O A:HOH703 3.1 52.4 1.0 CD A:GLN366 3.7 49.3 1.0 NE2 A:GLN366 3.8 49.6 1.0 OD1 A:ASP362 3.8 30.4 1.0 O A:HOH756 4.2 48.5 1.0 CG A:ASP362 4.2 29.6 1.0 OD2 A:ASP362 4.5 29.8 1.0 CD1 A:PHE357 4.9 36.4 1.0 CE1 A:PHE357 4.9 37.4 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:59.4 occ:1.00 O A:HOH819 2.1 59.8 1.0 O A:ILE302 2.3 64.4 1.0 O A:CYS300 2.7 84.5 1.0 O A:ILE305 2.9 60.1 1.0 OP1 D:DC3 3.1 52.6 1.0 C A:ILE302 3.1 66.8 1.0 C A:CYS300 3.6 85.7 1.0 CA A:PRO303 3.7 69.0 1.0 N A:PRO303 3.7 72.1 1.0 N A:ILE305 3.8 52.3 1.0 N A:ILE302 3.8 72.3 1.0 C A:ILE305 3.8 57.8 1.0 N A:GLY304 4.0 53.1 1.0 C A:SER301 4.0 73.6 1.0 P D:DC3 4.0 53.7 1.0 CA A:ILE302 4.1 68.6 1.0 C A:PRO303 4.1 65.5 1.0 OP2 D:DC3 4.2 55.3 1.0 O A:SER301 4.2 74.3 1.0 CA A:ILE305 4.3 55.3 1.0 CA A:CYS300 4.3 86.6 1.0 N A:SER301 4.5 76.6 1.0 CB A:ILE305 4.5 57.6 1.0 O A:ALA299 4.7 68.4 1.0 CA A:SER301 4.7 76.9 1.0 C A:GLY304 4.8 52.0 1.0 CD A:PRO303 4.9 73.9 1.0 O3' D:DC2 4.9 46.3 1.0 CA A:GLY304 5.0 50.0 1.0 N A:GLY306 5.0 57.2 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