Sodium in PDB 7m4b: Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min, PDB code: 7m4b 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)	31.14 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.981, 62.634, 140.334, 90, 90, 90
R / Rfree (%)	18.1 / 20.2

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min (pdb code 7m4b). 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 MN2+ Product State Ternary Complex, 60 Min, PDB code: 7m4b:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 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, Ttp:at MN2+ Product State Ternary Complex, 60 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:22.8 occ:1.00 O A:SER339 2.3 18.2 0.4 O A:HOH796 2.4 29.4 1.0 O A:ALA344 2.4 21.0 1.0 OP1 P:DA5 2.4 21.0 1.0 O A:ILE341 2.4 23.1 1.0 O A:SER339 2.5 25.4 0.6 O P:HOH204 2.7 28.4 1.0 C A:ILE341 3.3 24.4 1.0 C A:SER339 3.4 23.3 0.4 C A:SER339 3.4 23.3 0.6 C A:ALA344 3.4 21.3 1.0 P P:DA5 3.5 23.1 1.0 O A:HOH723 3.7 32.9 0.7 OP2 P:DA5 3.7 22.4 1.0 N A:ALA344 3.7 22.4 1.0 N A:GLY343 3.9 23.0 1.0 CA A:TRP342 3.9 25.2 1.0 N A:TRP342 4.0 22.6 1.0 O P:HOH225 4.0 37.7 0.4 N A:ILE341 4.1 19.3 1.0 CA A:ALA344 4.1 22.3 1.0 CA A:SER339 4.1 23.6 0.6 C A:ASN340 4.2 20.2 1.0 CA A:SER339 4.2 24.1 0.4 C A:TRP342 4.3 27.0 1.0 N A:ASN340 4.3 20.3 1.0 CA A:ILE341 4.4 19.6 1.0 O3' P:DT4 4.4 21.8 1.0 CA A:ASN340 4.4 21.0 1.0 N A:GLY345 4.5 21.6 1.0 CB A:ALA344 4.6 23.6 1.0 O P:HOH225 4.6 38.2 0.6 O5' P:DA5 4.7 19.3 1.0 C A:GLY343 4.7 21.2 1.0 CB A:SER339 4.7 25.0 0.6 O A:HOH723 4.7 31.0 0.3 CA A:GLY345 4.7 21.3 1.0 O1 A:EDO611 4.7 56.0 1.0 O A:ASN340 4.8 24.5 1.0 O A:HOH858 4.8 45.7 1.0 CA A:GLY343 4.8 22.7 1.0 CB A:SER339 4.9 23.4 0.4

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 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, Ttp:at MN2+ Product State Ternary Complex, 60 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:55.8 occ:0.86 O A:HOH712 2.1 48.0 0.9 O A:ILE302 2.2 79.0 1.0 O A:CYS300 2.8 87.9 1.0 O A:ILE305 2.9 61.0 1.0 OP1 D:DC3 3.0 49.7 1.0 C A:ILE302 3.1 76.3 1.0 CA A:PRO303 3.6 70.6 1.0 N A:PRO303 3.7 75.3 1.0 C A:CYS300 3.8 88.4 1.0 N A:ILE305 3.8 55.6 1.0 P D:DC3 3.9 55.9 1.0 C A:ILE305 3.9 62.2 1.0 OP2 D:DC3 3.9 54.7 1.0 N A:GLY304 3.9 66.1 1.0 N A:ILE302 4.0 72.8 1.0 C A:PRO303 4.1 64.3 1.0 CA A:ILE302 4.2 71.6 1.0 CA A:ILE305 4.3 56.9 1.0 CA A:CYS300 4.3 85.7 1.0 C A:SER301 4.4 76.0 1.0 CB A:ILE305 4.5 61.2 1.0 O A:SER301 4.7 77.1 1.0 C A:GLY304 4.8 55.2 1.0 O3' D:DC2 4.9 43.5 1.0 O A:ALA299 4.9 71.5 1.0 CB A:PRO303 4.9 71.4 1.0 N A:SER301 4.9 80.4 1.0 CA A:GLY304 5.0 57.4 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min


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 MN2+ Product State Ternary Complex, 60 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:50.4 occ:1.00 NE2 A:GLN366 2.3 63.1 1.0 O A:HOH809 2.9 38.8 0.3 O A:HOH809 3.0 49.8 0.7 O A:HOH726 3.1 97.6 1.0 CD A:GLN366 3.3 62.0 1.0 OE1 A:GLN366 3.6 62.9 1.0 CG A:GLN366 4.7 45.2 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