Sodium in PDB 7m49: Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min, PDB code: 7m49 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)	40.11 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.146, 62.771, 140.568, 90, 90, 90
R / Rfree (%)	18.8 / 21.6

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min (pdb code 7m49). 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+ Reaction State Ternary Complex, 5 Min, PDB code: 7m49:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:23.7 occ:1.00 O A:SER339 2.3 20.2 0.3 O A:HOH808 2.4 32.7 1.0 O A:ALA344 2.4 23.2 1.0 OP1 P:DA5 2.4 23.8 1.0 O A:SER339 2.4 25.4 0.7 O A:ILE341 2.5 25.5 1.0 O P:HOH210 2.7 28.3 1.0 C A:ILE341 3.4 24.4 1.0 C A:SER339 3.4 24.8 0.3 C A:SER339 3.5 23.4 0.7 C A:ALA344 3.5 23.8 1.0 O A:HOH708 3.5 32.0 0.6 P P:DA5 3.5 22.1 1.0 OP2 P:DA5 3.7 25.9 1.0 N A:ALA344 3.7 23.0 1.0 O P:HOH225 3.8 48.4 1.0 CA A:TRP342 3.9 25.2 1.0 N A:GLY343 4.0 23.6 1.0 N A:TRP342 4.0 23.4 1.0 N A:ILE341 4.1 20.7 1.0 CA A:ALA344 4.1 23.9 1.0 CA A:SER339 4.2 25.2 0.7 C A:ASN340 4.2 22.7 1.0 CA A:SER339 4.3 23.8 0.3 C A:TRP342 4.3 25.7 1.0 N A:ASN340 4.4 22.1 1.0 O3' P:DT4 4.4 22.7 1.0 CA A:ILE341 4.4 20.9 1.0 CA A:ASN340 4.4 23.6 1.0 N A:GLY345 4.5 22.3 1.0 CB A:ALA344 4.6 24.6 1.0 O P:HOH231 4.6 49.5 1.0 O5' P:DA5 4.7 20.3 1.0 C A:GLY343 4.7 24.2 1.0 CB A:SER339 4.7 31.4 0.7 CA A:GLY345 4.7 21.0 1.0 O A:HOH708 4.8 31.8 0.4 O1 A:EDO609 4.8 77.8 1.0 O A:ASN340 4.8 24.6 1.0 CA A:GLY343 4.9 23.8 1.0 CB A:SER339 5.0 22.6 0.3 O A:HOH863 5.0 44.8 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:61.7 occ:1.00 O A:ILE302 2.1 75.7 1.0 O A:HOH790 2.2 56.6 1.0 O A:CYS300 2.7 86.4 1.0 O A:ILE305 2.9 62.1 1.0 C A:ILE302 2.9 77.1 1.0 OP1 D:DC3 3.1 52.5 1.0 N A:PRO303 3.5 77.5 1.0 CA A:PRO303 3.5 69.3 1.0 N A:ILE302 3.7 74.3 1.0 C A:CYS300 3.7 88.0 1.0 C A:ILE305 3.8 62.3 1.0 N A:ILE305 3.9 54.0 1.0 CA A:ILE302 3.9 72.7 1.0 OP2 D:DC3 4.0 66.4 1.0 P D:DC3 4.0 58.8 1.0 C A:SER301 4.1 84.0 1.0 N A:GLY304 4.1 63.7 1.0 C A:PRO303 4.1 66.8 1.0 O A:SER301 4.2 84.1 1.0 CA A:ILE305 4.3 57.3 1.0 CA A:CYS300 4.3 86.0 1.0 CB A:ILE305 4.5 60.2 1.0 N A:SER301 4.7 89.9 1.0 O A:ALA299 4.8 77.9 1.0 CD A:PRO303 4.8 78.4 1.0 CB A:PRO303 4.9 70.9 1.0 C A:GLY304 4.9 49.9 1.0 CA A:SER301 4.9 91.0 1.0 CB A:ILE302 5.0 74.8 1.0 O3' D:DC2 5.0 47.0 1.0 N A:GLY306 5.0 57.3 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 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+ Reaction State Ternary Complex, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:61.2 occ:1.00 NE2 A:GLN366 2.3 61.7 1.0 O A:HOH807 3.1 76.5 1.0 O A:HOH716 3.1 99.8 1.0 CD A:GLN366 3.4 63.1 1.0 OE1 A:GLN366 3.7 64.6 1.0 CG A:GLN366 4.6 42.0 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