Sodium in PDB 7m4c: Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min, PDB code: 7m4c 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)	35.87 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.021, 62.641, 140.12, 90, 90, 90
R / Rfree (%)	18.1 / 21.4

The structure of Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min (pdb code 7m4c). 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, 960 Min, PDB code: 7m4c:
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, 960 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, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:20.6 occ:1.00 O A:ALA344 2.3 19.2 1.0 O A:SER339 2.4 20.9 1.0 OP1 P:DA5 2.4 19.5 1.0 O A:ILE341 2.4 21.5 1.0 O A:HOH807 2.5 28.6 1.0 O P:HOH209 2.6 24.4 1.0 C A:ALA344 3.4 21.9 1.0 C A:ILE341 3.4 23.6 1.0 C A:SER339 3.4 22.4 1.0 P P:DA5 3.4 23.5 1.0 OP2 P:DA5 3.6 20.6 1.0 N A:ALA344 3.7 20.3 1.0 O A:HOH779 3.7 35.6 1.0 N A:GLY343 3.9 20.9 1.0 CA A:TRP342 4.0 22.7 1.0 N A:TRP342 4.0 22.2 1.0 CA A:SER339 4.1 22.0 1.0 CA A:ALA344 4.1 22.4 1.0 N A:ILE341 4.1 19.2 1.0 C A:ASN340 4.3 19.4 1.0 O3' P:DT4 4.3 21.7 1.0 C A:TRP342 4.3 23.3 1.0 N A:ASN340 4.4 20.8 1.0 N A:GLY345 4.4 20.6 1.0 CA A:ILE341 4.4 21.1 1.0 CA A:ASN340 4.4 19.5 1.0 O P:HOH227 4.5 23.5 0.5 CA A:GLY345 4.6 22.8 1.0 CB A:ALA344 4.6 24.4 1.0 O5' P:DA5 4.6 18.7 1.0 C A:GLY343 4.6 22.4 1.0 CB A:SER339 4.7 29.7 1.0 O P:HOH227 4.7 22.0 0.5 O A:HOH843 4.8 60.0 1.0 CA A:GLY343 4.8 20.7 1.0 O A:ASN340 4.9 22.6 1.0 O1 A:EDO609 4.9 32.8 0.7 O A:PHE338 5.0 20.1 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 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, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:69.6 occ:1.00 O A:ILE302 2.7 62.5 1.0 O A:ILE305 2.8 67.0 1.0 O A:CYS300 2.8 95.8 1.0 OP1 D:DC3 3.1 50.0 1.0 C A:ILE302 3.6 69.2 1.0 OP2 D:DC3 3.6 56.0 1.0 P D:DC3 3.8 53.8 1.0 C A:ILE305 3.8 61.4 1.0 C A:CYS300 3.9 93.0 1.0 CA A:PRO303 4.1 69.9 1.0 N A:ILE302 4.2 69.7 1.0 N A:PRO303 4.2 71.4 1.0 N A:ILE305 4.3 49.4 1.0 C A:SER301 4.4 70.0 1.0 N A:GLY304 4.5 55.5 1.0 CA A:ILE302 4.5 71.4 1.0 CA A:ILE305 4.6 54.7 1.0 CA A:CYS300 4.6 92.8 1.0 C A:PRO303 4.7 66.8 1.0 O A:SER301 4.7 68.2 1.0 N A:GLY306 4.8 59.9 1.0 N A:SER301 4.8 83.0 1.0 O3' D:DC2 4.9 46.3 1.0 CA A:GLY306 4.9 57.7 1.0 SG A:CYS300 5.0 93.3 1.0 O5' D:DC3 5.0 49.8 1.0 CA A:SER301 5.0 77.3 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 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, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:36.6 occ:0.66 NE2 A:GLN366 2.1 63.5 1.0 O A:HOH836 2.4 58.3 1.0 O A:HOH827 2.9 82.2 1.0 CD A:GLN366 3.2 58.4 1.0 O A:HOH828 3.3 55.5 1.0 OE1 A:GLN366 3.6 64.3 1.0 CG A:GLN366 4.6 45.5 1.0 CE1 A:PHE357 5.0 29.3 0.5

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