Sodium in PDB 7m4f: Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min, PDB code: 7m4f 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)	36.13 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.869, 62.065, 142.087, 90, 90, 90
R / Rfree (%)	20.8 / 24.1

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min (pdb code 7m4f). 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, Dctp:at MG2+ Product State Ternary Complex, 300 Min, PDB code: 7m4f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 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 MG2+ Product State Ternary Complex, 300 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:44.1 occ:1.00 OD2 A:ASP427 2.0 63.0 0.5 OD1 A:ASP429 2.2 51.0 1.0 O P:HOH113 2.4 41.8 0.5 OP1 P:DC7 2.4 49.9 1.0 OD2 A:ASP490 2.5 38.7 1.0 O3' P:DC6 2.7 47.2 1.0 CG A:ASP427 3.0 39.1 0.5 P P:DC7 3.0 50.8 1.0 OD1 A:ASP427 3.1 41.2 0.5 CG A:ASP429 3.3 84.0 1.0 CG A:ASP490 3.3 37.1 1.0 OD1 A:ASP427 3.4 47.3 0.5 MG A:MG604 3.4 44.5 1.0 CG A:ASP427 3.6 59.8 0.5 O A:HOH766 3.7 76.1 1.0 OD2 A:ASP429 3.8 46.7 1.0 C3' P:DC6 3.9 42.2 1.0 OP2 P:DC7 4.0 67.3 1.0 OD1 A:ASP490 4.1 41.1 1.0 CB A:ASP490 4.1 33.5 1.0 OD2 A:ASP427 4.1 36.3 0.5 C5' P:DC6 4.1 46.1 1.0 C4' P:DC6 4.1 47.4 1.0 O5' P:DC7 4.3 46.0 1.0 CB A:ASP427 4.3 34.5 0.5 CB A:ASP427 4.3 41.1 0.5 NH2 A:ARG488 4.5 37.8 1.0 C5' P:DC7 4.5 46.0 1.0 CB A:ASP429 4.5 45.8 1.0 O22 A:PPV605 4.8 47.7 0.9 O A:VAL428 4.8 34.7 1.0 O5' P:DC6 4.9 47.6 1.0 OP1 P:DC6 4.9 38.5 1.0 CA A:ASP429 5.0 38.0 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 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 MG2+ Product State Ternary Complex, 300 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:32.5 occ:1.00 O A:ALA344 2.2 34.7 1.0 O P:HOH115 2.4 43.8 1.0 O A:SER339 2.4 35.2 1.0 O A:ILE341 2.4 32.3 1.0 OP1 P:DA5 2.5 34.4 1.0 O P:HOH103 2.6 42.3 1.0 C A:ALA344 3.4 33.7 1.0 C A:ILE341 3.4 32.1 1.0 C A:SER339 3.4 31.9 1.0 P P:DA5 3.6 32.8 1.0 OP2 P:DA5 3.7 33.1 1.0 N A:ALA344 3.7 32.6 1.0 O A:HOH768 3.8 44.7 1.0 CA A:TRP342 4.0 34.7 1.0 N A:GLY343 4.0 31.8 1.0 N A:TRP342 4.0 32.8 1.0 CA A:SER339 4.0 32.1 1.0 CA A:ALA344 4.1 32.5 1.0 N A:ILE341 4.1 31.9 1.0 C A:TRP342 4.3 39.4 1.0 C A:ASN340 4.3 32.0 1.0 N A:GLY345 4.4 31.6 1.0 O3' P:DT4 4.4 42.2 1.0 N A:ASN340 4.4 33.5 1.0 CA A:ILE341 4.4 33.9 1.0 CA A:ASN340 4.5 34.2 1.0 CA A:GLY345 4.5 35.4 1.0 CB A:SER339 4.5 36.6 1.0 O P:HOH119 4.6 63.8 1.0 CB A:ALA344 4.6 34.0 1.0 C A:GLY343 4.7 32.4 1.0 O5' P:DA5 4.8 34.0 1.0 O A:ASN340 4.8 35.1 1.0 CA A:GLY343 4.9 33.3 1.0 O A:PHE338 4.9 33.6 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 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, Dctp:at MG2+ Product State Ternary Complex, 300 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:56.5 occ:1.00 NE2 A:GLN366 2.7 58.1 1.0 O A:HOH792 2.7 106.8 1.0 O A:HOH784 3.1 92.9 1.0 CD A:GLN366 3.8 89.0 1.0 OE1 A:GLN366 4.1 104.3 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