Sodium in PDB 7m4i: Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 Min, PDB code: 7m4i 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)	37.72 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.75, 62.317, 142.177, 90, 90, 90
R / Rfree (%)	22.2 / 24.7

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 Min also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 Min (pdb code 7m4i). 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 MN2+ Product State Ternary Complex, 420 Min, PDB code: 7m4i:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 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 MN2+ Product State Ternary Complex, 420 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:34.7 occ:1.00 OP1 P:DA5 2.3 36.7 1.0 O A:ALA344 2.3 35.5 1.0 O A:SER339 2.4 35.1 1.0 O A:ILE341 2.5 34.4 1.0 O A:HOH731 2.6 46.3 1.0 O P:HOH105 2.6 39.2 1.0 C A:ALA344 3.3 38.6 1.0 P P:DA5 3.4 39.4 1.0 C A:SER339 3.4 37.2 1.0 C A:ILE341 3.5 34.5 1.0 OP2 P:DA5 3.6 33.7 1.0 N A:ALA344 3.7 34.5 1.0 O A:HOH727 3.8 54.0 1.0 N A:GLY343 4.0 38.4 1.0 CA A:TRP342 4.0 35.2 1.0 CA A:ALA344 4.1 37.4 1.0 N A:TRP342 4.1 36.7 1.0 CA A:SER339 4.1 37.7 1.0 N A:ILE341 4.1 34.4 1.0 N A:GLY345 4.3 34.8 1.0 O A:HOH754 4.3 60.7 1.0 O3' P:DT4 4.3 35.1 1.0 C A:TRP342 4.4 36.3 1.0 C A:ASN340 4.4 34.2 1.0 N A:ASN340 4.4 34.5 1.0 CA A:ILE341 4.4 36.4 1.0 CA A:ASN340 4.5 34.3 1.0 CA A:GLY345 4.6 43.1 1.0 O5' P:DA5 4.6 35.9 1.0 C A:GLY343 4.6 38.2 1.0 CB A:ALA344 4.7 39.1 1.0 CB A:SER339 4.8 40.7 1.0 O1 A:EDO608 4.8 40.5 0.8 CA A:GLY343 4.9 40.8 1.0 O A:PHE338 5.0 35.5 1.0 O A:ASN340 5.0 36.5 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 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 MN2+ Product State Ternary Complex, 420 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:45.5 occ:0.66 NE2 A:GLN366 2.5 57.1 1.0 O A:HOH750 2.9 71.2 1.0 O A:HOH757 3.0 68.6 1.0 O A:HOH732 3.3 77.8 1.0 CD A:GLN366 3.5 65.8 1.0 OE1 A:GLN366 3.8 80.8 1.0 CG A:GLN366 4.9 61.5 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 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 MN2+ Product State Ternary Complex, 420 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:55.0 occ:0.54 O A:ILE302 2.4 86.5 1.0 OP1 D:DC3 2.7 65.3 1.0 O A:ILE305 2.9 76.7 1.0 O A:CYS300 3.2 102.2 1.0 OP2 D:DC3 3.3 65.2 1.0 C A:ILE302 3.4 90.2 1.0 P D:DC3 3.5 64.6 1.0 CA A:PRO303 3.8 80.7 1.0 C A:ILE305 3.9 68.7 1.0 N A:PRO303 3.9 88.3 1.0 C A:CYS300 4.1 99.8 1.0 N A:GLY304 4.1 64.5 1.0 N A:ILE305 4.1 63.2 1.0 N A:ILE302 4.3 84.1 1.0 C A:PRO303 4.3 74.3 1.0 CA A:ILE302 4.4 85.4 1.0 C A:SER301 4.5 91.5 1.0 O3' D:DC2 4.6 63.5 1.0 CA A:ILE305 4.6 70.7 1.0 O5' D:DC3 4.6 64.1 1.0 CA A:CYS300 4.6 100.2 1.0 O A:SER301 4.7 92.0 1.0 N A:GLY306 4.8 74.6 1.0 O A:ALA299 4.9 94.3 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