Sodium in PDB 7m4g: Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min

All present enzymatic activity of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min:
2.7.7.7;

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min, PDB code: 7m4g 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)	39.93 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.997, 62.235, 141.114, 90, 90, 90
R / Rfree (%)	21.2 / 24

The structure of Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min (pdb code 7m4g). 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, 960 Min, PDB code: 7m4g:
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, 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, Dctp:at MG2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:33.7 occ:1.00 O A:ALA344 2.3 31.4 1.0 O A:SER339 2.4 30.7 1.0 O A:HOH725 2.4 38.0 1.0 OP1 P:DA5 2.5 31.2 1.0 O P:HOH107 2.5 34.2 1.0 O A:ILE341 2.5 30.7 1.0 C A:ALA344 3.4 31.6 1.0 C A:SER339 3.4 33.3 1.0 C A:ILE341 3.4 30.9 1.0 P P:DA5 3.5 36.8 1.0 OP2 P:DA5 3.7 30.9 1.0 N A:ALA344 3.8 31.8 1.0 O A:HOH781 4.0 58.7 1.0 N A:GLY343 4.0 30.9 1.0 CA A:TRP342 4.0 35.3 1.0 N A:TRP342 4.1 31.8 1.0 N A:ILE341 4.1 31.3 1.0 CA A:SER339 4.1 31.6 1.0 CA A:ALA344 4.2 32.1 1.0 C A:ASN340 4.3 31.8 1.0 N A:ASN340 4.3 32.1 1.0 N A:GLY345 4.4 35.1 1.0 C A:TRP342 4.4 38.3 1.0 CA A:ASN340 4.4 32.0 1.0 CA A:ILE341 4.4 31.4 1.0 O P:HOH116 4.4 70.0 1.0 O3' P:DT4 4.5 30.4 1.0 CB A:SER339 4.6 39.2 1.0 CA A:GLY345 4.6 40.5 1.0 O5' P:DA5 4.7 31.7 1.0 CB A:ALA344 4.7 32.5 1.0 C A:GLY343 4.8 31.5 1.0 O1 A:EDO605 4.8 65.3 1.0 O A:ASN340 4.9 33.5 1.0 CA A:GLY343 5.0 32.3 1.0 O A:PHE338 5.0 31.7 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Dctp:at MG2+ 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, Dctp:at MG2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:46.0 occ:1.00 O A:HOH764 2.1 41.1 1.0 OD1 A:ASP429 2.1 70.6 1.0 OD2 A:ASP490 2.4 44.2 1.0 OP1 P:DC7 2.4 57.7 1.0 O3' P:DC6 2.8 55.0 1.0 OD1 A:ASP427 2.9 61.9 1.0 P P:DC7 3.1 51.4 1.0 CG A:ASP429 3.2 70.9 1.0 CG A:ASP427 3.2 66.1 1.0 CG A:ASP490 3.3 43.3 1.0 OD2 A:ASP427 3.6 81.9 1.0 OD2 A:ASP429 3.7 83.3 1.0 MG A:MG604 3.7 70.3 1.0 OP2 P:DC7 3.9 55.0 1.0 C5' P:DC6 3.9 50.1 1.0 C3' P:DC6 3.9 49.8 1.0 OD1 A:ASP490 3.9 40.4 1.0 CB A:ASP427 4.0 46.8 1.0 C4' P:DC6 4.0 57.2 1.0 O A:HOH760 4.1 43.3 1.0 CB A:ASP490 4.1 34.9 1.0 NH2 A:ARG488 4.2 38.8 1.0 CB A:ASP429 4.5 54.3 1.0 O5' P:DC7 4.5 54.4 1.0 OP1 P:DC6 4.7 42.2 1.0 O5' P:DC6 4.7 52.8 1.0 C5' P:DC7 4.8 58.2 1.0 O A:VAL428 4.9 39.0 1.0 CA A:ASP429 4.9 35.5 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Dctp:at MG2+ 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, Dctp:at MG2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:55.1 occ:1.00 O D:HOH103 2.2 72.4 1.0 O A:ILE302 2.7 63.8 1.0 O A:ILE305 2.7 68.4 1.0 O A:CYS300 2.7 84.4 1.0 OP1 D:DC3 2.9 68.8 1.0 OP2 D:DC3 3.5 61.9 1.0 C A:ILE302 3.5 77.9 1.0 P D:DC3 3.6 58.4 1.0 C A:CYS300 3.7 89.2 1.0 C A:ILE305 3.8 71.8 1.0 CA A:PRO303 3.9 77.3 0.6 CA A:PRO303 3.9 77.4 0.4 N A:PRO303 4.1 82.8 0.6 N A:PRO303 4.1 83.1 0.4 N A:ILE305 4.1 64.6 1.0 N A:GLY304 4.2 63.6 1.0 N A:ILE302 4.2 83.1 1.0 CA A:CYS300 4.4 86.8 1.0 C A:SER301 4.4 79.9 1.0 C A:PRO303 4.5 70.2 0.4 C A:PRO303 4.5 70.4 0.6 CA A:ILE305 4.5 76.2 1.0 CA A:ILE302 4.5 70.5 1.0 O3' D:DC2 4.7 57.7 1.0 O A:SER301 4.7 81.8 1.0 N A:SER301 4.7 82.4 1.0 N A:GLY306 4.8 62.6 1.0 O A:ALA299 4.8 78.3 1.0 O5' D:DC3 4.9 57.4 1.0 CB A:ILE305 4.9 77.4 1.0 CA A:SER301 5.0 90.5 1.0 CA A:GLY306 5.0 65.7 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