Sodium in PDB 7m4j: Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min

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

The structure of Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min, PDB code: 7m4j 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)	42.04 / 2.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.975, 63.66, 139.97, 90, 90, 90
R / Rfree (%)	22.6 / 26.1

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

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min (pdb code 7m4j). 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, 960 Min, PDB code: 7m4j:
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, 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 MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:34.9 occ:1.00 OP1 P:DA5 2.3 38.4 1.0 O A:ILE341 2.3 28.8 1.0 O A:SER339 2.4 33.7 1.0 O A:HOH729 2.4 35.5 1.0 O A:ALA344 2.5 29.6 1.0 O P:HOH104 2.6 35.4 1.0 C A:ILE341 3.3 28.7 1.0 P P:DA5 3.4 37.0 1.0 C A:SER339 3.5 34.0 1.0 C A:ALA344 3.6 29.9 1.0 OP2 P:DA5 3.7 36.7 1.0 N A:ALA344 3.8 29.4 1.0 O A:HOH738 3.8 35.4 1.0 CA A:TRP342 3.9 31.5 1.0 N A:TRP342 4.0 32.2 1.0 N A:GLY343 4.0 28.9 1.0 N A:ILE341 4.1 29.0 1.0 CA A:ALA344 4.2 29.8 1.0 C A:ASN340 4.3 33.6 1.0 C A:TRP342 4.3 31.4 1.0 CA A:SER339 4.3 35.0 1.0 CA A:ILE341 4.3 28.9 1.0 N A:ASN340 4.4 35.2 1.0 O3' P:DT4 4.4 30.0 1.0 CA A:ASN340 4.4 34.5 1.0 O5' P:DA5 4.6 39.5 1.0 N A:GLY345 4.6 34.5 1.0 CB A:ALA344 4.7 29.9 1.0 C A:GLY343 4.7 29.6 1.0 O1 A:EDO608 4.8 39.4 0.8 O A:ASN340 4.9 33.5 1.0 CA A:GLY343 4.9 29.3 1.0 CA A:GLY345 4.9 34.1 1.0 CB A:SER339 4.9 36.4 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda, Dctp: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, Dctp:at MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:62.6 occ:1.00 O A:ILE302 2.5 72.6 1.0 O A:CYS300 2.6 93.7 1.0 O A:ILE305 2.7 65.2 1.0 OP1 D:DC3 3.1 63.0 1.0 OP2 D:DC3 3.4 61.7 1.0 C A:ILE302 3.5 73.6 1.0 C A:CYS300 3.6 93.2 1.0 P D:DC3 3.7 61.1 1.0 C A:ILE305 3.8 64.7 1.0 N A:ILE305 4.2 64.5 1.0 CA A:PRO303 4.2 71.5 1.0 N A:ILE302 4.2 72.2 1.0 CA A:CYS300 4.2 91.6 1.0 N A:PRO303 4.3 72.8 1.0 C A:SER301 4.3 65.6 1.0 N A:GLY304 4.4 57.7 1.0 O A:SER301 4.5 65.5 1.0 CA A:ILE302 4.5 72.0 1.0 CA A:ILE305 4.5 65.0 1.0 N A:SER301 4.6 66.3 1.0 N A:GLY306 4.7 57.8 1.0 O3' D:DC2 4.7 59.8 1.0 C A:PRO303 4.8 58.8 1.0 O A:ALA299 4.8 85.1 1.0 CA A:GLY306 4.9 57.9 1.0 CA A:SER301 4.9 66.9 1.0 CB A:CYS300 5.0 91.7 1.0 CB A:ILE305 5.0 67.0 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda, Dctp: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, Dctp:at MN2+ Product State Ternary Complex, 960 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:33.4 occ:1.00 OD1 A:ASP429 2.2 37.4 1.0 OP1 P:DC7 2.4 53.5 1.0 OD2 A:ASP490 2.4 30.5 1.0 O3' P:DC6 3.0 58.9 1.0 CG A:ASP490 3.2 30.6 1.0 OD2 A:ASP427 3.2 43.3 1.0 P P:DC7 3.2 48.6 1.0 CG A:ASP427 3.3 41.9 1.0 CG A:ASP429 3.3 36.9 1.0 OD1 A:ASP427 3.4 45.4 1.0 MN A:MN601 3.6 30.6 0.8 OD2 A:ASP429 3.7 40.3 1.0 OD1 A:ASP490 3.8 30.1 1.0 CB A:ASP490 3.9 31.3 1.0 OP2 P:DC7 4.1 47.1 1.0 CB A:ASP427 4.1 37.7 1.0 C3' P:DC6 4.1 57.0 1.0 C5' P:DC6 4.2 50.0 1.0 NH2 A:ARG488 4.2 35.4 1.0 C4' P:DC6 4.2 54.1 1.0 O5' P:DC7 4.5 49.5 1.0 CB A:ASP429 4.6 34.8 1.0 O A:VAL428 4.8 39.9 1.0 C5' P:DC7 4.8 51.3 1.0 OP1 P:DC6 4.9 42.5 1.0 CZ A:ARG488 4.9 34.7 1.0 O1 A:PO4606 4.9 69.7 1.0 O5' P:DC6 4.9 46.9 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