Sodium in PDB 7m4k: Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex

All present enzymatic activity of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex:
2.7.7.7;

The structure of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex, PDB code: 7m4k 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)	31.12 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.001, 62.507, 140.191, 90, 90, 90
R / Rfree (%)	19.6 / 22.7

The structure of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex (pdb code 7m4k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex, PDB code: 7m4k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex


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, Ttpas:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:48.7 occ:1.00 OD1 A:ASP429 2.3 47.5 1.0 OD2 A:ASP427 2.3 48.6 1.0 OD2 A:ASP490 2.4 37.2 1.0 O1A A:YQS612 2.4 66.7 1.0 OD1 A:ASP427 2.8 47.5 1.0 CG A:ASP427 2.9 57.2 1.0 CG A:ASP490 3.3 43.9 1.0 CG A:ASP429 3.4 59.2 1.0 O3' P:DC6 3.5 48.9 1.0 PA A:YQS612 3.6 50.8 1.0 C3' P:DC6 3.7 64.6 1.0 CA A:CA601 3.7 45.6 1.0 OD2 A:ASP429 3.8 54.8 1.0 O5' A:YQS612 3.9 80.7 1.0 OD1 A:ASP490 4.0 34.3 1.0 CB A:ASP490 4.0 31.2 1.0 C5' A:YQS612 4.1 69.3 1.0 CB A:ASP427 4.3 52.9 1.0 S2A A:YQS612 4.3 42.7 1.0 NH2 A:ARG488 4.5 30.5 1.0 C4' P:DC6 4.5 65.7 1.0 C5' P:DC6 4.6 45.6 1.0 CB A:ASP429 4.6 49.1 1.0 O A:VAL428 4.7 29.9 1.0 C2' P:DC6 4.9 58.0 1.0 O5' P:DC6 4.9 33.5 1.0 O1G A:YQS612 4.9 96.2 1.0 O A:HOH764 4.9 40.5 1.0 C A:VAL428 4.9 28.3 1.0 OP1 P:DC6 5.0 27.2 1.0 O3A A:YQS612 5.0 106.5 1.0

Sodium binding site 2 out of 4 in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex


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, Ttpas:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:24.9 occ:1.00 O A:SER339 2.4 24.1 1.0 O A:ALA344 2.4 23.3 1.0 O A:HOH749 2.4 31.3 1.0 OP1 P:DA5 2.4 25.5 1.0 O A:ILE341 2.4 26.0 1.0 O P:HOH106 2.7 32.3 1.0 C A:ILE341 3.4 26.7 1.0 C A:SER339 3.4 22.3 1.0 C A:ALA344 3.4 22.7 1.0 P P:DA5 3.5 24.6 1.0 OP2 P:DA5 3.7 25.3 1.0 O A:HOH776 3.7 40.0 1.0 N A:ALA344 3.8 23.8 1.0 N A:GLY343 3.9 23.5 1.0 CA A:TRP342 4.0 24.8 1.0 N A:TRP342 4.0 23.7 1.0 CA A:SER339 4.1 24.0 1.0 N A:ILE341 4.1 21.7 1.0 CA A:ALA344 4.2 25.9 1.0 C A:ASN340 4.3 23.4 1.0 C A:TRP342 4.3 31.6 1.0 N A:ASN340 4.4 23.2 1.0 O3' P:DT4 4.4 22.9 1.0 CA A:ILE341 4.4 21.2 1.0 CA A:ASN340 4.4 22.5 1.0 N A:GLY345 4.4 23.8 1.0 O A:HOH818 4.5 45.0 1.0 CB A:ALA344 4.6 27.2 1.0 O5' P:DA5 4.6 22.4 1.0 CB A:SER339 4.7 33.7 1.0 CA A:GLY345 4.7 26.1 1.0 O1 A:EDO606 4.7 50.3 1.0 C A:GLY343 4.7 22.2 1.0 O A:ASN340 4.8 25.5 1.0 CA A:GLY343 4.9 26.0 1.0 O A:HOH819 4.9 50.4 1.0 O A:PHE338 5.0 23.9 1.0

Sodium binding site 3 out of 4 in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex


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, Ttpas:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:58.9 occ:1.00 O A:CYS300 2.6 106.8 1.0 O A:ILE305 2.7 61.7 1.0 O A:ILE302 2.7 64.0 1.0 OP1 D:DC3 3.0 65.1 1.0 C A:CYS300 3.6 101.5 1.0 OP2 D:DC3 3.7 60.4 1.0 C A:ILE302 3.8 85.9 1.0 C A:ILE305 3.8 61.2 1.0 P D:DC3 3.8 57.2 1.0 CA A:CYS300 4.1 104.8 1.0 N A:ILE305 4.1 57.3 1.0 CA A:PRO303 4.2 72.1 1.0 N A:PRO303 4.4 78.0 1.0 N A:GLY304 4.4 62.5 1.0 CA A:ILE305 4.4 62.9 1.0 N A:ILE302 4.5 95.2 1.0 C A:SER301 4.6 77.9 1.0 CB A:CYS300 4.6 100.8 1.0 N A:SER301 4.7 78.4 1.0 C A:PRO303 4.8 70.2 1.0 O A:SER301 4.8 82.5 1.0 N A:GLY306 4.8 56.3 1.0 CA A:ILE302 4.8 95.5 1.0 CB A:ILE305 4.8 60.1 1.0 O3' D:DC2 4.9 48.2 1.0 O A:ALA299 4.9 79.1 1.0

Sodium binding site 4 out of 4 in the Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:60.0 occ:1.00 OE1 A:GLN366 2.3 110.2 1.0 O A:HOH713 3.0 95.6 1.0 CD A:GLN366 3.2 94.5 1.0 O A:HOH757 3.4 68.8 1.0 NE2 A:GLN366 3.5 117.8 1.0 CG A:GLN366 4.6 58.2 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