Sodium in PDB 5yur: Dna Polymerase IV - Dna Ternary Complex 1

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 1:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 1, PDB code: 5yur was solved by J.Kottur, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.29 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.560, 57.010, 110.431, 90.00, 94.79, 90.00
R / Rfree (%)	20.4 / 25.2

The binding sites of Sodium atom in the Dna Polymerase IV - Dna Ternary Complex 1 (pdb code 5yur). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase IV - Dna Ternary Complex 1, PDB code: 5yur:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase IV - Dna Ternary Complex 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase IV - Dna Ternary Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na901 b:65.8 occ:1.00 OD1 F:ASP8 2.3 48.7 1.0 O2A F:TTP900 2.3 42.6 1.0 OD2 F:ASP103 2.3 42.0 1.0 O F:MET9 2.4 47.7 1.0 O2B F:TTP900 2.5 31.6 1.0 O2G F:TTP900 2.7 46.8 1.0 PB F:TTP900 3.3 35.8 1.0 PA F:TTP900 3.4 40.1 1.0 CG F:ASP8 3.4 47.2 1.0 O F:HOH1036 3.5 63.6 1.0 CG F:ASP103 3.5 42.8 1.0 C F:MET9 3.5 49.8 1.0 O3A F:TTP900 3.6 36.4 1.0 PG F:TTP900 3.7 44.4 1.0 OD2 F:ASP8 3.8 53.8 1.0 O3B F:TTP900 4.0 50.8 1.0 OD1 F:ASP103 4.0 41.5 1.0 N F:MET9 4.0 34.5 1.0 C5' F:TTP900 4.0 33.0 1.0 NZ F:LYS157 4.1 43.8 1.0 O1G F:TTP900 4.1 52.8 1.0 O5' F:TTP900 4.2 35.5 1.0 CA F:MET9 4.3 45.3 1.0 C F:ASP8 4.4 33.2 1.0 N F:ASP10 4.6 40.5 1.0 CE F:LYS157 4.6 53.4 1.0 O1B F:TTP900 4.6 44.6 1.0 O1A F:TTP900 4.6 37.0 1.0 CB F:ASP8 4.6 39.3 1.0 N F:CYS11 4.7 30.4 1.0 CB F:PHE12 4.7 32.9 1.0 CB F:MET9 4.7 34.2 1.0 N F:PHE12 4.7 30.4 1.0 CB F:ASP103 4.7 32.0 1.0 OE1 F:GLU104 4.8 63.3 1.0 CA F:ASP10 4.8 30.5 1.0 CA F:ASP8 4.8 34.0 1.0 O F:ASP8 4.9 37.6 1.0 C F:ASP10 4.9 34.6 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase IV - Dna Ternary Complex 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase IV - Dna Ternary Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:41.6 occ:1.00 O2B A:TTP401 2.2 44.3 1.0 OD1 A:ASP8 2.3 70.4 1.0 OD2 A:ASP103 2.3 48.8 1.0 O2A A:TTP401 2.3 44.8 1.0 O A:MET9 2.3 40.6 1.0 O2G A:TTP401 2.7 65.5 1.0 PB A:TTP401 3.3 45.6 1.0 CG A:ASP103 3.4 48.6 1.0 PA A:TTP401 3.4 50.6 1.0 CG A:ASP8 3.5 66.3 1.0 C A:MET9 3.5 50.0 1.0 PG A:TTP401 3.7 61.6 1.0 O3A A:TTP401 3.7 49.4 1.0 O1G A:TTP401 3.8 54.1 1.0 OD1 A:ASP103 3.9 46.7 1.0 O A:HOH529 3.9 63.2 1.0 C5' A:TTP401 4.0 51.6 1.0 O3B A:TTP401 4.0 50.9 1.0 N A:MET9 4.0 48.0 1.0 NZ A:LYS157 4.0 60.0 1.0 OD2 A:ASP8 4.1 76.9 1.0 O5' A:TTP401 4.2 51.2 1.0 CA A:MET9 4.2 54.5 1.0 C A:ASP8 4.3 48.9 1.0 OE2 A:GLU104 4.4 73.0 1.0 N A:ASP10 4.5 49.1 1.0 CB A:ASP8 4.6 56.4 1.0 O1B A:TTP401 4.6 52.7 1.0 CB A:MET9 4.6 58.5 1.0 O1A A:TTP401 4.7 49.2 1.0 CB A:ASP103 4.7 53.7 1.0 N A:CYS11 4.7 46.9 1.0 CA A:ASP10 4.7 47.2 1.0 CB A:PHE12 4.7 57.2 1.0 O A:ASP8 4.7 50.7 1.0 N A:PHE12 4.7 49.3 1.0 CE A:LYS157 4.7 64.8 1.0 CA A:ASP8 4.8 51.9 1.0 C A:ASP10 4.9 48.0 1.0 CG A:GLU104 5.0 68.6 1.0

J.Kottur, D.T.Nair. Pyrophosphate Hydrolysis Is An Intrinsic and Critical Step of the Dna Synthesis Reaction Nucleic Acids Res. V. 46 5875 2018.
ISSN: ESSN 1362-4962
PubMed: 29850882
DOI: 10.1093/NAR/GKY402