Sodium in PDB 5yyd: Dna Polymerase IV - Ternary Complex 15

All present enzymatic activity of Dna Polymerase IV - Ternary Complex 15:
2.7.7.7;

The structure of Dna Polymerase IV - Ternary Complex 15, PDB code: 5yyd 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)	70.92 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.650, 57.050, 110.330, 90.00, 94.94, 90.00
R / Rfree (%)	19.5 / 23.7

The binding sites of Sodium atom in the Dna Polymerase IV - Ternary Complex 15 (pdb code 5yyd). 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 - Ternary Complex 15, PDB code: 5yyd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase IV - Ternary Complex 15


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 - Ternary Complex 15 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na901 b:28.7 occ:1.00 OD1 F:ASP8 2.3 47.8 1.0 O F:MET9 2.3 42.3 1.0 O2A F:TTW900 2.3 35.8 1.0 OD2 F:ASP103 2.3 41.9 1.0 O2G F:TTW900 2.3 38.7 1.0 O2B F:TTW900 2.4 34.9 1.0 PB F:TTW900 3.4 34.1 1.0 CG F:ASP8 3.4 49.0 1.0 C F:MET9 3.5 41.4 1.0 CG F:ASP103 3.5 39.8 1.0 PA F:TTW900 3.5 36.4 1.0 PG F:TTW900 3.5 40.0 1.0 O3A F:TTW900 3.7 39.2 1.0 N F:MET9 3.9 36.7 1.0 OD2 F:ASP8 3.9 51.9 1.0 OD1 F:ASP103 4.0 36.0 1.0 N3B F:TTW900 4.0 42.0 1.0 O F:HOH1038 4.0 44.1 1.0 O1G F:TTW900 4.0 44.1 1.0 C5' F:TTW900 4.1 32.0 1.0 O F:HOH1066 4.1 39.8 1.0 CA F:MET9 4.2 37.7 1.0 O5' F:TTW900 4.3 32.5 1.0 C F:ASP8 4.3 34.0 1.0 OE1 F:GLU104 4.4 47.6 1.0 N F:ASP10 4.5 36.2 1.0 CB F:ASP8 4.6 43.1 1.0 N F:CYS11 4.6 29.0 1.0 CB F:MET9 4.6 30.9 1.0 O1A F:TTW900 4.7 30.4 1.0 O1B F:TTW900 4.7 31.9 1.0 CB F:ASP103 4.7 35.1 1.0 CA F:ASP10 4.7 31.1 1.0 N F:PHE12 4.7 30.9 1.0 O3G F:TTW900 4.8 36.5 1.0 O F:ASP8 4.8 35.3 1.0 CB F:PHE12 4.8 30.9 1.0 CA F:ASP8 4.8 38.1 1.0 C F:ASP10 4.9 35.6 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase IV - Ternary Complex 15


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 - Ternary Complex 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:32.3 occ:1.00 OD1 A:ASP8 2.1 53.1 1.0 O2A A:TTW900 2.2 35.1 1.0 O A:MET9 2.3 46.9 1.0 O2G A:TTW900 2.3 56.6 1.0 O2B A:TTW900 2.3 34.3 1.0 OD2 A:ASP103 2.4 45.4 1.0 CG A:ASP8 3.3 60.5 1.0 PB A:TTW900 3.3 39.5 1.0 PA A:TTW900 3.4 44.8 1.0 PG A:TTW900 3.5 48.6 1.0 C A:MET9 3.5 44.9 1.0 CG A:ASP103 3.5 46.9 1.0 O3A A:TTW900 3.7 47.9 1.0 OD1 A:ASP103 3.8 38.9 1.0 N3B A:TTW900 3.9 43.2 1.0 OD2 A:ASP8 3.9 70.6 1.0 O A:HOH1036 3.9 50.1 1.0 O1G A:TTW900 3.9 45.9 1.0 N A:MET9 4.0 49.2 1.0 C5' A:TTW900 4.0 40.6 1.0 NZ A:LYS157 4.1 43.6 1.0 O5' A:TTW900 4.2 45.8 1.0 CA A:MET9 4.2 46.1 1.0 C A:ASP8 4.3 54.3 1.0 OE2 A:GLU104 4.4 58.7 1.0 CB A:ASP8 4.4 52.8 1.0 N A:ASP10 4.5 49.6 1.0 O1A A:TTW900 4.6 44.3 1.0 N A:CYS11 4.6 42.3 1.0 O1B A:TTW900 4.7 44.4 1.0 CA A:ASP10 4.7 38.9 1.0 N A:PHE12 4.7 43.5 1.0 CB A:MET9 4.7 45.6 1.0 O3G A:TTW900 4.7 46.8 1.0 CA A:ASP8 4.7 53.2 1.0 CE A:LYS157 4.8 54.0 1.0 O A:ASP8 4.8 51.9 1.0 CB A:ASP103 4.8 51.7 1.0 CB A:PHE12 4.9 45.1 1.0 C A:ASP10 4.9 42.0 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