Sodium in PDB 2e5x: Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3

All present enzymatic activity of Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3:
3.6.1.19;

The structure of Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3, PDB code: 2e5x was solved by H.Mizutani, N.K.Lokanath, N.Kunishima, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.080, 75.080, 84.470, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 22.2

The binding sites of Sodium atom in the Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3 (pdb code 2e5x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3, PDB code: 2e5x:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:39.2 occ:1.00 O A:HOH595 1.8 45.6 1.0 O2G A:ITT201 2.5 26.8 1.0 O A:GLU64 2.6 12.6 1.0 OD1 A:ASP65 2.6 27.5 1.0 O2A A:ITT201 2.9 30.6 1.0 OE2 A:GLU36 3.1 28.9 1.0 OH A:TYR34 3.3 24.2 1.0 CG A:ASP65 3.5 25.4 1.0 CA A:ASP65 3.5 16.3 1.0 O1A A:ITT201 3.5 32.2 1.0 NA A:NA302 3.5 29.0 1.0 C A:GLU64 3.6 15.1 1.0 CB A:ASP65 3.7 20.4 1.0 PG A:ITT201 3.7 24.9 1.0 NA A:NA303 3.7 38.7 1.0 O1G A:ITT201 3.7 23.5 1.0 PA A:ITT201 3.7 36.8 1.0 O A:HOH414 3.9 14.8 1.0 N A:ASP65 4.0 16.4 1.0 NZ A:LYS12 4.2 28.2 1.0 CD A:GLU36 4.3 29.6 1.0 O3A A:ITT201 4.3 34.2 1.0 CZ A:TYR34 4.5 22.4 1.0 OD2 A:ASP65 4.6 28.8 1.0 O3G A:ITT201 4.7 24.8 1.0 O A:HOH450 4.8 34.2 1.0 C A:ASP65 4.9 16.5 1.0 O3B A:ITT201 4.9 29.7 1.0 O2B A:ITT201 4.9 31.1 1.0 CA A:GLU64 4.9 14.5 1.0 PB A:ITT201 4.9 28.7 1.0 N A:GLU64 5.0 14.2 1.0

Sodium binding site 2 out of 3 in the Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:29.0 occ:1.00 O A:HOH580 2.2 47.5 1.0 O2G A:ITT201 2.3 26.8 1.0 OE2 A:GLU36 2.4 28.9 1.0 O1A A:ITT201 2.5 32.2 1.0 O2B A:ITT201 2.5 31.1 1.0 OE1 A:GLU36 2.8 31.9 1.0 CD A:GLU36 2.9 29.6 1.0 O A:HOH450 3.1 34.2 1.0 O A:HOH579 3.3 35.2 1.0 NA A:NA303 3.3 38.7 1.0 NA A:NA301 3.5 39.2 1.0 PG A:ITT201 3.6 24.9 1.0 PB A:ITT201 3.7 28.7 1.0 PA A:ITT201 3.7 36.8 1.0 O3G A:ITT201 4.1 24.8 1.0 O3A A:ITT201 4.1 34.2 1.0 O3B A:ITT201 4.2 29.7 1.0 O A:HOH551 4.2 46.0 1.0 O A:HOH595 4.4 45.6 1.0 CG A:GLU36 4.4 26.1 1.0 O2A A:ITT201 4.4 30.6 1.0 OD1 A:ASP65 4.6 27.5 1.0 O1G A:ITT201 4.8 23.5 1.0 O1B A:ITT201 4.9 31.1 1.0 O5' A:ITT201 5.0 34.8 1.0

Sodium binding site 3 out of 3 in the Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:38.7 occ:1.00 O A:HOH579 2.1 35.2 1.0 OD1 A:ASP65 2.5 27.5 1.0 O1A A:ITT201 2.6 32.2 1.0 OE2 A:GLU36 2.7 28.9 1.0 O A:HOH445 3.0 29.7 1.0 NA A:NA302 3.3 29.0 1.0 CG A:ASP65 3.4 25.4 1.0 CD A:GLU36 3.5 29.6 1.0 O A:HOH440 3.6 22.4 1.0 OD2 A:ASP65 3.7 28.8 1.0 PA A:ITT201 3.7 36.8 1.0 NA A:NA301 3.7 39.2 1.0 O2A A:ITT201 3.7 30.6 1.0 O A:HOH595 3.8 45.6 1.0 OE1 A:GLU36 4.0 31.9 1.0 O A:VAL79 4.2 18.0 1.0 O5' A:ITT201 4.3 34.8 1.0 O A:HOH580 4.4 47.5 1.0 O2G A:ITT201 4.5 26.8 1.0 CG A:GLU36 4.5 26.1 1.0 CG1 A:VAL45 4.6 11.4 1.0 CB A:GLU36 4.7 23.6 1.0 CB A:ASP65 4.8 20.4 1.0 O2B A:ITT201 4.9 31.1 1.0

H.Mizutani, N.K.Lokanath, N.Kunishima. Structure of Nucleotide Triphosphate Pyrophosphatase From Pyrococcus Horikoshii OT3 To Be Published.