Sodium in PDB 4nyo: The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3

The structure of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3, PDB code: 4nyo was solved by B.Bagautdinov, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.10 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.085, 124.250, 50.458, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.5

The structure of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 (pdb code 4nyo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3, PDB code: 4nyo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta 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 The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:39.4 occ:1.00 O A:HOH307 2.2 29.7 1.0 O B:HOH308 2.2 27.7 1.0 O B:HOH314 2.3 34.6 1.0 O C:HOH310 2.3 30.2 1.0 O A:HOH335 2.5 29.0 1.0 O C:HOH329 2.5 30.0 1.0 O B:HOH324 4.0 35.8 1.0 OD2 B:ASP86 4.1 22.1 1.0 OD2 A:ASP86 4.1 19.2 1.0 O A:ASP84 4.3 19.7 1.0 OD1 B:ASP86 4.3 21.8 1.0 OD1 A:ASP86 4.3 24.9 1.0 OD2 C:ASP86 4.4 21.3 1.0 OD1 C:ASP86 4.5 20.6 1.0 O C:ASP84 4.5 18.4 1.0 O B:ASP84 4.6 22.0 1.0 CG B:ASP86 4.6 22.6 1.0 CG A:ASP86 4.6 22.6 1.0 CG C:ASP86 4.8 20.7 1.0

Sodium binding site 2 out of 2 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta 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 The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na3001 b:38.7 occ:0.33 O F:HOH307 2.3 26.9 1.0 O E:HOH4115 2.3 19.4 1.0 O D:HOH3138 2.4 34.3 1.0 O D:HOH3142 2.4 29.6 1.0 O F:HOH375 2.4 42.3 1.0 O E:HOH4144 2.4 24.0 1.0 O E:HOH4215 3.6 32.3 1.0 O F:HOH356 3.9 45.7 1.0 OD2 F:ASP86 4.1 18.6 1.0 OD2 D:ASP86 4.2 21.5 1.0 OD2 E:ASP86 4.2 20.7 1.0 O E:ASP84 4.4 18.8 1.0 OD1 F:ASP86 4.4 20.5 1.0 OD1 E:ASP86 4.4 22.0 1.0 OD1 D:ASP86 4.5 20.8 1.0 O F:ASP84 4.5 16.5 1.0 O D:ASP84 4.5 19.6 1.0 CG F:ASP86 4.7 19.7 1.0 O F:HOH320 4.7 27.1 1.0 CG E:ASP86 4.7 19.4 1.0 CG D:ASP86 4.8 20.4 1.0

B.Bagautdinov, B.Bagautdinov, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi). N/A N/A.
ISSN: ISSN 2053-230X
PubMed: 24699729
DOI: 10.1107/S2053230X14003422