Sodium in PDB 4nyp: The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+

The structure of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+, PDB code: 4nyp 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)	32.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.822, 123.774, 50.667, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.9

The binding sites of Sodium atom in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ (pdb code 4nyp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+, PDB code: 4nyp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:22.1 occ:1.00 OE2 C:GLU47 2.1 22.8 1.0 OE2 F:GLU15 2.3 36.2 1.0 OE2 A:GLU15 2.4 40.8 1.0 OE1 F:GLU15 2.5 37.6 1.0 OE1 A:GLU15 2.5 40.4 1.0 CD F:GLU15 2.7 34.9 1.0 CD A:GLU15 2.8 37.7 1.0 CD C:GLU47 3.1 25.2 1.0 OE1 C:GLU47 3.4 25.1 1.0 NH1 E:ARG36 3.9 43.2 1.0 O F:HOH282 3.9 50.8 1.0 NH2 E:ARG36 4.2 43.2 1.0 CG A:GLU15 4.2 34.4 1.0 CG F:GLU15 4.2 31.5 1.0 CB F:TRP11 4.3 20.7 1.0 CE2 C:PHE38 4.3 21.1 1.0 NZ A:LYS19 4.4 33.5 1.0 CZ E:ARG36 4.4 43.4 1.0 CG C:GLU47 4.5 24.5 1.0 OE1 F:GLU12 4.5 36.8 1.0 CZ C:PHE38 4.5 22.6 1.0 O E:HOH374 4.6 39.4 1.0 O F:TRP11 4.7 17.7 1.0 C F:TRP11 4.7 19.0 1.0 CB C:GLU47 4.7 24.4 1.0 CE A:LYS19 4.9 30.3 1.0 CB A:GLU15 4.9 28.1 1.0 N F:GLU12 4.9 20.2 1.0 O F:HOH251 5.0 41.7 1.0

Sodium binding site 2 out of 3 in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:26.8 occ:1.00 O B:HOH314 2.2 23.2 1.0 O A:HOH1107 2.3 23.5 1.0 O C:HOH311 2.3 36.9 1.0 O B:HOH308 2.4 37.2 1.0 O A:HOH1127 2.4 23.1 1.0 O C:HOH329 2.5 24.2 1.0 O A:HOH1199 4.0 31.6 1.0 OD2 B:ASP86 4.1 19.7 1.0 OD2 C:ASP86 4.2 18.9 1.0 OD1 A:ASP86 4.2 26.9 1.0 OD2 A:ASP86 4.2 24.0 1.0 OD1 B:ASP86 4.2 18.8 1.0 OD1 C:ASP86 4.3 17.0 1.0 O C:HOH337 4.4 53.4 1.0 O A:ASP84 4.5 22.0 1.0 O C:ASP84 4.5 21.9 1.0 CG B:ASP86 4.6 19.7 1.0 CG A:ASP86 4.7 26.1 1.0 O B:ASP84 4.7 22.4 1.0 CG C:ASP86 4.7 17.7 1.0

Sodium binding site 3 out of 3 in the The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii CUTA1 Complexed with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:26.8 occ:1.00 O E:HOH312 2.3 31.3 1.0 O D:HOH349 2.3 35.6 1.0 O F:HOH278 2.3 31.9 1.0 O D:HOH341 2.4 39.4 1.0 O F:HOH206 2.4 19.8 1.0 O E:HOH341 2.5 20.9 1.0 OD2 D:ASP86 4.1 18.6 1.0 OD2 F:ASP86 4.2 21.5 1.0 OD2 E:ASP86 4.3 22.0 1.0 O F:HOH276 4.3 33.7 1.0 OD1 E:ASP86 4.4 21.9 1.0 OD1 D:ASP86 4.4 22.5 1.0 O F:ASP84 4.5 21.5 1.0 OD1 F:ASP86 4.5 23.6 1.0 O D:ASP84 4.5 19.1 1.0 O E:ASP84 4.5 17.9 1.0 O F:HOH217 4.7 46.4 1.0 CG D:ASP86 4.7 20.0 1.0 CG F:ASP86 4.8 19.9 1.0 CG E:ASP86 4.8 20.7 1.0

B.Bagautdinov, T.H.Tahirov. The 2.0 Angstrom Crystal Structure of Pyrococcus Horikoshii Complexed with Na+ To Be Published.