Sodium in PDB 5d74: The Crystal Structure of LY7917

The structure of The Crystal Structure of LY7917, PDB code: 5d74 was solved by L.Wu, W.H.Ji, J.H.Sun, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.64 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.009, 97.701, 174.668, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.4

The structure of The Crystal Structure of LY7917 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the The Crystal Structure of LY7917 (pdb code 5d74). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Crystal Structure of LY7917, PDB code: 5d74:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the The Crystal Structure of LY7917


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of LY7917 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:28.0 occ:1.00 O A:HOH476 2.6 29.3 1.0 O A:HOH527 3.0 22.1 1.0 NE A:ARG180 3.2 25.5 1.0 NH2 A:ARG180 3.3 24.5 1.0 O A:HOH451 3.3 16.1 1.0 ND2 A:ASN178 3.7 28.0 1.0 CZ A:ARG180 3.7 27.7 1.0 CB A:ASN178 3.9 26.1 1.0 CB A:ALA13 4.1 13.9 1.0 O A:HOH595 4.2 31.8 1.0 CG A:ASN178 4.3 31.4 1.0 CD A:ARG180 4.4 28.1 1.0 CB A:ALA227 4.5 9.7 1.0 CG2 A:THR185 4.5 15.6 1.0 N A:ASN178 4.7 22.8 1.0 O A:HOH570 4.8 32.3 1.0 O A:ASN178 4.8 18.1 1.0 CA A:ASN178 4.8 23.4 1.0 O A:ALA13 4.9 19.7 1.0

Sodium binding site 2 out of 7 in the The Crystal Structure of LY7917


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of LY7917 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:25.6 occ:1.00 N A:ASP40 3.3 22.6 1.0 C A:SER38 3.6 16.7 1.0 CA A:SER38 3.6 13.7 1.0 CB A:ASP40 3.6 25.7 1.0 N A:PRO39 3.7 15.2 1.0 O A:HOH401 3.8 43.4 1.0 CA A:ASP40 3.8 30.1 1.0 CD A:PRO39 3.8 15.9 1.0 N A:ALA41 3.8 23.4 1.0 O A:HOH448 4.0 23.9 1.0 C A:ASP40 4.0 31.1 1.0 CB A:SER38 4.1 13.5 1.0 O A:SER38 4.1 17.6 1.0 OD2 A:ASP40 4.4 40.8 1.0 C A:PRO39 4.4 20.9 1.0 CG A:ASP40 4.4 34.4 1.0 CG A:PRO39 4.4 21.2 1.0 O A:HOH506 4.5 34.0 1.0 O A:HOH597 4.5 42.1 1.0 CA A:PRO39 4.6 15.9 1.0 OG A:SER38 4.7 14.8 1.0 O A:ILE37 4.8 18.2 1.0 CA A:ALA41 4.8 23.3 1.0 O A:ASP40 4.9 22.8 1.0 N A:SER38 4.9 14.6 1.0

Sodium binding site 3 out of 7 in the The Crystal Structure of LY7917


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of LY7917 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:41.5 occ:1.00 O A:GLY187 3.2 48.9 1.0 C A:GLY187 3.6 57.2 1.0 CA A:GLY187 3.6 45.4 1.0 O A:HOH587 3.7 40.5 1.0 CB A:ARG181 4.2 31.9 1.0 CB A:ALA182 4.5 25.3 1.0 N A:GLN188 4.6 57.1 1.0 O A:SER186 4.7 48.3 1.0 N A:ALA182 4.8 19.3 1.0 C A:ARG181 4.8 27.8 1.0 N A:GLY187 4.9 46.5 1.0 CA A:ARG181 4.9 21.1 1.0 CB A:GLN188 5.0 56.7 1.0

Sodium binding site 4 out of 7 in the The Crystal Structure of LY7917


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of LY7917 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:29.0 occ:1.00 O B:HOH463 3.2 21.6 1.0 NE B:ARG180 3.4 25.1 1.0 NH2 B:ARG180 3.5 33.6 1.0 ND2 B:ASN178 3.7 30.8 1.0 CZ B:ARG180 3.9 31.4 1.0 CB B:ASN178 4.0 27.8 1.0 O B:HOH606 4.1 38.2 1.0 CB B:ALA13 4.2 19.0 1.0 CB B:ALA227 4.4 20.5 1.0 CG B:ASN178 4.4 34.4 1.0 CD B:ARG180 4.5 26.6 1.0 N B:ASN178 4.7 27.1 1.0 CG2 B:THR185 4.8 21.4 1.0 O B:ALA13 4.9 20.1 1.0 CA B:ASN178 4.9 28.8 1.0 CZ3 B:TRP241 5.0 22.6 1.0

Sodium binding site 5 out of 7 in the The Crystal Structure of LY7917


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of LY7917 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:22.8 occ:1.00 O B:HOH593 2.6 40.4 1.0 N B:ALA62 3.2 18.6 1.0 O B:HOH428 3.3 46.1 1.0 CB B:TYR100 3.6 39.7 1.0 CD2 B:TYR27 3.7 25.3 1.0 CB B:ALA62 3.7 20.5 1.0 CE2 B:TYR27 3.8 31.9 1.0 CA B:SER61 3.9 22.6 1.0 C B:SER61 4.0 22.8 1.0 CA B:ALA62 4.0 20.6 1.0 O B:TYR100 4.3 23.4 1.0 CG B:TYR100 4.3 52.6 1.0 CB B:SER61 4.4 27.8 1.0 CD2 B:TYR100 4.7 51.2 1.0 C B:TYR100 4.7 26.7 1.0 CA B:TYR100 4.7 37.1 1.0 O B:ILE60 4.7 22.8 1.0 SG B:CYS26 4.8 20.5 1.0 CG B:TYR27 4.9 21.4 1.0

Sodium binding site 6 out of 7 in the The Crystal Structure of LY7917


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of LY7917 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:37.3 occ:1.00 O B:HOH611 3.2 45.1 1.0 NH1 B:ARG195 3.6 37.2 1.0 CA B:THR173 3.8 23.0 1.0 O B:THR173 3.8 35.6 1.0 CB B:THR173 3.9 24.9 1.0 CG B:ARG195 3.9 28.9 1.0 CD B:ARG195 4.0 36.5 1.0 CG2 B:THR173 4.1 27.6 1.0 C B:THR173 4.2 26.8 1.0 CZ B:ARG195 4.6 41.9 1.0 O B:VAL172 4.7 28.4 1.0 O B:HOH485 4.7 32.0 1.0 NE B:ARG195 4.8 42.8 1.0

Sodium binding site 7 out of 7 in the The Crystal Structure of LY7917


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of LY7917 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:53.6 occ:1.00 N B:SER219 3.4 69.9 1.0 CA B:GLY218 3.8 52.5 1.0 C B:GLY218 3.8 58.1 1.0 O B:HOH562 4.1 52.2 1.0 CA B:SER219 4.2 67.2 1.0 CE1 B:TYR216 4.2 36.8 1.0 OG B:SER219 4.2 67.8 1.0 CB B:SER219 4.4 66.1 1.0 OH B:TYR216 4.8 36.9 1.0 O B:GLY218 4.8 55.7 1.0 OH B:TYR193 5.0 37.0 1.0 CZ B:TYR216 5.0 37.8 1.0

L.Wu, W.H.Ji, J.H.Sun, J.H.Zhou. The Crystal Structure of LY7917 To Be Published.