Sodium in PDB 8wc0: Crystal Structure of Ecthsa

The structure of Crystal Structure of Ecthsa, PDB code: 8wc0 was solved by Q.Chen, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.19 / 2.25
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	250.64, 250.64, 50.701, 90, 90, 90
R / Rfree (%)	18.8 / 22.8

The binding sites of Sodium atom in the Crystal Structure of Ecthsa (pdb code 8wc0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Ecthsa, PDB code: 8wc0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Ecthsa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ecthsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:29.6 occ:1.00 H A:GLY405 2.3 36.6 1.0 HZ3 A:LYS394 2.5 56.2 1.0 HD3 A:LYS394 3.0 40.6 1.0 HA3 A:GLY405 3.1 26.1 1.0 HB1 A:ALA403 3.1 31.3 1.0 N A:GLY405 3.1 30.5 1.0 O A:HOH779 3.1 46.5 1.0 NZ A:LYS394 3.4 46.8 1.0 O A:HOH790 3.5 47.0 1.0 HE2 A:LYS394 3.5 44.9 1.0 CA A:GLY405 3.6 21.7 1.0 H A:ASP404 3.7 24.5 1.0 HA A:ALA403 3.7 27.7 1.0 CE A:LYS394 3.7 37.4 1.0 CD A:LYS394 3.8 33.8 1.0 HZ1 A:LYS394 3.8 56.2 1.0 N A:ASP404 3.8 20.4 1.0 HZ2 A:LYS394 3.9 56.2 1.0 CB A:ALA403 3.9 26.0 1.0 HH22 A:ARG377 4.0 45.5 1.0 C A:ALA403 4.1 21.2 1.0 CA A:ALA403 4.1 23.1 1.0 HA2 A:GLY405 4.2 26.1 1.0 C A:ASP404 4.2 28.5 1.0 H A:VAL406 4.3 24.4 1.0 HB2 A:ALA403 4.3 31.3 1.0 HB3 A:ASP404 4.4 43.8 1.0 HD2 A:LYS394 4.4 40.6 1.0 HG2 A:LYS394 4.5 36.6 1.0 CA A:ASP404 4.5 27.9 1.0 HB3 A:ALA403 4.6 31.3 1.0 O1 A:SO4502 4.6 70.1 1.0 HH12 A:ARG377 4.6 48.2 1.0 O A:HOH838 4.7 32.6 1.0 HE3 A:LYS394 4.7 44.9 1.0 HG A:SER292 4.7 32.3 1.0 C A:GLY405 4.7 25.1 1.0 NH2 A:ARG377 4.7 37.9 1.0 CG A:LYS394 4.8 30.5 1.0 O A:ALA403 4.8 24.8 1.0 N A:VAL406 4.8 20.2 1.0 HB3 A:LYS394 4.9 31.9 1.0 CB A:ASP404 4.9 36.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Ecthsa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ecthsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:36.2 occ:1.00 HZ3 B:LYS394 2.2 81.6 1.0 H B:GLY405 2.4 37.4 1.0 O B:HOH700 2.9 45.8 1.0 HB1 B:ALA403 3.0 40.5 1.0 HD3 B:LYS394 3.0 52.4 1.0 HA3 B:GLY405 3.1 33.3 1.0 NZ B:LYS394 3.1 68.0 1.0 N B:GLY405 3.2 31.1 1.0 HZ2 B:LYS394 3.5 81.6 1.0 HZ1 B:LYS394 3.6 81.6 1.0 CA B:GLY405 3.7 27.7 1.0 HE2 B:LYS394 3.7 73.0 1.0 H B:ASP404 3.7 38.8 1.0 CE B:LYS394 3.7 60.8 1.0 OD1 B:ASP404 3.7 95.0 1.0 CD B:LYS394 3.8 43.6 1.0 CB B:ALA403 3.9 33.7 1.0 N B:ASP404 3.9 32.2 1.0 HA B:ALA403 4.0 41.3 1.0 O2 B:SO4501 4.0 90.6 1.0 CG B:ASP404 4.0 78.9 1.0 O4 B:SO4501 4.0 86.2 1.0 OD2 B:ASP404 4.1 85.3 1.0 HH22 B:ARG377 4.1 53.7 1.0 C B:ALA403 4.2 35.9 1.0 H B:VAL406 4.3 33.1 1.0 CA B:ALA403 4.3 34.4 1.0 HD2 B:LYS394 4.3 52.4 1.0 HA2 B:GLY405 4.3 33.3 1.0 HB2 B:ALA403 4.3 40.5 1.0 C B:ASP404 4.3 35.5 1.0 HB3 B:ALA403 4.5 40.5 1.0 HG B:SER292 4.6 37.4 1.0 CA B:ASP404 4.6 38.3 1.0 HH12 B:ARG377 4.6 55.7 1.0 HE3 B:LYS394 4.7 73.0 1.0 S B:SO4501 4.7 149.9 1.0 C B:GLY405 4.7 27.4 1.0 N B:VAL406 4.8 27.5 1.0 HG2 B:LYS394 4.8 51.0 1.0 NH2 B:ARG377 4.8 44.7 1.0 O B:HOH839 4.9 35.5 1.0 CG B:LYS394 4.9 42.5 1.0 HB3 B:LYS394 4.9 35.8 1.0 HG23 B:VAL406 4.9 33.7 1.0 CB B:ASP404 4.9 46.9 1.0 O B:ALA403 5.0 35.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Ecthsa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ecthsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:55.4 occ:1.00 H B:GLY329 2.4 36.0 1.0 O A:HOH782 2.9 31.8 1.0 OG B:SER332 3.0 29.4 0.4 HB3 B:SER332 3.0 31.6 0.6 N B:GLY329 3.2 29.9 1.0 HG B:SER332 3.3 35.3 0.4 HG B:SER332 3.4 41.8 0.6 HB2 B:SER332 3.4 36.2 0.4 H B:SER332 3.4 23.4 0.4 H B:SER332 3.4 23.4 0.6 HB3 A:SER332 3.4 37.6 1.0 HA B:TRP328 3.4 33.0 1.0 OG B:SER332 3.5 34.8 0.6 HA2 B:GLY329 3.6 52.0 1.0 CB B:SER332 3.7 26.3 0.6 CB B:SER332 3.7 30.1 0.4 CA B:GLY329 3.9 43.3 1.0 OG A:SER332 4.1 59.2 1.0 N B:SER332 4.1 19.5 1.0 CB A:SER332 4.1 31.3 1.0 O B:HOH805 4.2 38.8 1.0 H B:ILE330 4.2 38.1 1.0 C B:TRP328 4.2 31.7 1.0 CA B:TRP328 4.2 27.4 1.0 O B:GLY327 4.4 28.6 1.0 CE3 B:TRP328 4.4 36.8 1.0 HB2 A:SER332 4.4 37.6 1.0 HB2 B:SER332 4.4 31.6 0.6 O B:HOH713 4.5 28.7 1.0 HE3 B:TRP328 4.5 44.2 1.0 HB3 B:SER332 4.5 36.2 0.4 H B:GLY331 4.5 24.5 1.0 CD2 B:TRP328 4.5 35.7 1.0 CA B:SER332 4.5 28.8 0.6 CA B:SER332 4.5 23.9 0.4 N B:ILE330 4.6 31.7 1.0 C B:GLY329 4.6 44.4 1.0 HG A:SER332 4.6 71.1 1.0 CZ3 A:TRP328 4.7 51.5 1.0 H A:GLY329 4.7 30.7 1.0 HZ3 A:TRP328 4.7 61.9 1.0 HA3 B:GLY329 4.8 52.0 1.0 CH2 A:TRP328 4.8 45.9 1.0 CZ3 B:TRP328 4.8 44.0 1.0 CG B:TRP328 4.8 40.9 1.0 HH2 A:TRP328 4.9 55.2 1.0 N B:GLY331 4.9 20.4 1.0 HA B:SER332 4.9 34.6 0.6 HA B:SER332 4.9 28.8 0.4 CE2 B:TRP328 4.9 35.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Ecthsa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ecthsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:58.5 occ:1.00 O B:HOH696 2.6 47.7 1.0 O B:HOH672 2.9 29.5 1.0 O B:HOH858 3.0 44.3 1.0 O B:HOH863 3.0 42.5 1.0 HB2 B:PHE307 3.1 33.7 1.0 HZ3 B:TRP299 3.5 32.7 1.0 HB3 B:ARG465 3.6 33.7 1.0 HD1 B:PHE307 3.9 33.5 1.0 O B:ARG465 4.0 34.2 1.0 HG2 B:GLU303 4.1 38.2 1.0 CB B:PHE307 4.1 28.0 1.0 HB2 B:ARG465 4.2 33.7 1.0 HH2 B:TRP299 4.2 40.4 1.0 CZ3 B:TRP299 4.3 27.2 1.0 HG3 B:GLU303 4.3 38.2 1.0 CB B:ARG465 4.3 28.1 1.0 HA B:ALA466 4.3 38.2 1.0 HA B:PHE307 4.3 31.5 1.0 C B:ARG465 4.5 37.1 1.0 CD1 B:PHE307 4.5 27.9 1.0 HB3 B:PHE307 4.6 33.7 1.0 CG B:GLU303 4.6 31.8 1.0 HD22 B:ASN306 4.6 59.4 1.0 CH2 B:TRP299 4.6 33.6 1.0 CG B:PHE307 4.7 29.3 1.0 CA B:PHE307 4.7 26.2 1.0 O B:GLU303 4.7 24.2 1.0 O B:HOH711 4.7 35.6 1.0 OE2 B:GLU303 4.8 30.4 1.0 HD3 B:ARG465 4.9 33.9 1.0

Q.Chen, Y.Yu. Self-Association Activates Thsb Nad+ Hydrolase For Defense Against Phage Infection To Be Published.