Sodium in PDB 3a66: Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate

All present enzymatic activity of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate:
3.5.1.46;

The structure of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate, PDB code: 3a66 was solved by Y.Kawashima, N.Shibata, Y.Higuchi, M.Takeo, S.Negoro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.99 / 1.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.524, 96.524, 113.089, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 22.5

The binding sites of Sodium atom in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate (pdb code 3a66). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate, PDB code: 3a66:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate


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 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:39.0 occ:1.00 OD2 A:ASP127 2.2 29.2 1.0 OD1 A:ASP127 2.3 27.9 1.0 CG A:ASP127 2.5 27.0 1.0 O A:GLY123 2.7 16.8 1.0 CB A:TRP299 3.0 14.1 1.0 O A:HOH593 3.1 35.6 1.0 OG A:SER296 3.1 16.9 1.0 N A:SER296 3.3 15.0 1.0 CG A:TRP299 3.5 17.4 1.0 C A:GLY123 3.5 15.1 1.0 CB A:SER296 3.8 16.1 1.0 CB A:VAL295 3.8 18.4 1.0 CD2 A:TRP299 3.8 14.6 1.0 CB A:ASP127 3.9 19.3 1.0 CE3 A:TRP299 3.9 16.0 1.0 CA A:GLY123 4.0 12.0 1.0 CA A:VAL295 4.1 13.2 1.0 CA A:SER296 4.1 15.9 1.0 C A:VAL295 4.2 14.3 1.0 CG1 A:VAL295 4.2 14.5 1.0 N A:ASP127 4.2 18.9 1.0 CA A:TRP299 4.3 14.1 1.0 CD1 A:TRP299 4.4 14.8 1.0 N A:ALA124 4.4 13.6 1.0 CA A:ASP127 4.4 21.9 1.0 N A:TRP299 4.5 13.6 1.0 O A:SER296 4.6 13.7 1.0 O A:HOH587 4.6 29.7 1.0 CA A:ALA124 4.8 16.3 1.0 O A:HOH783 4.8 46.0 1.0 C A:SER296 4.8 16.5 1.0 CB A:VAL126 4.9 17.6 1.0 CE2 A:TRP299 4.9 14.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate


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 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N/D370Y Mutant with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:50.3 occ:1.00 O1 A:GOL606 2.4 48.2 1.0 O A:HOH549 2.4 31.4 1.0 O A:HOH397 2.5 56.0 1.0 O A:HOH399 3.7 46.8 1.0 C1 A:GOL606 3.7 45.4 1.0 CD2 A:TYR215 3.7 19.2 1.0 OD2 A:ASP314 3.9 32.8 1.0 CB A:TYR215 4.0 12.0 1.0 O2 A:GOL607 4.0 45.8 1.0 CG A:TYR215 4.1 14.2 1.0 C2 A:GOL607 4.2 43.2 1.0 O3 A:GOL607 4.4 34.6 1.0 O A:HOH642 4.4 33.5 1.0 CE2 A:TYR215 4.6 20.5 1.0 CH2 A:TRP331 4.6 17.8 1.0 O A:HOH463 4.6 19.3 1.0 O A:HOH398 4.7 56.0 1.0 O2 A:GOL606 4.7 41.3 1.0 C2 A:GOL606 4.8 44.5 1.0 CZ2 A:TRP331 4.8 13.6 1.0 CG A:ASP314 4.9 27.1 1.0 C3 A:GOL607 4.9 42.3 1.0 OE2 A:GLU168 5.0 73.8 1.0

Y.Kawashima, K.Yasuhira, N.Shibata, Y.Matsuura, Y.Tanaka, M.Taniguchi, Y.Miyoshi, M.Takeo, D.Kato, Y.Higuchi, S.Negoro. Enzymatic Synthesis of Nylon-6 Units in Organic Sol Contained Low-Water: Structural Requirement of 6-Aminohexanoate-Dimer Hydrolase For Efficient Amid Synthesis To Be Published.