Sodium in PDB 3vwn: Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant

All present enzymatic activity of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant:
3.5.1.46;

The structure of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant, PDB code: 3vwn was solved by Y.Kawashima, N.Shibata, S.Negoro, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.640, 96.640, 112.996, 90.00, 90.00, 120.00
R / Rfree (%)	13 / 14.6

The binding sites of Sodium atom in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant (pdb code 3vwn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant, PDB code: 3vwn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant


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 G181D/R187G/H266N/D370Y Mutant within 5.0Å range: probe atom residue distance (Å) B Occ X:Na412 b:27.7 occ:1.00 OD1 X:ASP127 1.9 18.9 0.5 CG X:ASP127 2.1 17.9 0.5 OD2 X:ASP127 2.1 18.0 0.5 O X:GLY123 2.7 16.1 1.0 O X:HOH772 2.9 25.9 1.0 OG X:SER296 3.1 19.1 1.0 N X:SER296 3.1 17.3 1.0 CB X:TRP299 3.3 15.4 1.0 CB X:ASP127 3.5 21.1 0.5 CB X:ASP127 3.5 17.8 0.5 C X:GLY123 3.5 13.9 1.0 CB X:SER296 3.6 18.7 1.0 CG X:TRP299 3.8 14.5 1.0 N X:ASP127 3.9 18.1 1.0 CB X:VAL295 3.9 16.5 1.0 CA X:SER296 4.0 17.7 1.0 CA X:ASP127 4.0 21.8 0.5 CA X:GLY123 4.0 13.0 1.0 CA X:ASP127 4.1 21.0 0.5 CA X:VAL295 4.1 16.8 1.0 CD2 X:TRP299 4.1 14.9 1.0 CE3 X:TRP299 4.1 16.5 1.0 C X:VAL295 4.1 16.7 1.0 CG X:ASP127 4.1 24.3 0.5 CG1 X:VAL295 4.3 17.5 1.0 N X:ALA124 4.4 13.9 1.0 OD2 X:ASP127 4.5 31.2 0.5 CA X:TRP299 4.6 15.1 1.0 OD1 X:ASP127 4.6 27.9 0.5 O X:HOH865 4.7 40.5 1.0 N X:TRP299 4.7 15.5 1.0 CA X:ALA124 4.7 15.4 1.0 O X:HOH547 4.7 29.8 1.0 CD1 X:TRP299 4.7 17.3 1.0 O X:SER296 4.8 15.4 1.0 CB X:VAL126 4.8 16.7 1.0 C X:VAL126 4.8 19.2 1.0 C X:SER296 4.9 16.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant


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 G181D/R187G/H266N/D370Y Mutant within 5.0Å range: probe atom residue distance (Å) B Occ X:Na413 b:47.4 occ:1.00 OD2 X:ASP181 2.2 26.1 1.0 O X:HOH810 2.9 36.3 1.0 NE2 X:GLN178 3.0 43.0 1.0 CG X:ASP181 3.2 21.1 1.0 CB X:ASP181 3.3 17.9 1.0 O X:HOH745 3.9 24.3 1.0 O X:HOH698 4.0 27.0 1.0 CD X:GLN178 4.1 36.3 1.0 OD1 X:ASP181 4.4 23.6 1.0 CA X:GLN178 4.7 20.5 1.0 OE1 X:GLN178 4.8 49.1 1.0 CA X:ASP181 4.9 16.0 1.0 CG X:GLN178 5.0 32.0 1.0 O X:VAL177 5.0 20.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant


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 6-Aminohexanoate-Dimer Hydrolase G181D/R187G/H266N/D370Y Mutant within 5.0Å range: probe atom residue distance (Å) B Occ X:Na414 b:42.7 occ:1.00 OE2 X:GLU297 2.3 35.4 1.0 O X:ASP285 2.8 20.1 1.0 CD X:GLU297 3.3 27.3 1.0 CG2 X:VAL288 3.7 24.1 1.0 CA X:GLY286 3.7 17.9 1.0 OE1 X:GLU297 3.7 32.3 1.0 C X:ASP285 3.8 16.6 1.0 NH2 X:ARG293 3.8 23.9 1.0 O X:GLY286 3.9 17.9 1.0 C X:GLY286 4.0 16.6 1.0 N X:GLY286 4.2 17.0 1.0 CB X:VAL288 4.4 20.0 1.0 CG X:GLU297 4.5 23.5 1.0 NH1 X:ARG293 4.6 20.1 1.0 CZ X:ARG293 4.7 21.5 1.0 N X:GLY287 4.8 15.6 1.0 N X:VAL288 4.8 16.3 1.0 CA X:ASP285 4.9 16.5 1.0

S.Negoro, Y.Kawashima, N.Shibata, Y.Shigeta, T.Kobayashi, H.Nishiguchi, T.Matsui, T.Baba, Y.Lee, K.Kamiya, D.Kato, M.Takeo, Y.Higuchi. Structural, Kinetic and Theoretical Analyses of Hydrolase Mutants Altering in the Directionality and Equilibrium Point of Reversible Amide-Synthetic/Hydrolytic Reaction To Be Published.