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Sodium in PDB 3a65: Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N Mutant with Substrate

Enzymatic activity of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N Mutant with Substrate

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

Protein crystallography data

The structure of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N Mutant with Substrate, PDB code: 3a65 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) 31.56 / 1.70
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.414, 96.414, 112.869, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 20.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N Mutant with Substrate (pdb code 3a65). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N Mutant with Substrate, PDB code: 3a65:

Sodium binding site 1 out of 1 in 3a65

Go back to Sodium Binding Sites List in 3a65
Sodium binding site 1 out of 1 in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/H266N 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 Mutant with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:34.8
occ:1.00
 OD2 A:ASP127 2.2 41.1 1.0
OD1 A:ASP127 2.2 37.8 1.0
CG A:ASP127 2.5 35.0 1.0
O A:GLY123 2.8 17.4 1.0
O A:HOH643 2.9 29.5 1.0
CB A:TRP299 3.0 15.3 1.0
OG A:SER296 3.0 18.2 1.0
N A:SER296 3.2 16.5 1.0
CG A:TRP299 3.5 14.3 1.0
C A:GLY123 3.6 15.3 1.0
CB A:SER296 3.7 19.7 1.0
CB A:VAL295 3.8 20.1 1.0
CD2 A:TRP299 3.9 14.7 1.0
CB A:ASP127 3.9 19.9 1.0
CE3 A:TRP299 3.9 14.0 1.0
CA A:SER296 4.0 18.4 1.0
CA A:VAL295 4.0 12.9 1.0
C A:VAL295 4.1 14.7 1.0
CA A:GLY123 4.1 12.5 1.0
CG1 A:VAL295 4.2 16.6 1.0
N A:ASP127 4.2 21.4 1.0
CA A:TRP299 4.3 13.7 1.0
CA A:ASP127 4.4 22.9 1.0
CD1 A:TRP299 4.5 17.2 1.0
N A:TRP299 4.5 15.3 1.0
N A:ALA124 4.5 13.3 1.0
O A:HOH639 4.5 27.4 1.0
O A:SER296 4.6 15.1 1.0
C A:SER296 4.7 18.2 1.0
O A:HOH434 4.8 53.8 1.0
CB A:VAL126 4.9 19.9 1.0
CA A:ALA124 4.9 15.4 1.0
CE2 A:TRP299 4.9 18.7 1.0

Reference:

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.
Page generated: Mon Oct 7 05:44:25 2024

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