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Sodium in PDB 3vwp: Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate

Enzymatic activity of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate

All present enzymatic activity of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate:
3.5.1.46;

Protein crystallography data

The structure of Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate, PDB code: 3vwp 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) 24.18 / 1.55
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.390, 96.390, 112.870, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 21.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate (pdb code 3vwp). 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/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate, PDB code: 3vwp:

Sodium binding site 1 out of 1 in 3vwp

Go back to Sodium Binding Sites List in 3vwp
Sodium binding site 1 out of 1 in the Crystal Structure of 6-Aminohexanoate-Dimer Hydrolase S112A/G181D/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate


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/R187S/H266N/D370Y Mutant Complexd with 6-Aminohexanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:34.6
occ:1.00
 OD2 A:ASP127 2.2 33.6 1.0
OD1 A:ASP127 2.3 33.9 1.0
CG A:ASP127 2.4 33.2 1.0
O A:GLY123 2.7 17.9 1.0
O A:HOH754 3.1 31.9 1.0
CB A:TRP299 3.1 16.7 1.0
OG A:SER296 3.1 18.6 1.0
N A:SER296 3.3 19.1 1.0
C A:GLY123 3.4 16.0 1.0
CG A:TRP299 3.6 16.0 1.0
CB A:SER296 3.7 18.6 1.0
CB A:ASP127 3.8 20.6 1.0
CD2 A:TRP299 3.8 15.5 1.0
CE3 A:TRP299 3.9 18.2 1.0
CB A:VAL295 3.9 20.1 1.0
CA A:GLY123 3.9 13.6 1.0
N A:ASP127 4.1 19.8 1.0
CA A:SER296 4.1 19.0 1.0
CA A:VAL295 4.1 16.9 1.0
C A:VAL295 4.2 17.4 1.0
CG1 A:VAL295 4.3 19.2 1.0
CA A:ASP127 4.3 23.1 1.0
CA A:TRP299 4.4 16.6 1.0
N A:ALA124 4.4 15.5 1.0
CD1 A:TRP299 4.5 18.8 1.0
O A:HOH788 4.6 33.2 1.0
N A:TRP299 4.6 16.2 1.0
CB A:VAL126 4.7 19.4 1.0
O A:SER296 4.7 16.4 1.0
CA A:ALA124 4.8 17.6 1.0
C A:SER296 4.9 19.0 1.0
CE2 A:TRP299 4.9 16.4 1.0
O A:HOH939 4.9 47.9 1.0
CZ3 A:TRP299 4.9 24.0 1.0
C A:VAL126 5.0 22.9 1.0
CG1 A:VAL126 5.0 19.3 1.0

Reference:

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.
Page generated: Tue Dec 15 06:29:23 2020

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