Sodium in PDB 9dys: X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol

The structure of X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol, PDB code: 9dys was solved by N.Capra, F.Meilleur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.73 / 1.85
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.879, 96.511, 105.188, 90, 90, 90
R / Rfree (%)	15.1 / 17.2

The binding sites of Sodium atom in the X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol (pdb code 9dys). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol, PDB code: 9dys:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:17.3 occ:1.00 OG1 A:THR227 2.8 14.4 1.0 ND2 A:ASN180 3.1 17.3 1.0 N A:TYR105 3.3 14.8 1.0 CB A:THR227 3.4 12.5 1.0 O A:HOH591 3.4 33.1 1.0 CB A:TYR105 3.5 17.4 1.0 N A:THR227 3.6 12.8 1.0 CA A:TYR105 3.9 16.4 1.0 O A:TYR105 4.1 16.7 1.0 CA A:THR227 4.1 12.4 1.0 C A:ILE104 4.3 13.5 1.0 CA A:ILE104 4.3 13.2 1.0 CG A:ASN180 4.3 16.0 1.0 O A:VAL265 4.3 17.8 1.0 O A:ASN180 4.4 12.9 1.0 CD1 A:LEU220 4.4 39.6 1.0 C A:TYR105 4.5 16.9 1.0 CB A:ILE104 4.6 15.5 1.0 CG2 A:THR227 4.6 12.9 1.0 CG A:TYR105 4.8 17.5 1.0 CB A:ASN180 4.9 13.1 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (NYLON66) Hydrolase NYL50 at Room Temperature Bound to Tetraethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:18.3 occ:1.00 O B:HOH546 2.7 35.5 1.0 OG1 B:THR227 2.9 14.8 1.0 ND2 B:ASN180 3.1 15.4 1.0 N B:TYR105 3.3 16.0 1.0 CB B:THR227 3.4 13.1 1.0 CB B:TYR105 3.5 17.7 1.0 O B:HOH562 3.6 33.2 1.0 N B:THR227 3.7 13.2 1.0 CA B:TYR105 3.9 16.1 1.0 O1 B:PG4401 4.0 38.9 0.5 C1 B:PG4401 4.0 45.0 0.5 O B:TYR105 4.1 16.9 1.0 CA B:THR227 4.2 12.5 1.0 C B:ILE104 4.3 15.0 1.0 CA B:ILE104 4.3 13.3 1.0 C1 B:PG4401 4.3 35.5 0.5 CG B:ASN180 4.4 15.6 1.0 O B:VAL265 4.4 16.4 1.0 O B:ASN180 4.4 12.1 1.0 C B:TYR105 4.5 16.4 1.0 CB B:ILE104 4.5 13.7 1.0 CG2 B:THR227 4.6 13.2 1.0 CG B:TYR105 4.7 18.2 1.0 CB B:ASN180 4.9 15.3 1.0 CD1 B:LEU220 5.0 57.5 1.0 CD2 B:LEU220 5.0 48.9 1.0

E.E.Drufva, J.F.Cahill, P.M.B.Saint-Vincent, A.N.Williams, V.Bocharova, N.Capra, F.Meilleur, D.L.Carper, C.Bourgery, K.Miyazaki, M.Yonemura, Y.Shiraishi, J.M.Parks, M.Zhou, I.T.Dishner, J.C.Foster, S.J.Koehler, H.R.Valentino, A.Sedova, V.Kertesz, D.P.Vasileva, L.H.Hochanadel, C.A.Figg, S.Negoro, D.I.Kato, S.H.Chen, J.K.Michener. Identification and Characterization of Substrate- and Product-Selective Nylon Hydrolases. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39605696
DOI: 10.1101/2024.11.14.623603