Sodium in PDB 7yu0: Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant

All present enzymatic activity of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant:
3.5.1.117;

The structure of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant, PDB code: 7yu0 was solved by S.Negoro, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.01 / 1.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.242, 144.345, 129.178, 90, 90, 90
R / Rfree (%)	11.1 / 13.9

The binding sites of Sodium atom in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant (pdb code 7yu0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant, PDB code: 7yu0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:51.6 occ:1.00 OE2 A:GLU136 2.5 29.1 1.0 O A:HOH1281 2.7 27.9 1.0 O A:HOH1352 2.8 52.7 1.0 H A:GLY133 3.0 19.0 1.0 CD A:GLU136 3.4 34.4 1.0 HA3 A:GLY133 3.5 19.8 1.0 HB3 A:ARG131 3.5 21.8 1.0 H A:THR132 3.6 18.0 1.0 N A:GLY133 3.6 18.6 1.0 OE1 A:GLU136 3.7 41.6 1.0 CA A:GLY133 4.0 20.0 1.0 HA2 A:GLY133 4.2 19.7 1.0 HD2 A:ARG131 4.2 34.0 1.0 HA A:ARG131 4.3 18.8 1.0 HG2 A:ARG131 4.3 26.4 1.0 N A:THR132 4.3 18.1 1.0 CB A:ARG131 4.4 21.7 1.0 O B:HOH608 4.6 47.5 1.0 C A:THR132 4.7 18.5 1.0 CG A:ARG131 4.7 26.4 1.0 HD2 B:PHE30 4.7 78.1 1.0 CA A:ARG131 4.7 18.8 1.0 HB2 B:PHE30 4.8 67.3 1.0 CD A:ARG131 4.8 34.3 1.0 CD2 B:PHE30 4.8 79.9 1.0 CG A:GLU136 4.8 30.9 1.0 HB3 B:PHE30 4.8 68.5 1.0 O A:HOH1189 4.9 32.3 1.0 HD3 A:ARG131 4.9 34.4 1.0 C A:ARG131 4.9 18.0 1.0 HG3 A:GLU136 5.0 30.3 1.0

Sodium binding site 2 out of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:38.7 occ:1.00 O B:HOH704 2.2 39.9 1.0 O B:HOH754 2.3 30.9 1.0 O B:THR315 2.5 21.1 1.0 O B:HOH628 2.5 20.2 1.0 O B:HOH805 2.6 47.7 1.0 C B:THR315 3.5 17.8 1.0 HB B:THR315 3.7 19.0 1.0 HA B:THR315 3.7 17.0 1.0 HB2 B:ASP316 3.8 21.9 1.0 O B:HOH690 3.9 26.1 1.0 O B:HOH786 4.0 19.8 1.0 HB1 B:ALA79 4.0 22.1 1.0 CA B:THR315 4.1 16.9 1.0 HB3 B:ALA79 4.2 22.6 1.0 O B:GLY80 4.3 17.6 1.0 CB B:THR315 4.4 18.8 1.0 HG3 B:GLU317 4.4 21.3 1.0 O B:HOH543 4.4 18.8 1.0 CB B:ALA79 4.5 22.6 1.0 HG2 B:GLU317 4.6 21.5 1.0 N B:ASP316 4.6 17.6 1.0 CB B:ASP316 4.6 21.9 1.0 O B:ASP316 4.7 23.9 1.0 C B:ASP316 4.8 19.1 1.0 HB2 B:ALA79 4.9 22.1 1.0 HB3 B:ASP316 4.9 21.4 1.0 CA B:ASP316 4.9 19.2 1.0 HA B:ALA81 5.0 15.5 1.0 CG B:GLU317 5.0 21.7 1.0

Sodium binding site 3 out of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, H130Y/N266A/T267A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na409 b:50.9 occ:1.00 OE1 B:GLU136 2.5 30.9 1.0 O B:HOH696 2.7 35.5 1.0 O B:HOH778 3.0 48.7 1.0 H B:GLY133 3.0 20.5 1.0 CD B:GLU136 3.3 37.5 1.0 OE2 B:GLU136 3.5 43.7 1.0 HA3 B:GLY133 3.5 21.0 1.0 HB3 B:ARG131 3.6 24.6 1.0 HD1 A:PHE30 3.6 62.0 1.0 H B:THR132 3.7 19.7 1.0 N B:GLY133 3.7 20.4 1.0 HE1 A:PHE30 3.9 67.7 1.0 CD1 A:PHE30 3.9 63.4 1.0 CE1 A:PHE30 4.0 68.8 1.0 HG2 B:ARG131 4.1 27.3 1.0 CA B:GLY133 4.1 21.1 1.0 HD2 B:ARG131 4.1 35.6 1.0 HA B:ARG131 4.3 21.0 1.0 HA2 B:GLY133 4.3 20.8 1.0 O A:HOH1332 4.4 51.4 1.0 CB B:ARG131 4.4 24.4 1.0 N B:THR132 4.4 19.5 1.0 O A:HOH1169 4.4 44.8 1.0 CG B:ARG131 4.5 26.6 1.0 O B:HOH776 4.5 45.8 1.0 HB3 A:PHE30 4.6 51.1 1.0 CD B:ARG131 4.7 36.7 1.0 CG A:PHE30 4.7 56.4 1.0 HD3 B:ARG131 4.7 36.9 1.0 CG B:GLU136 4.7 32.8 1.0 CA B:ARG131 4.7 21.0 1.0 C B:THR132 4.8 20.0 1.0 O B:HOH560 4.9 37.6 1.0 HG3 B:GLU136 4.9 32.2 1.0 CZ A:PHE30 4.9 71.3 1.0 C B:ARG131 5.0 20.1 1.0

S.Negoro, N.Shibata, D.I.Kato, Y.Tanaka, K.Yasuhira, K.Nagai, S.Oshima, Y.Furuno, R.Yokoyama, K.Miyazaki, M.Takeo, K.Hengphasatporn, Y.Shigeta, Y.H.Lee, Y.Higuchi. X-Ray Crystallographic and Mutational Analysis of the Nylc Precursor: Catalytic Mechanism of Autocleavage and Substrate Hydrolysis of Nylon Hydrolase. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 36799721
DOI: 10.1111/FEBS.16755