Sodium in PDB 7yu1: Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, D122G/H130Y/T267C Mutant

All present enzymatic activity of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, D122G/H130Y/T267C Mutant:
3.5.1.117;

The structure of Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, D122G/H130Y/T267C Mutant, PDB code: 7yu1 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)	28.27 / 1.13
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	69.879, 144.004, 129.284, 90, 90, 90
R / Rfree (%)	12.9 / 15.5

The binding sites of Sodium atom in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, D122G/H130Y/T267C Mutant (pdb code 7yu1). 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, D122G/H130Y/T267C Mutant, PDB code: 7yu1:
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, D122G/H130Y/T267C 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, D122G/H130Y/T267C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1005 b:37.7 occ:1.00 H A:GLU173 2.1 17.7 1.0 O A:VAL170 2.1 21.5 1.0 H A:ILE60 2.2 16.3 1.0 O A:GLU173 2.7 17.6 1.0 HB A:ILE60 2.9 19.6 1.0 N A:ILE60 2.9 16.1 1.0 N A:GLU173 2.9 17.5 1.0 H A:GLY172 3.1 23.1 1.0 HA A:SER59 3.2 19.5 1.0 N A:GLY172 3.2 24.2 1.0 C A:VAL170 3.3 20.8 1.0 HZ A:PHE53 3.3 27.4 1.0 HA A:PRO171 3.4 26.4 1.0 C A:PRO171 3.4 23.6 1.0 HG13 A:ILE60 3.4 23.3 1.0 C A:GLU173 3.5 15.7 1.0 CB A:ILE60 3.6 19.7 1.0 O A:ILE60 3.6 16.8 1.0 HB2 A:GLU173 3.6 18.9 1.0 CA A:ILE60 3.6 15.7 1.0 CA A:GLU173 3.7 17.9 1.0 CA A:PRO171 3.7 27.7 1.0 HG23 A:VAL170 3.7 26.3 1.0 H A:VAL170 3.8 22.1 1.0 C A:SER59 3.8 17.8 1.0 CA A:SER59 3.9 19.7 1.0 C A:GLY172 3.9 17.4 1.0 CZ A:PHE53 3.9 28.8 1.0 CG1 A:ILE60 3.9 24.4 1.0 N A:PRO171 3.9 26.9 1.0 O A:PRO171 4.0 23.0 1.0 HE2 A:PHE53 4.0 24.9 1.0 HD11 A:ILE60 4.0 23.8 1.0 CA A:GLY172 4.0 22.3 1.0 C A:ILE60 4.1 15.1 1.0 O A:HOH1214 4.1 24.1 1.0 CB A:GLU173 4.2 18.7 1.0 CE2 A:PHE53 4.2 24.4 1.0 HA2 A:GLY172 4.3 22.5 1.0 HG21 A:VAL170 4.4 26.6 1.0 N A:VAL170 4.4 21.9 1.0 CA A:VAL170 4.4 24.3 1.0 CG2 A:VAL170 4.5 26.4 1.0 CD1 A:ILE60 4.5 23.7 1.0 HB3 A:SER59 4.5 21.9 1.0 HA A:ILE60 4.5 15.8 1.0 O A:VAL58 4.6 33.7 1.0 HA A:GLU173 4.6 17.7 1.0 HG3 A:GLU173 4.6 21.0 1.0 N A:PHE174 4.8 14.5 1.0 HG12 A:ILE60 4.8 23.7 1.0 CB A:SER59 4.8 21.1 1.0 O A:SER59 4.9 17.5 1.0 CG2 A:ILE60 4.9 21.4 1.0 HA3 A:GLY172 4.9 22.2 1.0 CE1 A:PHE53 4.9 25.0 1.0 HB3 A:GLU173 4.9 18.9 1.0 N A:SER59 5.0 19.5 1.0 HD12 A:ILE60 5.0 23.3 1.0

Sodium binding site 2 out of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, D122G/H130Y/T267C 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, D122G/H130Y/T267C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:27.3 occ:1.00 O B:HOH642 2.0 33.1 1.0 O B:THR315 2.4 15.4 1.0 O B:HOH773 2.5 23.4 1.0 O B:HOH799 2.6 24.7 1.0 O B:HOH629 2.6 14.4 1.0 O B:HOH832 2.8 37.2 1.0 C B:THR315 3.4 13.6 1.0 HB B:THR315 3.6 12.9 1.0 HB2 B:ASP316 3.7 16.9 1.0 HA B:THR315 3.7 12.5 1.0 O B:HOH817 3.9 14.9 1.0 O B:HOH691 4.0 19.8 1.0 CA B:THR315 4.0 12.5 1.0 HB1 B:ALA79 4.1 14.8 1.0 HG3 B:GLU317 4.2 16.1 1.0 HB3 B:ALA79 4.2 15.1 1.0 CB B:THR315 4.3 12.9 1.0 O B:GLY80 4.4 12.7 1.0 HG2 B:GLU317 4.5 16.4 1.0 N B:ASP316 4.5 13.2 1.0 O B:HOH532 4.5 13.2 1.0 CB B:ASP316 4.5 16.8 1.0 O B:ASP316 4.5 16.9 1.0 CB B:ALA79 4.6 14.9 1.0 C B:ASP316 4.6 14.8 1.0 CA B:ASP316 4.7 14.5 1.0 HB3 B:ASP316 4.8 16.2 1.0 CG B:GLU317 4.8 16.2 1.0 HB2 B:ALA79 4.9 14.4 1.0

Sodium binding site 3 out of 3 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase Nylc Precursor, D122G/H130Y/T267C 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, D122G/H130Y/T267C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:30.7 occ:1.00 H B:GLU173 2.1 16.8 1.0 H B:ILE60 2.2 12.6 1.0 O B:VAL170 2.3 18.8 1.0 O B:GLU173 2.7 16.0 1.0 N B:ILE60 2.8 12.7 1.0 H B:GLY172 2.8 19.7 1.0 HA B:SER59 2.9 16.0 1.0 N B:GLU173 3.0 16.2 1.0 HZ B:PHE53 3.0 18.9 1.0 HB B:ILE60 3.0 14.6 1.0 N B:GLY172 3.1 19.0 1.0 HG13 B:ILE60 3.4 19.6 1.0 C B:VAL170 3.4 21.9 1.0 C B:GLU173 3.5 14.4 1.0 C B:PRO171 3.6 20.0 1.0 HA B:PRO171 3.6 18.4 1.0 CZ B:PHE53 3.6 18.8 1.0 C B:SER59 3.6 13.1 1.0 CB B:ILE60 3.6 13.9 1.0 HE2 B:PHE53 3.6 17.9 1.0 CA B:SER59 3.7 16.2 1.0 CA B:ILE60 3.7 11.3 1.0 HD11 B:ILE60 3.7 22.8 1.0 CA B:GLU173 3.8 15.8 1.0 HB2 B:GLU173 3.8 18.1 1.0 O B:ILE60 3.8 13.4 1.0 C B:GLY172 3.9 17.1 1.0 CG1 B:ILE60 3.9 20.3 1.0 CA B:PRO171 3.9 18.8 1.0 CE2 B:PHE53 3.9 17.6 1.0 CA B:GLY172 4.0 22.4 1.0 H B:VAL170 4.1 17.6 1.0 N B:PRO171 4.2 17.8 1.0 HA2 B:GLY172 4.2 20.8 1.0 C B:ILE60 4.2 11.8 1.0 O B:PRO171 4.3 19.2 1.0 CD1 B:ILE60 4.3 23.2 1.0 HB3 B:SER59 4.3 17.9 1.0 O B:VAL58 4.3 24.1 1.0 CB B:GLU173 4.3 17.7 1.0 HB B:VAL170 4.4 24.3 1.0 O B:HOH619 4.5 22.1 1.0 HA B:ILE60 4.5 12.0 1.0 CA B:VAL170 4.6 20.9 1.0 CB B:SER59 4.6 17.5 1.0 CE1 B:PHE53 4.6 20.3 1.0 N B:VAL170 4.6 17.7 1.0 HA B:GLU173 4.6 15.8 1.0 N B:SER59 4.7 15.3 1.0 O B:SER59 4.7 13.1 1.0 N B:PHE174 4.7 12.9 1.0 HD12 B:ILE60 4.8 22.2 1.0 HE1 B:PHE53 4.8 19.4 1.0 HG12 B:ILE60 4.8 19.3 1.0 HA3 B:GLY172 4.9 22.3 1.0 HA B:PHE174 4.9 12.5 1.0 C B:VAL58 4.9 18.6 1.0 HG3 B:GLU173 5.0 22.7 1.0 HG11 B:VAL170 5.0 25.1 1.0 HB2 B:PHE174 5.0 11.8 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