Sodium in PDB 5y0l: Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D122G/H130Y Muntant

The structure of Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D122G/H130Y Muntant, PDB code: 5y0l was solved by S.Negoro, N.Shibata, K.Nagai, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.00 / 1.39
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	69.880, 144.003, 129.283, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20

The binding sites of Sodium atom in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D122G/H130Y Muntant (pdb code 5y0l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D122G/H130Y Muntant, PDB code: 5y0l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D122G/H130Y Muntant


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 From Arthrobacter Sp. KI72., D122G/H130Y Muntant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:37.8 occ:1.00 O A:HOH1356 2.3 26.1 1.0 O A:HOH1328 2.4 23.8 1.0 O A:PHE38 2.6 29.5 1.0 O A:ASN35 2.6 24.1 1.0 O A:HOH1355 2.7 39.2 1.0 C A:ASN35 3.6 22.5 1.0 C A:PHE38 3.8 25.1 1.0 CA A:ASP36 4.1 26.0 1.0 CD1 A:LEU40 4.2 24.6 1.0 CG A:LEU40 4.2 25.6 1.0 O A:HOH1362 4.3 40.6 1.0 N A:ASP36 4.3 22.9 1.0 N A:LEU40 4.5 26.1 1.0 N A:PHE38 4.5 25.8 1.0 C A:ASP36 4.5 24.6 1.0 CA A:ASN35 4.5 20.2 1.0 CA A:ASP39 4.6 32.0 1.0 O A:HOH1128 4.6 21.3 1.0 CB A:ASN35 4.6 19.8 1.0 O B:HOH800 4.6 43.5 1.0 N A:ASP39 4.6 29.1 1.0 CA A:PHE38 4.7 25.4 1.0 O A:HOH1159 4.7 21.7 1.0 O A:ASP36 4.8 28.4 1.0 CB A:LEU40 4.8 23.5 1.0

Sodium binding site 2 out of 2 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D122G/H130Y Muntant


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 From Arthrobacter Sp. KI72., D122G/H130Y Muntant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:40.0 occ:1.00 O B:HOH688 2.4 37.1 1.0 O B:HOH741 2.4 24.8 1.0 O B:THR315 2.5 21.1 1.0 O B:HOH583 2.7 13.8 1.0 C B:THR315 3.5 20.7 1.0 O B:HOH686 3.9 18.7 1.0 O B:HOH783 4.0 15.1 1.0 CA B:THR315 4.1 18.1 1.0 CB B:THR315 4.3 17.4 1.0 O B:GLY80 4.4 17.0 1.0 O B:HOH534 4.5 12.0 1.0 CB B:ASP316 4.5 21.2 1.0 O B:ASP316 4.6 22.7 1.0 N B:ASP316 4.6 20.3 1.0 C B:ASP316 4.7 22.3 1.0 CB B:ALA79 4.7 22.5 1.0 CA B:ASP316 4.8 17.8 1.0 CG B:GLU317 4.9 27.1 1.0

S.Negoro, N.Shibata, Y.H.Lee, I.Takehara, R.Kinugasa, K.Nagai, Y.Tanaka, D.I.Kato, M.Takeo, Y.Goto, Y.Higuchi. Structural Basis of the Correct Subunit Assembly, Aggregation, and Intracellular Degradation of Nylon Hydrolase Sci Rep V. 8 9725 2018.
ISSN: ESSN 2045-2322
PubMed: 29950566
DOI: 10.1038/S41598-018-27860-W