Chlorine in PDB 5y0m: Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant

The structure of Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant, PDB code: 5y0m 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)	72.21 / 1.03
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.418, 144.424, 128.268, 90.00, 90.00, 90.00
R / Rfree (%)	11.6 / 13.4

The binding sites of Chlorine atom in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant (pdb code 5y0m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant, PDB code: 5y0m:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1008 b:19.5 occ:1.00 O1 A:GOL1006 2.1 34.6 1.0 C1 A:GOL1006 3.0 19.6 1.0 NZ A:LYS189 3.0 11.0 1.0 O A:HOH1258 3.1 15.1 1.0 O2 A:GOL1006 3.4 40.9 1.0 O A:TYR146 3.5 9.9 1.0 CH2 A:TRP192 3.5 14.1 0.3 CZ3 A:TRP192 3.5 17.5 0.3 CE A:LYS189 3.6 10.8 1.0 C2 A:GOL1006 3.7 27.4 1.0 CD A:LYS189 3.8 11.3 1.0 CD1 A:TYR146 3.8 12.0 1.0 ND2 A:ASN219 3.8 10.1 1.0 CZ3 A:TRP192 3.8 21.2 0.7 CH2 A:TRP192 4.1 19.1 0.7 CZ B:PHE134 4.2 24.5 0.3 O A:HOH1162 4.2 10.7 1.0 C3 A:GOL1006 4.3 22.1 1.0 CE1 A:TYR146 4.4 13.4 1.0 OD1 A:ASN219 4.5 9.8 1.0 CG A:ASN219 4.5 8.3 1.0 C A:TYR146 4.5 8.2 1.0 OG A:SER186 4.6 11.0 1.0 CE1 B:PHE134 4.6 23.9 0.3 CB A:SER149 4.6 18.6 1.0 CG A:TYR146 4.7 10.0 1.0 CZ2 A:TRP192 4.8 19.6 0.3 O A:HOH1306 4.8 11.1 1.0 CB A:TYR146 4.8 9.7 1.0 OG A:SER149 4.8 22.9 1.0 CE3 A:TRP192 4.8 16.7 0.3 CE3 A:TRP192 5.0 16.0 0.7 CG A:LYS189 5.0 12.1 1.0

Chlorine binding site 2 out of 4 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1009 b:28.4 occ:1.00 O A:HOH1336 3.0 37.0 1.0 N A:ARG227 3.1 10.1 1.0 O A:HOH1362 3.3 45.7 1.0 CB A:ARG227 3.4 11.4 1.0 CG A:ARG227 3.4 11.2 1.0 CD1 A:LEU351 3.7 12.7 1.0 CB A:ASP226 3.7 10.7 1.0 CA A:ARG227 3.9 10.7 1.0 CD A:ARG227 3.9 11.1 1.0 NH2 A:ARG227 4.0 13.2 1.0 C A:ASP226 4.1 8.8 1.0 CA A:ASP226 4.2 9.6 1.0 CG A:ASP226 4.4 10.9 1.0 OD2 A:ASP226 4.7 13.9 1.0 NE A:ARG227 4.8 10.2 1.0 CZ A:ARG227 4.9 10.1 1.0 C A:ARG227 4.9 11.8 1.0 N A:ALA228 4.9 11.8 1.0 O A:HOH1165 4.9 27.7 1.0 OD1 A:ASP226 4.9 11.2 1.0 O A:HOH1341 5.0 46.1 1.0

Chlorine binding site 3 out of 4 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl408 b:17.3 occ:1.00 O2 B:GOL403 3.0 29.6 1.0 C2 B:GOL403 3.0 36.2 1.0 NZ B:LYS189 3.0 9.3 1.0 O B:HOH597 3.1 14.6 1.0 O B:TYR146 3.4 8.5 1.0 C1 B:GOL403 3.4 44.7 1.0 CH2 B:TRP192 3.5 12.0 0.3 CZ3 B:TRP192 3.5 10.0 0.3 CE B:LYS189 3.6 8.8 1.0 CD B:LYS189 3.7 8.6 1.0 CD1 B:TYR146 3.7 11.4 1.0 CZ3 B:TRP192 3.8 13.9 0.7 ND2 B:ASN219 3.8 8.3 1.0 OG B:SER149 4.0 14.2 0.3 CH2 B:TRP192 4.1 19.1 0.7 O B:HOH571 4.2 8.6 1.0 C3 B:GOL403 4.4 20.5 1.0 CE1 B:TYR146 4.4 12.8 1.0 CB B:SER149 4.4 14.7 0.7 OD1 B:ASN219 4.5 8.3 1.0 C B:TYR146 4.5 7.3 1.0 CG B:ASN219 4.5 7.0 1.0 OG B:SER186 4.5 9.7 1.0 CG B:TYR146 4.7 8.8 1.0 O1 B:GOL403 4.7 49.1 1.0 CB B:TYR146 4.8 8.5 1.0 CZ2 B:TRP192 4.8 16.5 0.3 OG B:SER149 4.8 16.3 0.7 CE3 B:TRP192 4.8 10.7 0.3 CZ A:PHE134 4.8 23.5 0.5 O3 B:GOL404 4.8 11.0 1.0 CE3 B:TRP192 5.0 14.0 0.7 CG B:LYS189 5.0 9.9 1.0 CB B:SER149 5.0 10.6 0.3

Chlorine binding site 4 out of 4 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of 6-Aminohexanoate-Oligomer Hydrolase From Arthrobacter Sp. KI72., D36A/D122G/H130Y/E263Q Muntant within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl409 b:37.3 occ:1.00 O B:HOH739 2.5 33.6 1.0 O B:HOH629 2.7 21.8 1.0 O B:LEU166 2.8 11.2 1.0 NH2 B:ARG127 2.9 26.3 1.0 NH1 B:ARG127 3.2 27.9 1.0 CZ B:ARG127 3.5 20.9 1.0 C B:LEU166 3.8 9.8 1.0 CA B:GLU167 4.1 11.9 1.0 O B:GLU167 4.3 13.5 1.0 CG B:LEU166 4.3 11.0 1.0 CB B:ALA169 4.3 11.5 1.0 O B:HOH707 4.3 40.1 1.0 CD1 B:LEU166 4.3 11.7 1.0 C B:GLU167 4.4 11.3 1.0 N B:GLU167 4.4 10.8 1.0 ND1 B:HIS76 4.5 13.5 1.0 O B:ALA169 4.6 14.7 1.0 N B:ALA169 4.6 10.2 1.0 O B:HOH673 4.7 15.5 1.0 NE B:ARG127 4.8 21.3 1.0 CE1 B:HIS76 4.8 16.1 1.0 CA B:LEU166 4.9 9.8 1.0 CA B:ALA169 4.9 9.9 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