Chlorine in PDB 5u81: Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved

All present enzymatic activity of Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved:
3.5.1.23;

The structure of Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved, PDB code: 5u81 was solved by A.Gebai, A.Gorelik, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.39 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.767, 53.913, 48.802, 90.00, 104.41, 90.00
R / Rfree (%)	12.2 / 15.8

The binding sites of Chlorine atom in the Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved (pdb code 5u81). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved, PDB code: 5u81:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl416 b:21.5 occ:1.00 HO6 A:MAN403 2.2 30.0 1.0 HH11 A:ARG44 2.5 19.4 1.0 HD2 A:ARG44 3.1 17.7 1.0 HD3 A:PRO184 3.1 14.8 1.0 O6 A:NAG405 3.1 16.8 1.0 O A:HOH780 3.1 44.9 1.0 O6 A:MAN403 3.2 25.0 1.0 NH1 A:ARG44 3.2 16.1 1.0 HO6 A:NAG405 3.4 20.1 1.0 HB3 A:PRO184 3.4 16.3 1.0 HD13 A:LEU385 3.5 16.4 1.0 HH12 A:ARG44 3.5 19.4 1.0 HG2 A:ARG44 3.5 19.5 1.0 HB3 A:LYS183 3.6 15.6 1.0 HG3 A:ARG44 3.7 19.5 1.0 HA A:PRO184 3.7 15.9 1.0 H62 A:NAG405 3.9 20.5 1.0 CD A:ARG44 3.9 14.8 1.0 C6 A:NAG405 3.9 17.1 1.0 CG A:ARG44 3.9 16.2 1.0 H61 A:NAG405 3.9 20.5 1.0 CD A:PRO184 3.9 12.4 1.0 HB2 A:LYS183 3.9 15.6 1.0 N A:PRO184 3.9 11.2 1.0 H61 A:MAN403 4.1 27.9 1.0 C6 A:MAN403 4.1 23.2 1.0 HD12 A:LEU385 4.1 16.4 1.0 CB A:PRO184 4.1 13.6 1.0 CD1 A:LEU385 4.1 13.7 1.0 CA A:PRO184 4.2 13.2 1.0 CB A:LYS183 4.2 13.0 1.0 C A:LYS183 4.3 11.7 1.0 CZ A:ARG44 4.3 16.1 1.0 HD11 A:LEU385 4.4 16.4 1.0 H62 A:MAN403 4.4 27.9 1.0 O A:HOH552 4.5 16.4 1.0 CG A:PRO184 4.5 13.3 1.0 HG3 A:PRO184 4.5 15.9 1.0 NE A:ARG44 4.5 16.6 1.0 HD3 A:ARG44 4.6 17.7 1.0 HD2 A:PRO184 4.7 14.8 1.0 O A:LYS183 4.7 12.5 1.0 O A:HOH574 4.9 26.4 1.0 CA A:LYS183 4.9 13.0 1.0 HB2 A:PRO184 5.0 16.3 1.0

Chlorine binding site 2 out of 2 in the Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Acid Ceramidase (ASAH1, Acdase) From Naked Mole Rat, CYS143ALA, Uncleaved within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl417 b:20.4 occ:1.00 H A:ILE178 2.4 19.5 1.0 H A:GLY168 2.4 28.4 1.0 H A:LEU167 2.6 23.5 1.0 HG12 A:ILE178 2.7 25.2 0.6 HB A:ILE178 2.9 19.6 0.4 HB3 A:TRP176 3.0 25.3 1.0 HB A:ILE178 3.0 20.4 0.6 O A:HOH660 3.0 21.4 1.0 N A:ILE178 3.2 16.2 1.0 H A:VAL177 3.2 22.2 1.0 N A:GLY168 3.2 23.6 1.0 HB2 A:LEU167 3.2 24.4 1.0 N A:LEU167 3.3 19.6 1.0 HG23 A:ILE165 3.4 26.3 1.0 CG1 A:ILE178 3.4 21.0 0.6 HG13 A:ILE178 3.4 22.0 0.4 HB A:VAL177 3.4 29.2 1.0 HE1 A:MET83 3.4 20.0 0.5 H A:PHE166 3.4 23.6 1.0 HD12 A:ILE178 3.5 21.6 0.4 HG22 A:ILE165 3.5 26.3 1.0 O A:GLY168 3.5 32.6 1.0 CB A:ILE178 3.6 17.0 0.6 N A:VAL177 3.6 18.5 1.0 HE3 A:TRP176 3.6 38.8 1.0 CB A:ILE178 3.6 16.3 0.4 HG13 A:ILE178 3.7 25.2 0.6 HA A:PHE166 3.8 24.2 1.0 H A:THR179 3.8 16.5 1.0 CG2 A:ILE165 3.9 21.9 1.0 CG1 A:ILE178 3.9 18.3 0.4 N A:PHE166 3.9 19.7 1.0 CB A:TRP176 3.9 21.1 1.0 CA A:LEU167 4.0 21.9 1.0 CA A:ILE178 4.0 14.9 0.6 CA A:ILE178 4.0 15.0 0.4 CB A:LEU167 4.0 20.3 1.0 C A:LEU167 4.1 19.7 1.0 CA A:GLY168 4.1 28.4 1.0 HA3 A:GLY168 4.1 34.1 1.0 C A:PHE166 4.1 19.6 1.0 C A:TRP176 4.1 14.6 1.0 CD1 A:ILE178 4.1 18.0 0.4 CA A:PHE166 4.1 20.2 1.0 C A:VAL177 4.2 14.3 1.0 CA A:VAL177 4.2 18.9 1.0 CB A:VAL177 4.2 24.3 1.0 C A:GLY168 4.2 26.9 1.0 HG21 A:ILE165 4.2 26.3 1.0 HA A:TRP176 4.3 21.2 1.0 CE A:MET83 4.3 16.6 0.5 CE3 A:TRP176 4.4 32.3 1.0 HB2 A:TRP176 4.4 25.3 1.0 CA A:TRP176 4.4 17.7 1.0 HB3 A:LEU167 4.5 24.4 1.0 N A:THR179 4.5 13.8 1.0 HE3 A:MET83 4.6 20.0 0.5 H A:ILE165 4.6 22.7 1.0 CD1 A:ILE178 4.7 20.7 0.6 HD11 A:ILE178 4.7 21.6 0.4 HA A:ILE178 4.7 18.0 1.0 HD13 A:ILE178 4.8 24.8 0.6 HG12 A:VAL177 4.8 30.1 1.0 C A:ILE165 4.8 19.4 1.0 CG A:TRP176 4.8 27.6 1.0 HG12 A:ILE178 4.8 22.0 0.4 C A:ILE178 4.8 12.8 1.0 HD13 A:ILE178 4.8 21.6 0.4 O A:TRP176 4.9 14.6 1.0 HA A:LEU167 4.9 26.3 1.0 HD11 A:ILE178 4.9 24.8 0.6 CD2 A:TRP176 4.9 28.7 1.0 HD12 A:LEU167 4.9 25.9 1.0 CG2 A:ILE178 4.9 17.0 0.4 SD A:MET83 4.9 17.8 0.5 HG23 A:VAL177 5.0 32.4 1.0 HA2 A:GLY168 5.0 34.1 1.0 CG2 A:ILE178 5.0 18.3 0.6

A.Gebai, A.Gorelik, Z.Li, K.Illes, B.Nagar. Structural Basis For the Activation of Acid Ceramidase. Nat Commun V. 9 1621 2018.
ISSN: ESSN 2041-1723
PubMed: 29692406
DOI: 10.1038/S41467-018-03844-2