Chlorine in PDB 7yct: Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile

The structure of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile, PDB code: 7yct was solved by S.Chaikaew, Y.Watanabe, D.Zheng, F.Motojima, Y.Asano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.66 / 2.01
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	123.79, 123.79, 129.5, 90, 90, 120
R / Rfree (%)	17.1 / 20

The binding sites of Chlorine atom in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile (pdb code 7yct). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile, PDB code: 7yct:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:45.0 occ:1.00 CL1 A:IJ5201 0.0 45.0 1.0 C8 A:IJ5201 1.7 39.0 1.0 C7 A:IJ5201 2.7 32.5 1.0 C3 A:IJ5201 2.7 36.1 1.0 H6 A:IJ5201 2.8 34.7 1.0 C1 A:IJ5201 2.9 45.4 1.0 H1 A:IJ5201 3.0 41.4 1.0 C2 A:IJ5201 3.0 40.1 1.0 HA A:LEU27 3.0 23.0 1.0 HA A:ASN125 3.2 23.5 1.0 O A:PRO26 3.2 22.5 1.0 N1 A:IJ5201 3.4 29.7 1.0 HG2 A:GLN28 3.5 26.7 1.0 HB1 C:ALA48 3.5 26.2 1.0 H A:GLN28 3.6 23.7 1.0 HB3 A:ASN125 3.6 23.5 1.0 HB3 A:GLN28 3.6 24.3 1.0 HB2 A:ASN125 3.6 23.5 1.0 CA A:LEU27 3.7 22.8 1.0 C A:LEU27 3.7 23.6 1.0 N A:GLN28 3.7 23.8 1.0 HG2 A:PRO26 3.8 23.5 1.0 O A:ASN124 3.9 22.7 1.0 C A:PRO26 3.9 25.1 1.0 CB A:ASN125 3.9 23.4 1.0 C6 A:IJ5201 4.0 35.3 1.0 CA A:ASN125 4.0 23.1 1.0 C4 A:IJ5201 4.0 34.5 1.0 N A:LEU27 4.2 20.2 1.0 HB2 C:ALA48 4.2 26.2 1.0 CG A:GLN28 4.2 27.2 1.0 O A:HOH375 4.2 39.4 1.0 CB A:GLN28 4.3 23.4 1.0 CB C:ALA48 4.3 26.1 1.0 O A:LEU27 4.3 23.7 1.0 HB2 A:PRO26 4.4 23.7 1.0 O1 A:IJ5201 4.4 46.6 1.0 C5 A:IJ5201 4.5 31.0 1.0 O A:HOH370 4.5 21.9 1.0 HE2 A:PHE163 4.6 34.0 1.0 CA A:GLN28 4.6 23.6 1.0 H2 A:IJ5201 4.6 46.5 0.0 CG A:PRO26 4.7 23.1 1.0 CD A:GLN28 4.7 29.5 1.0 H5 A:IJ5201 4.7 33.8 1.0 H3 A:IJ5201 4.8 34.2 1.0 C A:ASN124 4.8 22.5 1.0 CB A:PRO26 4.9 24.0 1.0 HB3 C:ALA48 4.9 26.2 1.0 N A:ASN125 4.9 23.0 1.0 C A:ASN125 4.9 25.0 1.0 H A:LEU27 5.0 21.9 1.0 HB1 A:ALA164 5.0 30.0 1.0 HA C:ALA48 5.0 26.2 1.0

Chlorine binding site 2 out of 6 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:84.3 occ:1.00 CL1 A:IJ5202 0.0 84.3 1.0 C8 A:IJ5202 1.7 64.2 1.0 C7 A:IJ5202 2.6 65.4 1.0 H6 A:IJ5202 2.7 65.8 1.0 C3 A:IJ5202 2.8 59.4 1.0 H1 A:IJ5202 2.8 49.8 1.0 HE1 A:TYR44 3.0 26.2 1.0 HH12 A:ARG42 3.1 31.0 0.0 HB2 A:ALA58 3.2 22.9 1.0 C2 A:IJ5202 3.3 60.3 1.0 HH A:TYR44 3.4 30.6 0.0 HD11 A:LEU81 3.4 27.9 1.0 HD23 A:LEU81 3.5 27.5 1.0 HB3 A:ALA58 3.5 22.9 1.0 NH1 A:ARG42 3.7 31.0 1.0 CD1 A:PHE71 3.7 23.9 1.0 CE1 A:TYR44 3.8 27.9 1.0 CB A:ALA58 3.8 23.2 1.0 HD1 A:PHE71 3.8 23.8 1.0 C1 A:IJ5202 3.8 42.6 1.0 CE1 A:PHE71 3.9 24.2 1.0 C6 A:IJ5202 3.9 69.8 1.0 HH11 A:ARG42 4.0 31.0 0.0 C4 A:IJ5202 4.0 59.3 1.0 O A:HOH412 4.0 54.3 1.0 HE1 A:PHE71 4.1 24.0 1.0 OH A:TYR44 4.1 30.8 1.0 CG A:PHE71 4.2 23.0 1.0 HB1 A:ALA58 4.2 22.9 1.0 CD1 A:LEU81 4.3 28.7 1.0 HB3 A:PHE71 4.3 23.7 1.0 CD2 A:LEU81 4.4 28.1 1.0 CZ A:PHE71 4.4 23.5 1.0 CZ A:TYR44 4.4 27.1 1.0 C5 A:IJ5202 4.5 55.8 1.0 HG A:LEU81 4.5 26.9 1.0 CZ A:ARG42 4.5 30.0 1.0 N1 A:IJ5202 4.5 39.4 1.0 O1 A:IJ5202 4.5 32.3 1.0 CD2 A:PHE71 4.6 25.8 1.0 HZ A:PHE94 4.6 26.5 1.0 HH22 A:ARG42 4.6 30.1 1.0 H5 A:IJ5202 4.6 65.1 1.0 NH2 A:ARG42 4.6 30.1 1.0 HD13 A:LEU81 4.6 27.9 1.0 CG A:LEU81 4.7 26.2 1.0 CE2 A:PHE71 4.7 24.8 1.0 CB A:PHE71 4.7 23.9 1.0 H3 A:IJ5202 4.8 58.3 1.0 CD1 A:TYR44 4.8 22.6 1.0 HD1 A:TYR44 4.8 23.5 1.0 H2 A:IJ5202 4.8 32.1 0.0 HZ A:PHE71 4.8 24.0 1.0 HB2 A:PHE71 4.9 23.7 1.0 HD22 A:LEU81 4.9 27.5 1.0 HD21 A:LEU81 4.9 27.5 1.0 HD12 A:LEU81 5.0 27.9 1.0

Chlorine binding site 3 out of 6 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:46.2 occ:1.00 CL1 B:IJ5201 0.0 46.2 1.0 C8 B:IJ5201 1.8 44.5 1.0 C7 B:IJ5201 2.7 34.4 1.0 C3 B:IJ5201 2.7 40.4 1.0 H6 B:IJ5201 2.8 37.6 1.0 H1 B:IJ5201 3.0 44.6 1.0 C2 B:IJ5201 3.1 43.8 1.0 HA B:LEU27 3.1 22.9 1.0 C1 B:IJ5201 3.1 45.4 1.0 HA B:ASN125 3.1 25.4 1.0 O B:PRO26 3.2 21.1 1.0 HG2 B:GLN28 3.5 29.8 1.0 HB3 B:GLN28 3.6 27.7 1.0 H B:GLN28 3.6 24.8 1.0 N1 B:IJ5201 3.6 26.6 1.0 HB1 D:ALA48 3.6 26.0 1.0 HB3 B:ASN125 3.6 23.9 1.0 C B:LEU27 3.7 26.0 1.0 HB2 B:ASN125 3.7 23.9 1.0 CA B:LEU27 3.7 22.2 1.0 N B:GLN28 3.7 23.6 1.0 HG2 B:PRO26 3.8 21.5 1.0 C B:PRO26 3.8 22.5 1.0 O B:ASN124 3.9 25.8 1.0 O B:HOH372 3.9 34.6 1.0 CA B:ASN125 4.0 24.2 1.0 CB B:ASN125 4.0 23.9 1.0 C6 B:IJ5201 4.0 37.8 1.0 C4 B:IJ5201 4.0 42.6 1.0 N B:LEU27 4.1 21.0 1.0 CG B:GLN28 4.2 31.0 1.0 CB B:GLN28 4.2 26.9 1.0 HB2 D:ALA48 4.3 26.0 1.0 O B:LEU27 4.3 22.5 1.0 HB2 B:PRO26 4.3 21.7 1.0 CB D:ALA48 4.4 25.4 1.0 O1 B:IJ5201 4.4 50.9 1.0 O B:HOH360 4.5 21.5 1.0 C5 B:IJ5201 4.5 34.4 1.0 CA B:GLN28 4.6 26.5 1.0 CG B:PRO26 4.6 21.3 1.0 HE2 B:PHE163 4.6 34.3 1.0 CD B:GLN28 4.6 30.2 1.0 H2 B:IJ5201 4.7 50.6 0.0 H5 B:IJ5201 4.7 36.6 1.0 HD21 B:LEU27 4.7 29.6 1.0 C B:ASN124 4.7 28.9 1.0 H3 B:IJ5201 4.8 40.0 1.0 N B:ASN125 4.8 28.1 1.0 CB B:PRO26 4.8 22.3 1.0 HA D:ALA48 4.9 26.2 1.0 H B:LEU27 4.9 21.6 1.0 HE21 B:GLN28 4.9 29.3 0.0 C B:ASN125 5.0 27.4 1.0 CA B:PRO26 5.0 20.7 1.0 HB1 B:ALA164 5.0 26.9 1.0 HG1 B:THR41 5.0 28.7 0.0 NE2 B:GLN28 5.0 29.4 1.0

Chlorine binding site 4 out of 6 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:50.5 occ:1.00 CL1 C:IJ5201 0.0 50.5 1.0 C8 C:IJ5201 1.7 48.4 1.0 C3 C:IJ5201 2.7 42.9 1.0 C7 C:IJ5201 2.7 43.8 1.0 H6 C:IJ5201 2.8 45.9 1.0 H1 C:IJ5201 2.9 46.0 1.0 C2 C:IJ5201 3.0 47.0 1.0 HA C:LEU27 3.0 25.3 1.0 C1 C:IJ5201 3.0 43.0 1.0 O C:PRO26 3.1 21.4 1.0 HA C:ASN125 3.3 28.3 1.0 HG2 C:PRO26 3.5 22.1 1.0 HB1 A:ALA48 3.5 27.6 1.0 HB3 C:ASN125 3.5 28.4 1.0 N1 C:IJ5201 3.5 30.8 1.0 H C:GLN28 3.6 27.1 1.0 HB2 C:ASN125 3.6 28.4 1.0 HG2 C:GLN28 3.6 32.7 1.0 CA C:LEU27 3.7 24.5 1.0 C C:LEU27 3.7 27.6 1.0 C C:PRO26 3.7 22.7 1.0 HB3 C:GLN28 3.8 29.8 1.0 N C:GLN28 3.8 26.3 1.0 CB C:ASN125 3.9 28.1 1.0 O C:ASN124 4.0 26.5 1.0 C6 C:IJ5201 4.0 47.7 1.0 C4 C:IJ5201 4.0 51.5 1.0 N C:LEU27 4.0 23.0 1.0 CA C:ASN125 4.0 28.1 1.0 HB2 A:ALA48 4.2 27.6 1.0 CB A:ALA48 4.3 27.8 1.0 O1 C:IJ5201 4.3 50.2 1.0 CG C:GLN28 4.4 32.6 1.0 HB2 C:PRO26 4.4 21.8 1.0 O C:LEU27 4.4 25.9 1.0 O C:HOH330 4.4 24.8 1.0 CB C:GLN28 4.4 29.3 1.0 O C:HOH354 4.4 45.2 1.0 CG C:PRO26 4.4 22.2 1.0 C5 C:IJ5201 4.5 44.6 1.0 H2 C:IJ5201 4.6 50.1 0.0 HE2 C:PHE163 4.6 34.9 1.0 HB1 C:ALA164 4.7 30.0 1.0 CA C:GLN28 4.7 28.1 1.0 H5 C:IJ5201 4.7 46.1 1.0 H3 C:IJ5201 4.7 47.6 1.0 CB C:PRO26 4.8 21.4 1.0 CD C:GLN28 4.8 36.7 1.0 H C:LEU27 4.8 23.3 1.0 C C:ASN124 4.8 28.9 1.0 HA A:ALA48 4.9 27.2 1.0 CA C:PRO26 4.9 22.3 1.0 HG22 C:THR41 4.9 30.3 1.0 HD21 C:LEU27 4.9 31.4 1.0 N C:ASN125 4.9 27.8 1.0 HB3 A:ALA48 4.9 27.6 1.0 HG3 C:PRO26 4.9 22.1 1.0

Chlorine binding site 5 out of 6 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:86.0 occ:1.00 CL1 C:IJ5202 0.0 86.0 1.0 C8 C:IJ5202 1.7 70.3 1.0 C7 C:IJ5202 2.7 64.7 1.0 H1 C:IJ5202 2.7 59.7 1.0 HB3 C:TRP92 2.7 28.8 1.0 H6 C:IJ5202 2.7 66.5 1.0 C3 C:IJ5202 2.8 67.3 1.0 HB1 C:ALA109 2.9 26.4 1.0 C2 C:IJ5202 3.2 64.1 1.0 CZ C:PHE94 3.4 34.3 1.0 CE2 C:PHE94 3.5 40.1 1.0 HE3 C:TRP92 3.5 29.1 1.0 HB2 C:ALA109 3.5 26.4 1.0 CB C:TRP92 3.5 28.9 1.0 HB2 C:TRP92 3.5 28.7 1.0 HZ C:PHE94 3.6 35.1 1.0 HE2 C:PHE94 3.6 37.7 1.0 CB C:ALA109 3.6 26.1 1.0 HB3 C:ALA79 3.8 37.0 1.0 CE1 C:PHE94 3.9 32.4 1.0 CD2 C:PHE94 3.9 37.3 1.0 C6 C:IJ5202 3.9 66.6 1.0 C1 C:IJ5202 4.0 52.3 1.0 C4 C:IJ5202 4.0 69.6 1.0 O C:TYR93 4.1 30.9 1.0 HB3 C:ALA109 4.1 26.4 1.0 CE3 C:TRP92 4.1 28.7 1.0 CG C:TRP92 4.2 29.3 1.0 C C:TYR93 4.3 30.4 1.0 HE1 C:PHE94 4.3 33.0 1.0 CD1 C:PHE94 4.3 32.3 1.0 HD11 C:LEU81 4.3 33.2 1.0 O1 C:IJ5202 4.4 51.5 1.0 CG C:PHE94 4.4 34.4 1.0 N C:TYR93 4.4 29.0 1.0 HD2 C:PHE94 4.4 36.9 1.0 CD2 C:TRP92 4.4 28.7 1.0 H C:TYR93 4.4 30.0 1.0 C C:TRP92 4.5 30.5 1.0 C5 C:IJ5202 4.5 67.9 1.0 HB2 C:ALA79 4.6 37.0 1.0 H C:TYR110 4.6 28.2 1.0 CB C:ALA79 4.6 37.1 1.0 CA C:TRP92 4.6 27.5 1.0 H2 C:IJ5202 4.6 55.2 0.0 H5 C:IJ5202 4.7 66.7 1.0 HA C:TYR93 4.8 30.9 1.0 CA C:TYR93 4.8 31.8 1.0 H3 C:IJ5202 4.8 68.5 1.0 N C:PHE94 4.8 28.2 1.0 HA C:ALA109 4.8 26.6 1.0 CA C:ALA109 4.9 26.8 1.0 O C:TRP92 4.9 29.8 1.0 N1 C:IJ5202 4.9 40.1 1.0 HA C:PHE94 4.9 29.8 1.0 HD1 C:PHE94 5.0 33.0 1.0 HB1 C:ALA79 5.0 37.0 1.0 HD12 C:LEU81 5.0 33.1 1.0

Chlorine binding site 6 out of 6 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis Complexed with (R)-2-Chloromandelonitrile within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:45.9 occ:1.00 CL1 D:IJ5201 0.0 45.9 1.0 C8 D:IJ5201 1.7 45.5 1.0 C3 D:IJ5201 2.7 39.0 1.0 C7 D:IJ5201 2.7 37.6 1.0 H6 D:IJ5201 2.8 40.8 1.0 C2 D:IJ5201 3.0 40.5 1.0 H1 D:IJ5201 3.0 40.6 1.0 C1 D:IJ5201 3.0 40.1 1.0 O D:PRO26 3.1 22.2 1.0 HA D:LEU27 3.1 22.7 1.0 HA D:ASN125 3.2 28.1 1.0 HG2 D:PRO26 3.5 21.9 1.0 HG2 D:GLN28 3.6 28.2 1.0 HB3 D:GLN28 3.6 25.8 1.0 H D:GLN28 3.6 22.6 1.0 N1 D:IJ5201 3.6 29.4 1.0 HB3 D:ASN125 3.7 27.7 1.0 C D:LEU27 3.7 23.8 1.0 HB2 D:ASN125 3.7 27.7 1.0 CA D:LEU27 3.7 21.6 1.0 HB1 B:ALA48 3.7 25.6 1.0 C D:PRO26 3.7 21.8 1.0 N D:GLN28 3.7 21.6 1.0 C6 D:IJ5201 3.9 43.8 1.0 O D:ASN124 3.9 22.0 1.0 C4 D:IJ5201 4.0 42.0 1.0 CB D:ASN125 4.0 28.3 1.0 N D:LEU27 4.0 23.9 1.0 CA D:ASN125 4.1 26.8 1.0 HB2 B:ALA48 4.2 25.6 1.0 O D:LEU27 4.2 20.0 1.0 CB D:GLN28 4.3 25.6 1.0 CG D:GLN28 4.3 28.1 1.0 O D:HOH310 4.3 50.6 1.0 O1 D:IJ5201 4.3 43.1 1.0 CB B:ALA48 4.4 25.9 1.0 HB2 D:PRO26 4.4 22.0 1.0 O D:HOH362 4.4 20.4 1.0 C5 D:IJ5201 4.4 41.7 1.0 CG D:PRO26 4.5 22.9 1.0 H2 D:IJ5201 4.6 42.9 0.0 CA D:GLN28 4.6 24.0 1.0 H5 D:IJ5201 4.7 41.7 1.0 CD D:GLN28 4.7 31.6 1.0 H3 D:IJ5201 4.7 41.2 1.0 HE2 D:PHE163 4.8 31.8 1.0 H D:LEU27 4.8 22.8 1.0 HA B:ALA48 4.8 24.7 1.0 HB1 D:ALA164 4.8 26.1 1.0 CB D:PRO26 4.8 21.9 1.0 C D:ASN124 4.8 27.9 1.0 CA D:PRO26 4.8 21.5 1.0 N D:ASN125 4.9 28.8 1.0 HD21 D:LEU27 5.0 30.1 1.0

S.Chaikaew, Y.Watanabe, D.Zheng, F.Motojima, Y.Asano. Structure-Based Site-Directed Mutagenesis of Hydroxynitrile Lyase From Cyanogenic Millipede, Oxidus Gracilis For Enhancing Catalytic Efficiency and Enantioselectivity To Be Published.