Chlorine in PDB 7ycf: Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis in Acetonitrile

The structure of Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis in Acetonitrile, PDB code: 7ycf 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)	53.37 / 2.01
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	123.11, 123.11, 129.59, 90, 90, 120
R / Rfree (%)	17.3 / 20.3

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

Chlorine binding site 1 out of 4 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis in Acetonitrile


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 in Acetonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:26.2 occ:1.00 HH A:TYR107 2.4 20.7 0.0 HH12 A:ARG42 2.4 23.6 0.0 HO6 A:CNH201 2.6 24.3 0.0 O6 A:CNH201 3.0 24.0 1.0 HE1 A:TYR107 3.0 21.1 1.0 HC21 A:CNH201 3.0 25.1 1.0 HH21 A:ARG42 3.0 23.8 1.0 HD2 A:LYS121 3.1 26.1 1.0 HB3 A:ALA109 3.1 19.7 1.0 O A:HOH376 3.1 29.4 1.0 NH1 A:ARG42 3.2 23.9 1.0 OH A:TYR107 3.2 20.9 1.0 HB2 A:LYS121 3.3 23.8 1.0 C4 A:CNH201 3.6 25.1 1.0 C1 A:CNH201 3.6 24.3 1.0 NH2 A:ARG42 3.6 23.8 1.0 CE1 A:TYR107 3.7 20.0 1.0 C2 A:CNH201 3.7 25.5 1.0 HH11 A:ARG42 3.8 23.6 0.0 CZ A:ARG42 3.8 23.9 1.0 CB A:ALA109 3.8 19.3 1.0 HZ3 A:TRP92 3.9 23.6 1.0 HH A:TYR44 3.9 23.0 0.0 CZ A:TYR107 3.9 21.4 1.0 HB2 A:ALA109 3.9 19.7 1.0 HB1 A:ALA109 3.9 19.7 1.0 CD A:LYS121 4.0 26.1 1.0 N5 A:CNH201 4.0 28.3 1.0 CB A:LYS121 4.1 24.6 1.0 HB3 A:LYS121 4.1 23.8 1.0 HD3 A:LYS121 4.1 26.1 1.0 HE1 A:PHE29 4.2 24.9 1.0 CZ3 A:TRP92 4.2 23.8 1.0 HC23 A:CNH201 4.2 25.1 1.0 OH A:TYR44 4.2 23.1 1.0 HE3 A:TRP92 4.4 23.5 1.0 HZ A:PHE29 4.4 24.7 1.0 HH22 A:ARG42 4.4 23.8 1.0 CE3 A:TRP92 4.4 22.8 1.0 HZ2 A:LYS121 4.5 27.6 1.0 HC22 A:CNH201 4.5 25.1 1.0 CG A:LYS121 4.6 23.9 1.0 HE1 A:PHE94 4.7 22.4 1.0 CE1 A:PHE29 4.7 25.0 1.0 CZ A:PHE29 4.8 23.5 1.0 CH2 A:TRP92 4.9 23.0 1.0 O A:LYS121 4.9 23.8 1.0 HG3 A:LYS121 4.9 24.6 1.0 CD1 A:TYR107 5.0 23.1 1.0

Chlorine binding site 2 out of 4 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis in Acetonitrile


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 in Acetonitrile within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl204 b:32.0 occ:1.00 HH B:TYR107 2.3 28.7 0.0 HH12 B:ARG42 2.4 29.4 0.0 HO6 B:CNH201 2.7 31.9 0.0 HH21 B:ARG42 2.9 28.4 1.0 HE1 B:TYR107 3.0 29.2 1.0 O6 B:CNH201 3.1 31.6 1.0 HC21 B:CNH201 3.1 36.0 1.0 O B:HOH361 3.1 39.8 1.0 OH B:TYR107 3.1 28.8 1.0 HD2 B:LYS121 3.1 36.3 1.0 NH1 B:ARG42 3.1 29.8 1.0 HB3 B:ALA109 3.1 30.2 1.0 HB2 B:LYS121 3.4 33.4 1.0 NH2 B:ARG42 3.6 28.0 1.0 C4 B:CNH201 3.6 39.7 1.0 C1 B:CNH201 3.7 35.5 1.0 CE1 B:TYR107 3.7 29.1 1.0 HH11 B:ARG42 3.7 29.4 0.0 CZ B:ARG42 3.8 29.1 1.0 C2 B:CNH201 3.8 36.3 1.0 CZ B:TYR107 3.8 28.3 1.0 CB B:ALA109 3.9 31.4 1.0 HH B:TYR44 3.9 26.2 0.0 HB2 B:ALA109 4.0 30.2 1.0 N5 B:CNH201 4.0 39.2 1.0 HB1 B:ALA109 4.0 30.2 1.0 HZ3 B:TRP92 4.1 32.0 1.0 CD B:LYS121 4.1 36.1 1.0 HE1 B:PHE29 4.1 32.4 1.0 HC23 B:CNH201 4.2 36.0 1.0 CB B:LYS121 4.2 33.7 1.0 HZ2 B:LYS121 4.2 37.5 1.0 CZ3 B:TRP92 4.3 32.5 1.0 HB3 B:LYS121 4.3 33.4 1.0 OH B:TYR44 4.3 26.1 1.0 HH22 B:ARG42 4.4 28.4 1.0 HZ B:PHE29 4.4 31.7 1.0 HE3 B:TRP92 4.4 31.1 1.0 CE3 B:TRP92 4.5 29.8 1.0 HD3 B:LYS121 4.5 36.3 1.0 HC22 B:CNH201 4.6 36.0 1.0 CG B:LYS121 4.6 34.4 1.0 CE1 B:PHE29 4.7 33.2 1.0 HE2 B:PHE94 4.7 30.4 1.0 HG3 B:LYS121 4.8 34.6 1.0 CZ B:PHE29 4.8 30.7 1.0 CD1 B:TYR107 4.9 31.2 1.0 CH2 B:TRP92 4.9 32.9 1.0 CE B:LYS121 4.9 39.0 1.0 NZ B:LYS121 5.0 36.9 1.0 HE3 B:LYS121 5.0 37.8 1.0

Chlorine binding site 3 out of 4 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis in Acetonitrile


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 in Acetonitrile within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl205 b:27.8 occ:1.00 HH C:TYR107 2.3 26.9 0.0 HH12 C:ARG42 2.5 21.3 0.0 HO6 C:CNH201 2.7 29.2 0.0 HE1 C:TYR107 2.9 26.8 1.0 HC21 C:CNH201 3.0 27.2 1.0 O6 C:CNH201 3.1 29.4 1.0 OH C:TYR107 3.1 27.0 1.0 HH21 C:ARG42 3.1 25.1 1.0 HD2 C:LYS121 3.1 29.6 1.0 O C:HOH361 3.1 28.1 1.0 HB3 C:ALA109 3.1 22.3 1.0 NH1 C:ARG42 3.2 21.6 1.0 HB2 C:LYS121 3.3 25.3 1.0 CE1 C:TYR107 3.6 27.1 1.0 NH2 C:ARG42 3.6 25.3 1.0 C4 C:CNH201 3.7 31.2 1.0 C1 C:CNH201 3.7 26.2 1.0 C2 C:CNH201 3.7 27.7 1.0 HH11 C:ARG42 3.8 21.3 0.0 CZ C:TYR107 3.8 28.1 1.0 CZ C:ARG42 3.8 24.6 1.0 CB C:ALA109 3.9 22.5 1.0 HE1 C:PHE29 3.9 27.2 1.0 HH C:TYR44 3.9 22.3 0.0 HB2 C:ALA109 3.9 22.3 1.0 CD C:LYS121 4.0 29.9 1.0 N5 C:CNH201 4.0 29.0 1.0 HD3 C:LYS121 4.0 29.6 1.0 HB1 C:ALA109 4.0 22.3 1.0 HB3 C:LYS121 4.1 25.3 1.0 HZ3 C:TRP92 4.1 26.8 1.0 CB C:LYS121 4.1 25.6 1.0 HC23 C:CNH201 4.2 27.2 1.0 OH C:TYR44 4.3 22.5 1.0 HZ C:PHE29 4.3 27.2 1.0 HH22 C:ARG42 4.3 25.1 1.0 CZ3 C:TRP92 4.4 27.3 1.0 HE3 C:TRP92 4.4 26.1 1.0 HZ2 C:LYS121 4.4 32.1 1.0 HC22 C:CNH201 4.5 27.2 1.0 CE3 C:TRP92 4.5 25.6 1.0 CE1 C:PHE29 4.5 27.2 1.0 HE2 C:PHE94 4.6 25.1 1.0 CG C:LYS121 4.6 25.9 1.0 CZ C:PHE29 4.8 26.6 1.0 CD1 C:TYR107 4.8 25.1 1.0 HG3 C:LYS121 4.9 26.8 1.0 HZ1 C:LYS121 4.9 32.1 1.0 O C:LYS121 5.0 24.6 1.0 NZ C:LYS121 5.0 31.7 1.0

Chlorine binding site 4 out of 4 in the Hydroxynitrile Lyase From the Millipede, Oxidus Gracilis in Acetonitrile


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 in Acetonitrile within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl206 b:31.0 occ:1.00 HH D:TYR107 2.3 26.8 0.0 HH12 D:ARG42 2.4 25.5 0.0 HO6 D:CNH201 2.7 27.1 0.0 HE1 D:TYR107 3.0 28.8 1.0 HC21 D:CNH201 3.0 28.6 1.0 O6 D:CNH201 3.1 26.9 1.0 OH D:TYR107 3.1 27.1 1.0 O D:HOH348 3.1 29.9 1.0 HB3 D:ALA109 3.1 26.5 1.0 HD2 D:LYS121 3.2 27.8 1.0 NH1 D:ARG42 3.2 25.6 1.0 HH21 D:ARG42 3.2 27.4 1.0 HB2 D:LYS121 3.3 27.8 1.0 CE1 D:TYR107 3.6 28.1 1.0 C1 D:CNH201 3.7 25.9 1.0 NH2 D:ARG42 3.7 27.5 1.0 C4 D:CNH201 3.7 30.9 1.0 C2 D:CNH201 3.7 29.9 1.0 HD3 D:LYS121 3.7 27.8 1.0 HH11 D:ARG42 3.8 25.5 0.0 CZ D:TYR107 3.8 28.9 1.0 CZ D:ARG42 3.8 27.3 1.0 CB D:ALA109 3.9 26.7 1.0 CD D:LYS121 3.9 26.8 1.0 HB2 D:ALA109 3.9 26.5 1.0 HH D:TYR44 3.9 24.2 0.0 HB3 D:LYS121 3.9 27.8 1.0 N5 D:CNH201 4.0 32.6 1.0 CB D:LYS121 4.1 27.8 1.0 HZ3 D:TRP92 4.1 31.6 1.0 HE1 D:PHE29 4.1 28.5 1.0 HB1 D:ALA109 4.1 26.5 1.0 HC23 D:CNH201 4.1 28.6 1.0 OH D:TYR44 4.3 24.1 1.0 CZ3 D:TRP92 4.3 31.7 1.0 HH22 D:ARG42 4.3 27.4 1.0 HZ D:PHE29 4.3 27.3 1.0 HE3 D:TRP92 4.4 31.5 1.0 HC22 D:CNH201 4.5 28.6 1.0 CE3 D:TRP92 4.5 33.3 1.0 HZ2 D:LYS121 4.5 29.0 1.0 CG D:LYS121 4.6 28.6 1.0 CE1 D:PHE29 4.7 28.6 1.0 HE2 D:PHE94 4.7 27.6 1.0 CZ D:PHE29 4.8 26.8 1.0 HZ1 D:LYS121 4.8 29.0 1.0 CD1 D:TYR107 4.9 31.2 1.0 CH2 D:TRP92 4.9 30.7 1.0 NZ D:LYS121 5.0 28.9 1.0 O D:LYS121 5.0 28.3 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.