Chlorine in PDB 7ycb: Hydroxynitrile Lyase From the Millipede

The structure of Hydroxynitrile Lyase From the Millipede, PDB code: 7ycb 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)	49.40 / 2.01
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	123.16, 123.16, 130.14, 90, 90, 120
R / Rfree (%)	20.6 / 23.5

The binding sites of Chlorine atom in the Hydroxynitrile Lyase From the Millipede (pdb code 7ycb). 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, PDB code: 7ycb:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hydroxynitrile Lyase From the Millipede


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:33.3 occ:1.00 HH A:TYR125 2.2 31.2 0.0 HH12 A:ARG60 2.4 29.2 0.0 HE1 A:TYR125 2.8 30.3 1.0 HH21 A:ARG60 2.9 32.5 1.0 OH A:TYR125 3.0 31.1 1.0 HD2 A:LYS139 3.0 33.2 1.0 HB2 A:LYS139 3.0 31.1 1.0 HB3 A:ALA127 3.1 27.6 1.0 NH1 A:ARG60 3.1 29.3 1.0 C1' A:HBX201 3.2 39.6 1.0 H1' A:HBX201 3.2 38.2 1.0 O A:HOH301 3.2 46.6 1.0 C1 A:HBX201 3.4 38.7 1.0 NH2 A:ARG60 3.5 31.9 1.0 CE1 A:TYR125 3.5 29.6 1.0 HB3 A:LYS139 3.7 31.1 1.0 HD3 A:LYS139 3.7 33.2 1.0 CZ A:ARG60 3.7 34.0 1.0 O1' A:HBX201 3.7 35.0 1.0 HE1 A:PHE47 3.7 34.2 1.0 HH11 A:ARG60 3.7 29.2 0.0 CZ A:TYR125 3.7 30.6 1.0 CD A:LYS139 3.7 33.5 1.0 C2 A:HBX201 3.8 40.8 1.0 CB A:LYS139 3.8 31.5 1.0 H2 A:HBX201 3.8 41.4 1.0 CB A:ALA127 3.8 27.3 1.0 HB2 A:ALA127 3.9 27.6 1.0 HB1 A:ALA127 4.0 27.6 1.0 C6 A:HBX201 4.0 39.2 1.0 HZ A:PHE47 4.1 33.8 1.0 HH22 A:ARG60 4.2 32.5 1.0 H6 A:HBX201 4.2 39.9 1.0 CE1 A:PHE47 4.3 34.2 1.0 HH A:TYR62 4.3 38.0 0.0 CG A:LYS139 4.3 31.6 1.0 HZ3 A:TRP110 4.4 27.7 1.0 OH A:TYR62 4.4 38.1 1.0 CZ A:PHE47 4.5 33.2 1.0 O A:LYS139 4.6 28.0 1.0 CZ3 A:TRP110 4.6 28.1 1.0 C3 A:HBX201 4.6 45.5 1.0 HZ2 A:LYS139 4.7 34.7 1.0 HE2 A:PHE112 4.8 32.5 1.0 CD1 A:TYR125 4.8 31.5 1.0 HE3 A:TRP110 4.8 28.0 1.0 HG3 A:LYS139 4.8 32.0 1.0 C5 A:HBX201 4.8 41.9 1.0 CE3 A:TRP110 4.8 27.1 1.0 HZ1 A:LYS139 4.8 34.7 1.0 NE A:ARG60 4.9 32.4 1.0 CE A:LYS139 5.0 34.3 1.0 CA A:LYS139 5.0 29.6 1.0

Chlorine binding site 2 out of 4 in the Hydroxynitrile Lyase From the Millipede


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:32.5 occ:1.00 HH B:TYR125 2.1 33.1 0.0 HH12 B:ARG60 2.6 23.3 0.0 HH21 B:ARG60 2.6 30.4 1.0 HE1 B:TYR125 2.8 30.4 1.0 OH B:TYR125 2.9 33.1 1.0 HD2 B:LYS139 3.0 34.1 1.0 HB2 B:LYS139 3.1 30.2 1.0 O B:HOH302 3.1 45.3 1.0 HB3 B:ALA127 3.2 28.4 1.0 NH1 B:ARG60 3.2 23.5 1.0 C1' B:HBX201 3.3 41.5 1.0 HE1 B:PHE47 3.3 31.8 1.0 NH2 B:ARG60 3.3 30.7 1.0 H1' B:HBX201 3.4 39.0 1.0 HD3 B:LYS139 3.4 34.1 1.0 CE1 B:TYR125 3.5 29.6 1.0 C1 B:HBX201 3.5 40.7 1.0 CZ B:ARG60 3.6 29.8 1.0 CD B:LYS139 3.6 34.0 1.0 HB3 B:LYS139 3.7 30.2 1.0 O1' B:HBX201 3.7 32.9 1.0 CZ B:TYR125 3.7 32.1 1.0 C6 B:HBX201 3.8 45.5 1.0 H6 B:HBX201 3.8 44.5 1.0 CB B:LYS139 3.8 30.2 1.0 HH11 B:ARG60 3.9 23.3 0.0 HZ B:PHE47 3.9 33.3 1.0 HB2 B:ALA127 4.0 28.4 1.0 CB B:ALA127 4.0 29.0 1.0 CE1 B:PHE47 4.1 31.3 1.0 HH22 B:ARG60 4.1 30.4 1.0 C2 B:HBX201 4.2 38.3 1.0 HH B:TYR62 4.2 34.2 0.0 HB1 B:ALA127 4.2 28.4 1.0 CG B:LYS139 4.3 31.4 1.0 OH B:TYR62 4.3 33.9 1.0 CZ B:PHE47 4.3 33.3 1.0 H2 B:HBX201 4.4 40.5 1.0 HZ3 B:TRP110 4.4 32.1 1.0 HZ2 B:LYS139 4.5 37.3 1.0 HE1 B:PHE112 4.6 31.3 1.0 C5 B:HBX201 4.6 47.4 1.0 CZ3 B:TRP110 4.7 32.2 1.0 HG3 B:LYS139 4.7 31.7 1.0 O B:LYS139 4.7 33.5 1.0 CD1 B:TYR125 4.7 30.8 1.0 NE B:ARG60 4.8 25.8 1.0 HE3 B:TRP110 4.9 31.5 1.0 CE B:LYS139 4.9 37.5 1.0 HZ1 B:LYS139 4.9 37.3 1.0 HB2 B:ALA141 4.9 29.6 1.0 CE3 B:TRP110 4.9 31.7 1.0 C3 B:HBX201 4.9 44.5 1.0 HG2 B:ARG60 5.0 26.1 1.0 HD1 B:TYR125 5.0 30.2 1.0

Chlorine binding site 3 out of 4 in the Hydroxynitrile Lyase From the Millipede


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl203 b:46.8 occ:1.00 HH C:TYR125 2.1 47.5 0.0 HH12 C:ARG60 2.6 43.1 0.0 HE1 C:TYR125 2.7 45.1 1.0 H1' C:HBX201 2.8 61.2 1.0 OH C:TYR125 2.9 47.7 1.0 C1' C:HBX201 2.9 60.4 1.0 HH21 C:ARG60 3.1 42.2 1.0 O C:HOH301 3.1 42.5 1.0 HD2 C:LYS139 3.1 50.0 1.0 HB2 C:LYS139 3.2 48.8 1.0 HB3 C:ALA127 3.2 42.9 1.0 NH1 C:ARG60 3.2 43.0 1.0 HD3 C:LYS139 3.3 50.0 1.0 C1 C:HBX201 3.3 62.9 1.0 CE1 C:TYR125 3.4 44.6 1.0 O1' C:HBX201 3.5 61.7 1.0 NH2 C:ARG60 3.6 40.9 1.0 CZ C:TYR125 3.6 45.7 1.0 CD C:LYS139 3.7 49.3 1.0 HE1 C:PHE47 3.7 43.5 1.0 CZ C:ARG60 3.7 45.2 1.0 C2 C:HBX201 3.7 62.9 1.0 HB3 C:LYS139 3.8 48.7 1.0 HH11 C:ARG60 3.8 43.1 0.0 H2 C:HBX201 3.8 62.7 1.0 HB2 C:ALA127 3.8 42.9 1.0 CB C:LYS139 3.9 49.1 1.0 CB C:ALA127 3.9 43.5 1.0 HH C:TYR62 3.9 40.2 0.0 C6 C:HBX201 4.0 63.8 1.0 HZ C:PHE47 4.0 42.3 1.0 H6 C:HBX201 4.1 63.8 1.0 HH22 C:ARG60 4.2 42.2 1.0 HB1 C:ALA127 4.3 42.9 1.0 CE1 C:PHE47 4.3 42.6 1.0 HZ3 C:TRP110 4.4 44.4 1.0 OH C:TYR62 4.4 40.6 1.0 CG C:LYS139 4.4 49.6 1.0 CZ C:PHE47 4.5 41.9 1.0 HZ2 C:LYS139 4.6 51.5 1.0 CZ3 C:TRP110 4.6 43.9 1.0 C3 C:HBX201 4.7 61.8 1.0 HZ1 C:LYS139 4.7 51.5 1.0 CD1 C:TYR125 4.7 46.3 1.0 HE3 C:TRP110 4.8 42.2 1.0 O C:LYS139 4.9 38.8 1.0 CE3 C:TRP110 4.9 40.0 1.0 C5 C:HBX201 4.9 65.2 1.0 CE C:LYS139 4.9 51.9 1.0 NE C:ARG60 4.9 40.9 1.0 HE2 C:PHE112 4.9 44.0 1.0 CE2 C:TYR125 4.9 43.5 1.0 NZ C:LYS139 4.9 51.3 1.0 H C:ALA127 4.9 39.0 1.0 HG3 C:LYS139 5.0 49.4 1.0

Chlorine binding site 4 out of 4 in the Hydroxynitrile Lyase From the Millipede


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl205 b:37.5 occ:1.00 HH D:TYR125 2.3 36.9 0.0 HH12 D:ARG60 2.4 28.8 0.0 HH21 D:ARG60 2.8 30.6 1.0 HE1 D:TYR125 2.9 37.3 1.0 HD2 D:LYS139 3.0 36.9 1.0 OH D:TYR125 3.0 36.7 1.0 HB2 D:LYS139 3.1 35.4 1.0 NH1 D:ARG60 3.2 28.9 1.0 HB3 D:ALA127 3.2 33.9 1.0 C1' D:HBX201 3.3 44.3 1.0 O D:HOH304 3.3 32.3 1.0 HD3 D:LYS139 3.3 36.9 1.0 NH2 D:ARG60 3.4 31.0 1.0 O1' D:HBX201 3.4 40.7 1.0 C1 D:HBX201 3.4 53.5 1.0 HB3 D:LYS139 3.5 35.4 1.0 H1' D:HBX201 3.5 45.3 1.0 CD D:LYS139 3.6 36.7 1.0 CE1 D:TYR125 3.6 36.5 1.0 CZ D:ARG60 3.7 29.6 1.0 H6 D:HBX201 3.7 49.0 1.0 C6 D:HBX201 3.7 47.7 1.0 HE1 D:PHE47 3.7 36.7 1.0 CZ D:TYR125 3.7 37.7 1.0 CB D:LYS139 3.7 36.1 1.0 HH11 D:ARG60 3.8 28.8 0.0 CB D:ALA127 4.0 34.5 1.0 HZ D:PHE47 4.0 36.5 1.0 HH22 D:ARG60 4.1 30.5 1.0 HB2 D:ALA127 4.1 33.9 1.0 HZ3 D:TRP110 4.1 36.0 1.0 C2 D:HBX201 4.1 49.5 1.0 CG D:LYS139 4.2 35.1 1.0 HB1 D:ALA127 4.3 33.9 1.0 CE1 D:PHE47 4.3 36.1 1.0 CZ3 D:TRP110 4.4 36.7 1.0 H2 D:HBX201 4.4 49.8 1.0 HZ2 D:LYS139 4.5 38.0 1.0 CZ D:PHE47 4.5 37.0 1.0 HH D:TYR62 4.5 31.6 0.0 OH D:TYR62 4.5 31.3 1.0 C5 D:HBX201 4.5 48.4 1.0 HE3 D:TRP110 4.7 35.5 1.0 CE3 D:TRP110 4.7 36.5 1.0 HG3 D:LYS139 4.8 35.7 1.0 O D:LYS139 4.8 34.1 1.0 CE D:LYS139 4.8 39.3 1.0 CD1 D:TYR125 4.9 39.3 1.0 HE2 D:PHE112 4.9 36.5 1.0 C3 D:HBX201 4.9 48.0 1.0 H D:ALA127 4.9 32.7 1.0 NE D:ARG60 4.9 27.5 1.0 NZ D:LYS139 5.0 37.4 1.0 CH2 D:TRP110 5.0 34.6 1.0 HZ1 D:LYS139 5.0 38.0 1.0 HG2 D:LYS139 5.0 35.7 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.