Magnesium in PDB 9clr: Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations

The structure of Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations, PDB code: 9clr was solved by P.Tan, E.L.Meixner, A.Nguyen, R.J.Kazlaukas, C.T.Pierce, R.L.Evans, K.Shi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.49 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.966, 80.751, 135.456, 90, 90, 90
R / Rfree (%)	22 / 25.3

The structure of Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations (pdb code 9clr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations, PDB code: 9clr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:44.9 occ:1.00 O A:CSO163 2.7 33.2 1.0 O A:GLY164 3.4 27.5 1.0 C A:GLY164 3.5 26.5 1.0 C A:CSO163 3.6 32.4 1.0 O A:TYR160 3.7 28.6 1.0 N A:PRO165 3.9 30.4 1.0 CA A:PRO165 4.1 30.5 1.0 CA A:GLY164 4.2 31.7 1.0 N A:GLY164 4.3 28.6 1.0 CB A:LEU168 4.3 22.7 1.0 CD2 A:LEU168 4.4 23.6 1.0 CA A:CSO163 4.6 28.3 1.0 CD A:PRO165 4.6 30.7 1.0 N A:CSO163 4.6 28.9 1.0 C A:TYR160 4.8 28.9 1.0 O A:GLN161 4.8 35.8 1.0 CB A:CSO163 4.8 29.3 1.0

Magnesium binding site 2 out of 5 in the Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:20.8 occ:0.62 OD1 A:ASP37 2.6 26.8 1.0 N A:TRP17 3.1 19.2 1.0 N A:GLY16 3.2 21.9 1.0 CD1 A:TRP17 3.2 20.3 1.0 OD2 A:ASP37 3.4 30.2 1.0 CG A:ASP37 3.4 27.5 1.0 O B:MET173 3.5 29.8 1.0 CA A:GLY16 3.7 19.1 1.0 CA A:GLY42 3.8 23.2 1.0 CD2 B:LEU174 3.8 19.6 1.0 C A:GLY16 3.8 21.0 1.0 CB A:TRP17 3.9 19.7 1.0 CG A:TRP17 3.9 21.0 1.0 C A:GLY15 4.0 22.4 1.0 CA A:TRP17 4.0 22.0 1.0 CA A:GLY15 4.3 21.5 1.0 N A:VAL43 4.3 25.3 1.0 NE1 A:TRP17 4.3 22.7 1.0 CB B:MET173 4.4 25.6 1.0 C B:MET173 4.4 28.5 1.0 C A:GLY42 4.6 25.3 1.0 CG B:LEU174 4.8 22.8 1.0 O A:GLY15 4.8 22.2 1.0 CB A:ASP37 4.9 28.5 1.0 N A:GLY42 4.9 22.3 1.0 CA B:MET173 4.9 24.8 1.0 O A:GLY16 5.0 20.9 1.0

Magnesium binding site 3 out of 5 in the Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:43.9 occ:1.00 OH B:TYR224 2.7 28.5 1.0 OG1 B:THR110 3.1 30.9 1.0 CE1 B:TYR224 3.4 29.3 1.0 CZ B:TYR224 3.5 29.3 1.0 CA B:GLY197 3.6 24.4 1.0 CG2 B:THR110 3.6 29.7 1.0 CB B:THR110 4.0 26.8 1.0 O B:GLY197 4.0 35.0 1.0 C B:GLY197 4.2 29.9 1.0 CG B:LYS193 4.2 36.1 1.0 CD1 B:TYR224 4.7 27.0 1.0 CE2 B:TYR224 4.8 25.4 1.0 N B:GLY197 4.8 27.3 1.0 CA B:LYS193 4.9 33.0 1.0 CB B:LYS193 4.9 33.5 1.0 N B:THR110 5.0 25.1 1.0

Magnesium binding site 4 out of 5 in the Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:35.8 occ:1.00 O B:ALA40 2.6 23.7 1.0 O B:PRO177 2.9 29.0 1.0 OG B:SER41 3.0 25.8 1.0 CA B:SER41 3.5 19.4 1.0 C B:ALA40 3.5 23.9 1.0 CB B:SER41 3.6 22.9 1.0 N B:SER41 3.9 25.6 1.0 C B:PRO177 3.9 26.3 1.0 CB B:ARG176 4.0 23.9 1.0 O B:ARG176 4.0 23.4 1.0 C B:ARG176 4.2 25.6 1.0 CA B:CYS13 4.3 23.8 1.0 CB B:SER178 4.4 29.3 1.0 CA B:SER178 4.4 27.2 1.0 N B:CYS13 4.5 19.1 1.0 O B:ALA39 4.5 24.1 1.0 O B:HIS14 4.6 27.8 1.0 N B:SER178 4.6 24.9 1.0 OG B:SER178 4.6 36.3 1.0 C B:CYS13 4.6 26.1 1.0 N B:PRO177 4.7 25.1 1.0 CA B:ARG176 4.7 25.8 1.0 CA B:ALA40 4.8 26.5 1.0 C B:SER41 4.8 21.1 1.0 CB B:ALA40 4.8 25.2 1.0 CD B:ARG176 4.9 23.6 1.0 CA B:PRO177 4.9 27.0 1.0 NE B:ARG176 5.0 27.3 1.0 CG B:ARG176 5.0 26.3 1.0

Magnesium binding site 5 out of 5 in the Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:34.1 occ:1.00 OD1 B:ASP109 2.7 25.0 1.0 O B:HOH415 2.8 25.7 1.0 O B:CYS113 2.9 24.7 1.0 N B:ASP109 3.1 25.9 1.0 O B:ASP109 3.2 27.2 1.0 O B:HIS112 3.3 26.4 1.0 O B:HOH411 3.5 27.1 1.0 CG B:ASP109 3.6 27.0 1.0 C B:ASP109 3.7 28.1 1.0 C B:HIS112 3.8 28.4 1.0 CB B:PHE116 3.8 26.8 1.0 CA B:ASP109 3.8 27.5 1.0 C B:CYS113 3.8 30.4 1.0 CB B:PRO108 3.9 27.6 1.0 C B:PRO108 4.0 25.7 1.0 CA B:PRO108 4.0 25.7 1.0 CB B:HIS112 4.0 26.4 1.0 O B:SER114 4.2 29.5 1.0 CA B:SER114 4.2 27.9 1.0 CB B:ASP109 4.3 25.4 1.0 CA B:HIS112 4.3 23.0 1.0 N B:HIS112 4.4 22.7 1.0 CD2 B:PHE116 4.4 25.9 1.0 C B:SER114 4.4 29.4 1.0 OD2 B:ASP109 4.4 27.4 1.0 N B:SER114 4.5 27.7 1.0 N B:CYS113 4.5 23.1 1.0 N B:PHE116 4.6 30.9 1.0 CG B:PHE116 4.6 25.6 1.0 N B:THR110 4.7 25.1 1.0 CA B:CYS113 4.8 29.4 1.0 CA B:PHE116 4.8 27.6 1.0 CG1 B:VAL117 4.8 28.6 1.0 N B:VAL117 4.9 26.1 1.0

P.Tan, C.T.Pierce, E.L.Meixner, A.Nguyen, K.Shi, H.Aihara, R.L.Evans, R.J.Kazlaukas. Hydroxynitrile Lyase From Hevea Brasiliensis with Seventy-One Mutations To Be Published.