Manganese in PDB 8oz8: Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola

The structure of Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola, PDB code: 8oz8 was solved by I.Bento, J.Coloma, P.-L.Hagedoorn, U.Hanefeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.84 / 1.85
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.049, 152.049, 109.92, 90, 90, 120
R / Rfree (%)	16.4 / 19.5

The structure of Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Manganese atom in the Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola (pdb code 8oz8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola, PDB code: 8oz8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:24.9 occ:0.80 O A:HOH303 2.1 22.5 0.8 OE1 A:GLN59 2.2 22.3 1.0 NE2 A:HIS53 2.2 23.8 1.0 O4 A:NM2202 2.2 28.3 0.8 NE2 A:HIS94 2.3 26.3 1.0 NE2 A:HIS55 2.4 28.5 1.0 HE22 A:GLN59 2.9 26.7 1.0 CD A:GLN59 3.0 24.7 1.0 CE1 A:HIS53 3.1 27.7 1.0 CD2 A:HIS53 3.2 24.1 1.0 HE1 A:HIS53 3.2 33.2 1.0 C5 A:NM2202 3.2 34.8 0.8 CD2 A:HIS94 3.3 24.8 1.0 NE2 A:GLN59 3.3 22.2 1.0 CE1 A:HIS55 3.3 24.6 1.0 CE1 A:HIS94 3.3 28.9 1.0 CD2 A:HIS55 3.3 28.2 1.0 HD2 A:HIS94 3.4 29.7 1.0 HD2 A:HIS53 3.4 28.9 1.0 HE1 A:HIS55 3.4 29.6 1.0 HD2 A:HIS55 3.5 33.9 1.0 HE1 A:HIS94 3.5 34.7 1.0 O7 A:NM2202 3.5 35.2 0.8 HE21 A:GLN59 4.1 26.7 1.0 HD21 A:LEU61 4.1 30.5 1.0 ND1 A:HIS53 4.2 28.8 1.0 CG A:HIS53 4.3 26.6 1.0 HB3 A:GLN59 4.3 28.4 1.0 CG A:GLN59 4.4 23.5 1.0 HD2 A:PHE88 4.4 31.1 1.0 ND1 A:HIS94 4.4 27.4 1.0 CG A:HIS94 4.4 23.8 1.0 ND1 A:HIS55 4.4 24.2 1.0 CG A:HIS55 4.5 27.3 1.0 C6 A:NM2202 4.6 37.0 0.8 HB2 A:GLN59 4.6 28.4 1.0 HE2 A:PHE88 4.7 35.1 1.0 CD2 A:PHE88 4.7 25.9 1.0 CB A:GLN59 4.7 23.7 1.0 HG2 A:GLN59 4.7 28.2 1.0 HD11 A:LEU61 4.7 34.8 1.0 H32C A:NM2202 4.8 48.0 0.8 HG21 A:THR50 4.8 33.7 1.0 CE2 A:PHE88 4.8 29.3 1.0 H62C A:NM2202 4.9 44.4 0.8 H31C A:NM2202 4.9 48.0 0.8 HD1 A:HIS53 4.9 34.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:18.5 occ:0.80 OE1 B:GLN59 2.1 20.2 1.0 NE2 B:HIS53 2.2 22.1 1.0 O4 B:NM2202 2.2 26.5 0.8 O B:HOH302 2.3 20.4 0.8 NE2 B:HIS55 2.3 21.2 1.0 NE2 B:HIS94 2.3 22.7 1.0 HE22 B:GLN59 2.8 29.2 1.0 CD B:GLN59 2.9 24.1 1.0 CE1 B:HIS53 3.1 24.3 1.0 CD2 B:HIS53 3.1 23.6 1.0 CD2 B:HIS55 3.1 26.4 1.0 HD2 B:HIS55 3.2 31.7 1.0 NE2 B:GLN59 3.2 24.4 1.0 C5 B:NM2202 3.2 35.9 0.8 CD2 B:HIS94 3.2 22.7 1.0 CE1 B:HIS94 3.3 23.2 1.0 HD2 B:HIS53 3.3 28.3 1.0 HE1 B:HIS53 3.3 29.1 1.0 CE1 B:HIS55 3.4 21.2 1.0 HD2 B:HIS94 3.4 27.2 1.0 HE1 B:HIS94 3.5 27.9 1.0 O7 B:NM2202 3.5 29.4 0.8 HE1 B:HIS55 3.6 25.5 1.0 HE21 B:GLN59 4.0 29.2 1.0 HD21 B:LEU61 4.2 26.1 1.0 HB3 B:GLN59 4.2 26.9 1.0 ND1 B:HIS53 4.2 22.8 1.0 CG B:HIS53 4.3 20.6 1.0 CG B:GLN59 4.3 25.2 1.0 HD2 B:PHE88 4.3 30.4 1.0 CG B:HIS55 4.3 22.2 1.0 ND1 B:HIS94 4.4 22.7 1.0 CG B:HIS94 4.4 20.8 1.0 ND1 B:HIS55 4.4 23.3 1.0 HB2 B:GLN59 4.5 26.9 1.0 H32C B:NM2202 4.5 40.4 0.8 CB B:GLN59 4.6 22.4 1.0 C6 B:NM2202 4.6 43.1 0.8 CD2 B:PHE88 4.6 25.3 1.0 HE2 B:PHE88 4.6 29.1 1.0 HG2 B:GLN59 4.6 30.3 1.0 HG21 B:THR50 4.7 27.7 1.0 CE2 B:PHE88 4.8 24.3 1.0 HD11 B:LEU61 4.9 30.3 1.0 HG3 B:GLN59 4.9 30.3 1.0 H61C B:NM2202 5.0 51.7 0.8

Manganese binding site 3 out of 4 in the Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn203 b:20.6 occ:0.80 OE1 C:GLN59 2.1 22.2 1.0 NE2 C:HIS53 2.2 22.6 1.0 NE2 C:HIS94 2.3 18.5 1.0 O C:HOH302 2.3 21.6 0.8 NE2 C:HIS55 2.3 24.8 1.0 O4 C:NM2202 2.3 24.7 0.8 HE22 C:GLN59 2.9 29.6 1.0 CD C:GLN59 3.0 21.9 1.0 CE1 C:HIS53 3.2 23.9 1.0 CE1 C:HIS94 3.2 21.7 1.0 CD2 C:HIS55 3.2 25.2 1.0 CD2 C:HIS53 3.2 24.1 1.0 CD2 C:HIS94 3.2 20.3 1.0 C5 C:NM2202 3.3 31.4 0.8 CE1 C:HIS55 3.3 22.8 1.0 NE2 C:GLN59 3.3 24.6 1.0 HE1 C:HIS53 3.3 28.7 1.0 HD2 C:HIS55 3.3 30.3 1.0 HE1 C:HIS94 3.4 26.0 1.0 HD2 C:HIS94 3.4 24.3 1.0 HD2 C:HIS53 3.4 29.0 1.0 HE1 C:HIS55 3.5 27.3 1.0 O7 C:NM2202 3.5 28.9 0.8 HE21 C:GLN59 4.1 29.6 1.0 HD21 C:LEU61 4.2 28.2 1.0 HB3 C:GLN59 4.2 27.1 1.0 HD2 C:PHE88 4.3 30.0 1.0 ND1 C:HIS53 4.3 21.2 1.0 CG C:GLN59 4.3 22.9 1.0 ND1 C:HIS94 4.3 22.1 1.0 CG C:HIS53 4.3 21.3 1.0 CG C:HIS94 4.4 20.2 1.0 ND1 C:HIS55 4.4 24.1 1.0 CG C:HIS55 4.4 21.2 1.0 H31C C:NM2202 4.5 41.3 0.8 HB2 C:GLN59 4.5 27.1 1.0 CD2 C:PHE88 4.6 25.0 1.0 C6 C:NM2202 4.6 34.9 0.8 CB C:GLN59 4.6 22.6 1.0 H32C C:NM2202 4.7 41.3 0.8 HG2 C:GLN59 4.7 27.4 1.0 HE2 C:PHE88 4.7 26.7 1.0 HG21 C:THR50 4.7 25.8 1.0 HD11 C:LEU61 4.7 30.1 1.0 C3 C:NM2202 4.9 34.4 0.8 CE2 C:PHE88 4.9 22.3 1.0 HG3 C:GLN59 5.0 27.4 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of An Hydroxynitrile Lyase Variant (H96A) From Granulicella Tundricola within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn202 b:29.7 occ:0.88 OE1 D:GLN59 2.1 29.8 1.0 NE2 D:HIS55 2.2 33.2 1.0 O D:HOH301 2.2 26.0 0.8 O7 D:NM2201 2.3 30.5 0.8 NE2 D:HIS53 2.3 29.9 1.0 NE2 D:HIS94 2.4 28.9 1.0 HE22 D:GLN59 2.8 42.1 1.0 CD D:GLN59 3.0 28.9 1.0 CE1 D:HIS53 3.2 30.9 1.0 CD2 D:HIS55 3.2 30.9 1.0 CE1 D:HIS55 3.2 31.3 1.0 NE2 D:GLN59 3.2 35.0 1.0 CD2 D:HIS53 3.2 37.1 1.0 C5 D:NM2201 3.2 32.0 0.8 CE1 D:HIS94 3.3 28.7 1.0 HD2 D:HIS55 3.3 37.0 1.0 HE1 D:HIS53 3.4 37.1 1.0 HE1 D:HIS55 3.4 37.6 1.0 CD2 D:HIS94 3.4 28.2 1.0 HD2 D:HIS53 3.4 44.5 1.0 O4 D:NM2201 3.4 35.2 0.8 HE1 D:HIS94 3.4 34.5 1.0 HD2 D:HIS94 3.5 33.8 1.0 HE21 D:GLN59 4.0 42.1 1.0 HD21 D:LEU61 4.2 37.8 1.0 HB3 D:GLN59 4.3 32.4 1.0 ND1 D:HIS53 4.3 31.4 1.0 HD2 D:PHE88 4.3 40.9 1.0 CG D:GLN59 4.3 29.4 1.0 ND1 D:HIS55 4.3 36.3 1.0 CG D:HIS53 4.3 26.9 1.0 CG D:HIS55 4.4 30.3 1.0 ND1 D:HIS94 4.4 30.8 1.0 CG D:HIS94 4.5 30.4 1.0 HB2 D:GLN59 4.5 32.4 1.0 CB D:GLN59 4.6 27.0 1.0 H32C D:NM2201 4.6 46.4 0.8 C6 D:NM2201 4.6 34.4 0.8 CD2 D:PHE88 4.7 34.1 1.0 HE2 D:PHE88 4.7 39.9 1.0 HG21 D:THR50 4.7 35.7 1.0 H31C D:NM2201 4.7 46.4 0.8 HG2 D:GLN59 4.7 35.2 1.0 HD11 D:LEU61 4.8 32.4 1.0 CE2 D:PHE88 4.9 33.2 1.0 HG3 D:GLN59 4.9 35.2 1.0 C3 D:NM2201 4.9 38.7 0.8

J.Coloma, P.L.Hagedoorn, I.Bento, U.Hanefeld. Can A Hydroxynitrile Lyase Catalyze An Oxidative Cleavage? Acs Catalysis V. 13 11182 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.3C02249