Manganese in PDB 4bif: Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria

The structure of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria, PDB code: 4bif was solved by I.Hajnal, A.Lyskowski, U.Hanefeld, K.Gruber, H.Schwab, K.Steiner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.722 / 2.46
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	126.310, 254.780, 82.470, 90.00, 90.00, 90.00
R / Rfree (%)	17.38 / 23.29

The binding sites of Manganese atom in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria (pdb code 4bif). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria, PDB code: 4bif:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1132 b:28.1 occ:1.00 NE2 A:HIS53 2.1 28.1 1.0 OE1 A:GLN59 2.1 24.4 1.0 NE2 A:HIS96 2.2 28.0 1.0 NE2 A:HIS55 2.3 32.9 1.0 NE2 A:HIS94 2.5 30.1 1.0 CE1 A:HIS53 2.9 27.9 1.0 CD A:GLN59 3.0 29.0 1.0 CD2 A:HIS55 3.1 31.4 1.0 CE1 A:HIS96 3.1 28.8 1.0 CD2 A:HIS53 3.2 28.7 1.0 CD2 A:HIS96 3.3 26.9 1.0 O A:HOH2047 3.3 32.4 1.0 NE2 A:GLN59 3.3 27.4 1.0 CE1 A:HIS94 3.3 28.2 1.0 CE1 A:HIS55 3.4 31.1 1.0 CD2 A:HIS94 3.5 29.7 1.0 ND1 A:HIS53 4.1 28.1 1.0 ND1 A:HIS96 4.2 26.8 1.0 CG A:HIS53 4.3 29.9 1.0 CG A:GLN59 4.3 27.0 1.0 CG A:HIS55 4.3 31.4 1.0 CG A:HIS96 4.4 31.2 1.0 ND1 A:HIS55 4.4 24.8 1.0 ND1 A:HIS94 4.4 32.6 1.0 CB A:GLN59 4.5 29.5 1.0 CG A:HIS94 4.6 32.8 1.0 CD2 A:PHE88 4.7 29.9 1.0 CE2 A:PHE88 4.8 31.1 1.0

Manganese binding site 2 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1132 b:27.6 occ:1.00 OE1 B:GLN59 1.6 30.4 1.0 NE2 B:HIS53 2.3 29.5 1.0 NE2 B:HIS94 2.4 27.1 1.0 NE2 B:HIS96 2.4 28.8 1.0 O B:HOH2057 2.5 25.1 1.0 NE2 B:HIS55 2.5 30.2 1.0 CD B:GLN59 2.6 28.5 1.0 CD2 B:HIS53 3.1 31.0 1.0 CD2 B:HIS55 3.2 32.7 1.0 CE1 B:HIS94 3.3 29.9 1.0 CD2 B:HIS96 3.3 29.1 1.0 CE1 B:HIS53 3.3 26.7 1.0 NE2 B:GLN59 3.4 26.5 1.0 CD2 B:HIS94 3.4 30.7 1.0 CE1 B:HIS96 3.5 27.3 1.0 CE1 B:HIS55 3.6 34.1 1.0 CG B:GLN59 3.7 28.6 1.0 CG B:HIS53 4.3 28.3 1.0 ND1 B:HIS53 4.3 32.0 1.0 ND1 B:HIS94 4.4 29.1 1.0 CG B:HIS55 4.5 33.3 1.0 CG B:HIS96 4.5 31.3 1.0 CG B:HIS94 4.5 29.9 1.0 ND1 B:HIS96 4.5 31.4 1.0 ND1 B:HIS55 4.6 32.6 1.0 CD2 B:PHE88 4.6 28.9 1.0 CE2 B:PHE88 4.8 28.5 1.0 CB B:GLN59 4.9 31.1 1.0

Manganese binding site 3 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1132 b:25.2 occ:1.00 NE2 C:HIS53 2.1 22.8 1.0 OE1 C:GLN59 2.2 25.6 1.0 NE2 C:HIS55 2.2 25.4 1.0 NE2 C:HIS94 2.3 19.8 1.0 NE2 C:HIS96 2.4 22.1 1.0 O C:HOH2052 2.6 19.4 1.0 CE1 C:HIS53 3.0 21.9 1.0 CE1 C:HIS94 3.1 22.6 1.0 CD2 C:HIS55 3.1 24.6 1.0 CD C:GLN59 3.1 22.2 1.0 CD2 C:HIS53 3.1 18.8 1.0 CE1 C:HIS55 3.2 24.9 1.0 CD2 C:HIS96 3.3 19.0 1.0 CE1 C:HIS96 3.4 22.4 1.0 CD2 C:HIS94 3.4 20.5 1.0 NE2 C:GLN59 3.6 25.1 1.0 ND1 C:HIS53 4.1 25.6 1.0 ND1 C:HIS94 4.2 23.5 1.0 CG C:HIS53 4.2 22.8 1.0 CG C:HIS55 4.3 25.8 1.0 ND1 C:HIS55 4.3 25.7 1.0 CG C:GLN59 4.3 23.5 1.0 CG C:HIS94 4.4 19.7 1.0 ND1 C:HIS96 4.4 23.9 1.0 CG C:HIS96 4.5 19.6 1.0 CD2 C:PHE88 4.6 23.6 1.0 CB C:GLN59 4.6 25.0 1.0 CE2 C:PHE88 4.7 24.0 1.0

Manganese binding site 4 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1132 b:25.5 occ:1.00 OE1 D:GLN59 1.8 29.4 1.0 NE2 D:HIS53 2.2 31.2 1.0 NE2 D:HIS96 2.3 28.2 1.0 NE2 D:HIS94 2.3 32.5 1.0 NE2 D:HIS55 2.4 27.9 1.0 O D:HOH2049 2.5 29.0 1.0 CD D:GLN59 3.0 28.4 1.0 CE1 D:HIS53 3.0 33.3 1.0 CD2 D:HIS96 3.1 27.2 1.0 CE1 D:HIS94 3.2 32.2 1.0 CD2 D:HIS53 3.2 29.0 1.0 CD2 D:HIS55 3.3 28.6 1.0 CD2 D:HIS94 3.3 30.3 1.0 CE1 D:HIS96 3.3 28.0 1.0 CE1 D:HIS55 3.4 23.9 1.0 NE2 D:GLN59 3.6 26.3 1.0 ND1 D:HIS53 4.2 31.6 1.0 CG D:GLN59 4.2 24.2 1.0 ND1 D:HIS94 4.3 29.9 1.0 O D:HOH2023 4.3 33.4 1.0 CG D:HIS53 4.3 29.9 1.0 CG D:HIS96 4.3 26.2 1.0 ND1 D:HIS96 4.4 28.4 1.0 CG D:HIS94 4.4 28.7 1.0 CG D:HIS55 4.5 27.8 1.0 ND1 D:HIS55 4.5 29.0 1.0 CB D:GLN59 4.6 22.7 1.0 CD2 D:PHE88 4.6 33.1 1.0 CE2 D:PHE88 4.7 28.8 1.0 O D:HOH2024 4.9 20.3 1.0

Manganese binding site 5 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1132 b:23.8 occ:1.00 OE1 E:GLN59 2.0 23.1 1.0 NE2 E:HIS94 2.2 22.8 1.0 NE2 E:HIS55 2.3 20.5 1.0 NE2 E:HIS53 2.3 23.2 1.0 NE2 E:HIS96 2.3 19.3 1.0 O E:HOH2061 2.5 21.2 1.0 CD E:GLN59 2.9 20.7 1.0 CE1 E:HIS94 3.1 22.5 1.0 CD2 E:HIS55 3.1 20.0 1.0 CD2 E:HIS53 3.2 24.1 1.0 CE1 E:HIS96 3.2 18.6 1.0 CD2 E:HIS94 3.2 23.8 1.0 CE1 E:HIS53 3.3 22.6 1.0 CE1 E:HIS55 3.3 21.0 1.0 CD2 E:HIS96 3.3 19.9 1.0 NE2 E:GLN59 3.4 17.6 1.0 ND1 E:HIS94 4.2 19.6 1.0 CG E:GLN59 4.2 21.9 1.0 CG E:HIS53 4.3 23.5 1.0 ND1 E:HIS53 4.3 24.9 1.0 CG E:HIS55 4.3 20.5 1.0 CG E:HIS94 4.3 21.6 1.0 ND1 E:HIS55 4.4 21.3 1.0 ND1 E:HIS96 4.4 22.0 1.0 CG E:HIS96 4.4 19.0 1.0 CB E:GLN59 4.5 20.7 1.0 CD2 E:PHE88 4.7 24.0 1.0 O E:HOH2033 4.8 34.2 1.0 CE2 E:PHE88 4.9 25.6 1.0

Manganese binding site 6 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1132 b:18.1 occ:1.00 OE1 F:GLN59 2.1 27.7 1.0 O F:HOH2062 2.2 19.6 1.0 NE2 F:HIS53 2.2 25.3 1.0 NE2 F:HIS94 2.3 19.4 1.0 NE2 F:HIS55 2.3 20.8 1.0 NE2 F:HIS96 2.4 18.9 1.0 CE1 F:HIS94 3.0 23.3 1.0 CD F:GLN59 3.1 21.6 1.0 CD2 F:HIS53 3.1 24.2 1.0 CD2 F:HIS55 3.2 20.2 1.0 CE1 F:HIS53 3.2 21.1 1.0 CD2 F:HIS96 3.2 19.2 1.0 CE1 F:HIS55 3.3 21.3 1.0 CD2 F:HIS94 3.4 18.3 1.0 CE1 F:HIS96 3.4 22.6 1.0 NE2 F:GLN59 3.6 22.1 1.0 ND1 F:HIS94 4.1 21.3 1.0 CG F:GLN59 4.3 20.9 1.0 CG F:HIS53 4.3 23.5 1.0 ND1 F:HIS53 4.3 20.9 1.0 CG F:HIS94 4.4 23.3 1.0 CG F:HIS55 4.4 19.9 1.0 ND1 F:HIS55 4.4 21.2 1.0 CG F:HIS96 4.4 18.4 1.0 ND1 F:HIS96 4.5 19.2 1.0 CB F:GLN59 4.7 26.6 1.0 CD2 F:PHE88 4.7 19.0 1.0 O F:HOH2033 4.9 14.8 1.0 CE2 F:PHE88 5.0 25.0 1.0

Manganese binding site 7 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn1132 b:34.3 occ:1.00 OE1 G:GLN59 2.1 26.7 1.0 NE2 G:HIS55 2.2 34.1 1.0 NE2 G:HIS53 2.2 30.5 1.0 NE2 G:HIS94 2.3 30.6 1.0 O G:HOH2031 2.4 27.8 1.0 NE2 G:HIS96 2.4 32.8 1.0 CD G:GLN59 3.0 32.0 1.0 CD2 G:HIS55 3.0 32.8 1.0 CE1 G:HIS94 3.1 33.4 1.0 CD2 G:HIS53 3.1 34.6 1.0 CE1 G:HIS53 3.3 28.3 1.0 CE1 G:HIS55 3.3 35.7 1.0 CD2 G:HIS96 3.3 27.1 1.0 CD2 G:HIS94 3.4 29.0 1.0 CE1 G:HIS96 3.5 30.7 1.0 NE2 G:GLN59 3.5 32.5 1.0 CG G:HIS55 4.2 32.1 1.0 CG G:GLN59 4.3 30.3 1.0 ND1 G:HIS94 4.3 33.7 1.0 CG G:HIS53 4.3 35.3 1.0 ND1 G:HIS55 4.3 34.3 1.0 ND1 G:HIS53 4.3 29.2 1.0 CB G:GLN59 4.4 32.6 1.0 CG G:HIS94 4.5 29.1 1.0 CG G:HIS96 4.5 31.1 1.0 ND1 G:HIS96 4.5 29.0 1.0 O G:HOH2017 4.6 34.5 1.0 CD2 G:PHE88 4.7 30.5 1.0 O G:HOH2016 4.9 30.7 1.0 CE2 G:PHE88 5.0 31.2 1.0

Manganese binding site 8 out of 8 in the Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Biochemical and Structural Characterisation of A Novel Manganese-Dependent Hydroxynitrile Lyase From Bacteria within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn1132 b:28.9 occ:1.00 OE1 H:GLN59 2.1 30.5 1.0 NE2 H:HIS53 2.2 30.1 1.0 NE2 H:HIS55 2.4 32.3 1.0 NE2 H:HIS96 2.5 32.0 1.0 O H:HOH2040 2.5 30.6 1.0 NE2 H:HIS94 2.6 34.4 1.0 CE1 H:HIS53 2.9 30.3 1.0 CD H:GLN59 3.0 34.2 1.0 CD2 H:HIS53 3.3 32.6 1.0 CD2 H:HIS55 3.3 30.3 1.0 CD2 H:HIS96 3.4 33.3 1.0 CE1 H:HIS55 3.4 36.3 1.0 CE1 H:HIS94 3.4 36.6 1.0 CE1 H:HIS96 3.5 30.8 1.0 NE2 H:GLN59 3.5 29.6 1.0 CD2 H:HIS94 3.5 32.7 1.0 ND1 H:HIS53 4.1 25.2 1.0 CG H:HIS53 4.3 32.0 1.0 CG H:GLN59 4.3 32.4 1.0 CG H:HIS55 4.5 36.0 1.0 O H:HOH2041 4.5 43.0 1.0 ND1 H:HIS55 4.5 31.0 1.0 ND1 H:HIS94 4.5 37.8 1.0 CG H:HIS96 4.6 29.6 1.0 ND1 H:HIS96 4.6 30.3 1.0 CB H:GLN59 4.6 32.0 1.0 CG H:HIS94 4.6 33.2 1.0 CD2 H:PHE88 4.7 31.5 1.0 CE2 H:PHE88 4.8 30.4 1.0

I.Hajnal, A.Lyskowski, U.Hanefeld, K.Gruber, H.Schwab, K.Steiner. Biochemical and Structural Characterisation of A Novel Bacterial Manganese-Dependent Hydroxynitrile Lyase. Febs J. V. 280 5815 2013.
ISSN: ISSN 1742-464X
PubMed: 23981508
DOI: 10.1111/FEBS.12501