Magnesium in PDB 6jdk: Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans

The structure of Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans, PDB code: 6jdk was solved by J.-S.Kim, T.D.Nguyen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.831, 55.049, 118.099, 90.00, 95.25, 90.00
R / Rfree (%)	20.7 / 27

The binding sites of Magnesium atom in the Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans (pdb code 6jdk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans, PDB code: 6jdk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:22.9 occ:1.00 OE1 A:GLU126 2.0 52.7 1.0 O B:HOH730 2.2 45.8 1.0 OD1 A:ASP129 2.3 53.3 1.0 OE1 B:GLN480 2.3 32.3 1.0 O A:GLU126 2.4 46.1 1.0 OE2 A:GLU126 2.5 53.6 1.0 CD A:GLU126 2.5 49.4 1.0 OE2 B:GLU483 2.9 78.3 1.0 CD B:GLN480 3.0 31.7 1.0 NE2 B:GLN480 3.1 26.1 1.0 CG A:ASP129 3.2 53.6 1.0 OD2 A:ASP129 3.5 58.8 1.0 C A:GLU126 3.5 26.9 1.0 CD B:GLU483 3.7 68.2 1.0 CG A:GLU126 4.0 26.0 1.0 CA A:GLU126 4.2 33.0 1.0 O A:HOH704 4.4 45.8 1.0 OE1 B:GLU483 4.4 82.6 1.0 CG B:GLU483 4.4 48.2 1.0 CB A:GLU126 4.5 23.5 1.0 CG B:GLN480 4.5 23.3 1.0 N A:ALA127 4.5 26.3 1.0 CB A:ASP129 4.6 37.7 1.0 N A:ASP129 4.6 23.1 1.0 CD A:ARG474 4.6 25.5 1.0 C A:ALA127 4.7 37.3 1.0 NE A:ARG474 4.7 24.2 1.0 CA A:ALA127 4.8 33.9 1.0 CB B:GLU483 4.9 35.0 1.0 CA A:ASP129 4.9 23.9 1.0 O A:ALA127 4.9 39.9 1.0 CB B:GLN480 5.0 34.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:26.8 occ:1.00 OD1 B:ASP129 1.9 33.9 1.0 OE2 B:GLU126 2.0 45.1 1.0 OE1 A:GLN480 2.0 32.5 1.0 O B:HOH749 2.2 45.8 1.0 OE1 A:GLU483 2.5 41.4 1.0 O B:GLU126 2.6 46.7 1.0 CG B:ASP129 2.9 37.4 1.0 CD A:GLN480 3.1 38.2 1.0 OD2 B:ASP129 3.1 52.9 1.0 CD B:GLU126 3.2 41.1 1.0 CD A:GLU483 3.5 41.8 1.0 NE2 A:GLN480 3.5 39.4 1.0 C B:GLU126 3.7 36.4 1.0 OE2 A:GLU483 3.7 49.7 1.0 OE1 B:GLU126 3.8 61.6 1.0 CD B:ARG474 3.9 32.3 1.0 CA B:GLU126 4.3 35.3 1.0 CB B:ASP129 4.3 34.6 1.0 CG B:GLU126 4.4 35.4 1.0 CG B:ARG474 4.4 37.0 1.0 CG A:GLN480 4.5 26.6 1.0 CB B:GLU126 4.5 30.9 1.0 N B:ASP129 4.6 37.8 1.0 CA B:ASP129 4.7 39.9 1.0 N B:ALA127 4.8 33.5 1.0 CB A:GLN480 4.8 32.0 1.0 CG A:GLU483 4.8 30.5 1.0 O B:ALA127 4.9 37.8 1.0 CA A:GLN480 5.0 39.2 1.0 C B:ALA127 5.0 43.2 1.0

T.D.Nguyen, G.E.Choi, D.H.Gu, P.W.Seo, J.W.Kim, J.B.Park, J.S.Kim. Structural Basis For the Selective Addition of An Oxygen Atom to Cyclic Ketones By Baeyer-Villiger Monooxygenase From Parvibaculum Lavamentivorans. Biochem. Biophys. Res. V. 512 564 2019COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30914200
DOI: 10.1016/J.BBRC.2019.03.114