Magnesium in PDB 3a28: Crystal Structure of L-2,3-Butanediol Dehydrogenase

The structure of Crystal Structure of L-2,3-Butanediol Dehydrogenase, PDB code: 3a28 was solved by M.Otagiri, G.Kurisu, S.Ui, M.Kusunoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.800, 69.200, 127.400, 96.10, 100.20, 109.60
R / Rfree (%)	19.3 / 24

The binding sites of Magnesium atom in the Crystal Structure of L-2,3-Butanediol Dehydrogenase (pdb code 3a28). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of L-2,3-Butanediol Dehydrogenase, PDB code: 3a28:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


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 L-2,3-Butanediol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg804 b:37.0 occ:1.00 O B:HOH1094 2.9 29.7 1.0 O C:HOH655 3.0 26.5 1.0 CA B:PHE235 3.9 16.3 1.0 CA C:PHE235 3.9 16.6 1.0 OD1 C:ASN240 4.0 22.4 1.0 CB B:PHE235 4.0 15.2 1.0 CB C:PHE235 4.0 15.2 1.0 OD1 B:ASN240 4.0 22.2 1.0 O B:HOH1418 4.0 33.9 1.0 CD1 B:PHE235 4.1 14.9 1.0 CD1 C:PHE235 4.1 16.4 1.0 N C:PHE235 4.4 15.0 1.0 OG B:SER238 4.4 19.1 1.0 N B:PHE235 4.4 16.3 1.0 OG C:SER238 4.5 17.6 1.0 CG B:PHE235 4.5 16.1 1.0 CG C:PHE235 4.6 17.4 1.0 CB B:ASN240 4.7 17.4 1.0 CB C:ASN240 4.8 15.8 1.0 CG C:ASN240 4.8 17.5 1.0 CG B:ASN240 4.8 20.0 1.0 C C:SER234 5.0 14.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


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 L-2,3-Butanediol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg805 b:41.1 occ:1.00 O A:HOH668 2.8 30.7 1.0 O D:HOH790 2.9 26.6 1.0 CB A:PHE235 3.8 17.9 1.0 CB D:PHE235 3.8 19.4 1.0 CA D:PHE235 3.8 19.1 1.0 CA A:PHE235 3.9 18.3 1.0 CD1 D:PHE235 4.0 21.4 1.0 OD1 D:ASN240 4.0 23.8 1.0 OD1 A:ASN240 4.1 23.2 1.0 CD1 A:PHE235 4.1 17.9 1.0 OG D:SER238 4.3 24.9 1.0 N A:PHE235 4.4 19.3 1.0 N D:PHE235 4.4 19.6 1.0 CG D:PHE235 4.4 19.9 1.0 O A:HOH1398 4.4 38.1 1.0 OG A:SER238 4.4 26.8 1.0 CG A:PHE235 4.4 19.3 1.0 CB D:ASN240 4.7 21.2 1.0 CG D:ASN240 4.8 22.5 1.0 CB A:ASN240 4.8 22.1 1.0 CG A:ASN240 4.9 23.2 1.0 C A:SER234 5.0 20.2 1.0 C D:SER234 5.0 20.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of L-2,3-Butanediol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1288 b:44.3 occ:1.00 O E:HOH1155 3.1 46.4 1.0 CA E:PHE235 3.9 29.9 1.0 OD1 H:ASN240 3.9 33.2 1.0 CB H:PHE235 3.9 30.3 1.0 CB E:PHE235 3.9 31.5 1.0 CA H:PHE235 4.0 30.1 1.0 CD1 H:PHE235 4.1 30.0 1.0 OD1 E:ASN240 4.2 29.2 1.0 CD1 E:PHE235 4.3 31.7 1.0 OG H:SER238 4.3 39.1 1.0 OG E:SER238 4.3 34.8 1.0 N E:PHE235 4.3 30.7 1.0 CG H:PHE235 4.5 30.2 1.0 N H:PHE235 4.6 30.9 1.0 CG E:PHE235 4.6 31.9 1.0 CB H:ASN240 4.6 35.1 1.0 CG H:ASN240 4.7 34.4 1.0 CB E:ASN240 4.9 27.4 1.0 C E:SER234 4.9 30.6 1.0 OG E:SER234 5.0 35.5 1.0 CG E:ASN240 5.0 28.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of L-2,3-Butanediol Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg948 b:34.0 occ:1.00 O F:HOH906 3.0 26.7 1.0 O G:HOH1023 3.2 29.6 1.0 OD1 F:ASN240 3.7 19.6 1.0 CB F:PHE235 3.7 15.5 1.0 CA F:PHE235 3.8 15.6 1.0 CB G:PHE235 3.8 15.4 1.0 CA G:PHE235 3.9 16.6 1.0 CD1 F:PHE235 3.9 15.9 1.0 CD1 G:PHE235 4.0 15.6 1.0 OD1 G:ASN240 4.2 17.1 1.0 CG F:PHE235 4.3 16.8 1.0 N F:PHE235 4.3 16.1 1.0 OG F:SER238 4.4 18.5 1.0 CG G:PHE235 4.4 16.6 1.0 N G:PHE235 4.4 14.8 1.0 O F:HOH1113 4.5 41.6 1.0 OG G:SER238 4.5 17.1 1.0 CB F:ASN240 4.6 16.0 1.0 CG F:ASN240 4.6 18.3 1.0 CB G:ASN240 4.9 14.5 1.0 C G:SER234 5.0 15.9 1.0 CE1 F:PHE235 5.0 16.6 1.0 C F:SER234 5.0 16.7 1.0 CG G:ASN240 5.0 17.0 1.0

M.Otagiri, S.Ui, Y.Takusagawa, T.Ohtsuki, G.Kurisu, M.Kusunoki. Structural Basis For Chiral Substrate Recognition By Two 2,3-Butanediol Dehydrogenases Febs Lett. V. 584 219 2010.
ISSN: ISSN 0014-5793
PubMed: 19941855
DOI: 10.1016/J.FEBSLET.2009.11.068