Magnesium in PDB 3a16: Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime

All present enzymatic activity of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime:
4.99.1.5;

The structure of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime, PDB code: 3a16 was solved by H.Sawai, H.Sugimoto, Y.Kato, Y.Asano, Y.Shiro, S.Aono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.710, 147.670, 78.910, 90.00, 90.01, 90.00
R / Rfree (%)	24.8 / 27.4

The structure of Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime (pdb code 3a16). 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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime, PDB code: 3a16:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime


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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg356 b:8.8 occ:1.00 O B:HOH416 2.0 14.9 1.0 O B:HOH472 2.1 13.2 1.0 O B:HOH423 2.1 15.1 1.0 O B:HOH451 2.1 15.6 1.0 O B:HOH480 2.1 16.2 1.0 O B:HOH364 2.4 13.7 1.0 OD2 B:ASP185 3.7 10.4 1.0 OD1 B:ASP326 4.0 11.0 1.0 O B:HOH467 4.1 13.1 1.0 OD2 B:ASP212 4.1 8.7 1.0 O B:HOH399 4.2 7.7 1.0 OD1 B:ASP185 4.3 10.6 1.0 ND2 B:ASN213 4.3 5.3 1.0 CG B:ASP185 4.4 9.4 1.0 OD1 B:ASP212 4.7 9.8 1.0 CG B:ASP212 4.7 7.2 1.0 OD1 B:ASN213 4.8 8.0 1.0 CG B:ASN213 5.0 5.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime


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 Aldoxime Dehydratase (Oxdre) in Complex with Propionaldoxime within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg356 b:5.5 occ:1.00 O D:HOH452 2.1 13.2 1.0 O D:HOH471 2.1 16.0 1.0 O D:HOH379 2.1 6.2 1.0 O A:HOH532 2.1 17.4 1.0 O D:HOH426 2.2 10.9 1.0 O A:HOH430 2.2 10.0 1.0 OD2 D:ASP185 3.8 10.3 1.0 OD1 D:ASP326 4.0 10.3 1.0 O A:HOH447 4.0 11.2 1.0 O D:HOH428 4.0 15.2 1.0 O D:HOH365 4.1 5.1 1.0 OD2 D:ASP212 4.1 2.0 0.4 OD1 A:ASP329 4.1 9.3 1.0 O A:HOH429 4.2 9.9 1.0 ND2 D:ASN213 4.2 6.5 1.0 OE1 A:GLN40 4.3 8.0 1.0 OD1 D:ASP212 4.3 6.1 0.4 OD1 D:ASP185 4.4 12.4 1.0 OD1 D:ASP212 4.5 9.6 0.6 O A:HOH495 4.5 16.6 1.0 CG D:ASP185 4.5 10.0 1.0 CG D:ASP212 4.6 4.7 0.4 NE2 A:GLN40 4.8 7.8 1.0 OD1 D:ASN213 4.9 7.9 1.0 OD2 A:ASP329 4.9 8.0 1.0 CG D:ASP326 5.0 9.5 1.0 CG A:ASP329 5.0 7.1 1.0 CD A:GLN40 5.0 7.9 1.0

H.Sawai, H.Sugimoto, Y.Kato, Y.Asano, Y.Shiro, S.Aono. X-Ray Crystal Structure of Michaelis Complex of Aldoxime Dehydratase J.Biol.Chem. V. 284 32089 2009.
ISSN: ISSN 0021-9258
PubMed: 19740758
DOI: 10.1074/JBC.M109.018762