Magnesium in PDB 5xm3: Crystal Structure of Methanol Dehydrogenase From Methylophaga Aminisulfidivorans

All present enzymatic activity of Crystal Structure of Methanol Dehydrogenase From Methylophaga Aminisulfidivorans:
1.1.2.7;

The structure of Crystal Structure of Methanol Dehydrogenase From Methylophaga Aminisulfidivorans, PDB code: 5xm3 was solved by T.P.Cao, J.M.Choi, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.72 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.926, 109.479, 95.554, 90.00, 100.48, 90.00
R / Rfree (%)	15.1 / 18.1

The binding sites of Magnesium atom in the Crystal Structure of Methanol Dehydrogenase From Methylophaga Aminisulfidivorans (pdb code 5xm3). 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 Methanol Dehydrogenase From Methylophaga Aminisulfidivorans, PDB code: 5xm3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Methanol Dehydrogenase From Methylophaga Aminisulfidivorans


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 Methanol Dehydrogenase From Methylophaga Aminisulfidivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:32.9 occ:1.00 O5 A:PQQ701 2.4 21.9 1.0 O7A A:PQQ701 2.5 29.9 1.0 OE2 A:GLU208 2.5 22.6 1.0 OE1 A:GLU208 2.5 14.1 1.0 OD1 A:ASN292 2.6 13.4 1.0 N6 A:PQQ701 2.7 30.5 1.0 CD A:GLU208 2.9 20.3 1.0 C5 A:PQQ701 3.2 29.6 1.0 OD1 A:ASP334 3.2 17.0 1.0 O A:HOH806 3.3 35.2 1.0 C6A A:PQQ701 3.3 31.9 1.0 C7X A:PQQ701 3.4 22.7 1.0 CG A:ASN292 3.4 12.7 1.0 C7 A:PQQ701 3.7 28.6 1.0 ND2 A:ASN292 3.7 14.2 1.0 O A:HOH955 3.9 13.3 1.0 CB A:ALA336 4.0 11.8 1.0 CG A:ASP334 4.1 18.8 1.0 OD2 A:ASP334 4.2 19.8 1.0 CG A:GLU208 4.3 21.4 1.0 CB A:ALA207 4.5 13.8 1.0 O7B A:PQQ701 4.5 19.1 1.0 NE1 A:TRP274 4.5 11.7 1.0 C4 A:PQQ701 4.5 31.2 1.0 NH1 A:ARG362 4.6 14.7 1.0 CZ2 A:TRP274 4.6 18.5 1.0 CB A:ASN292 4.7 10.9 1.0 C9A A:PQQ701 4.7 29.9 1.0 NE1 A:TRP296 4.8 14.9 1.0 CE2 A:TRP274 4.9 10.4 1.0 O A:HOH1066 4.9 15.8 1.0 CZ2 A:TRP296 5.0 17.1 1.0 C8 A:PQQ701 5.0 23.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Methanol Dehydrogenase From Methylophaga Aminisulfidivorans


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 Methanol Dehydrogenase From Methylophaga Aminisulfidivorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:34.9 occ:1.00 O7A C:PQQ701 2.3 35.0 1.0 O5 C:PQQ701 2.4 22.5 1.0 OD1 C:ASN292 2.5 13.6 1.0 OE2 C:GLU208 2.6 13.5 1.0 OE1 C:GLU208 2.6 22.1 1.0 N6 C:PQQ701 2.6 33.1 1.0 CD C:GLU208 2.9 17.1 1.0 OD1 C:ASP334 3.2 18.9 1.0 C5 C:PQQ701 3.2 30.6 1.0 C7X C:PQQ701 3.3 28.1 1.0 CG C:ASN292 3.4 15.1 1.0 C6A C:PQQ701 3.4 33.7 1.0 O C:HOH813 3.4 34.5 1.0 C7 C:PQQ701 3.7 28.7 1.0 ND2 C:ASN292 3.7 13.9 1.0 O C:HOH984 3.7 13.1 1.0 CB C:ALA336 4.0 10.7 1.0 CG C:ASP334 4.1 18.8 1.0 OD2 C:ASP334 4.2 19.6 1.0 O7B C:PQQ701 4.3 17.6 1.0 CB C:ALA207 4.4 12.9 1.0 CG C:GLU208 4.4 15.8 1.0 NE1 C:TRP274 4.5 15.7 1.0 C4 C:PQQ701 4.6 32.4 1.0 NH1 C:ARG362 4.6 13.3 1.0 CZ2 C:TRP274 4.6 15.8 1.0 CB C:ASN292 4.6 14.9 1.0 C9A C:PQQ701 4.7 30.5 1.0 CE2 C:TRP274 4.9 16.5 1.0 NE1 C:TRP296 4.9 15.0 1.0 O C:HOH1003 4.9 16.3 1.0 C8 C:PQQ701 5.0 23.6 1.0

T.P.Cao, J.M.Choi, S.W.Kim, S.H.Lee. The Crystal Structure of Methanol Dehydrogenase, A Quinoprotein From the Marine Methylotrophic Bacterium Methylophaga Aminisulfidivorans Mpt J. Microbiol. V. 56 246 2018.
ISSN: ESSN 1976-3794
PubMed: 29492864
DOI: 10.1007/S12275-018-7483-Y