Magnesium in PDB 5ikz: Glycerol Bound Structure of OBC1, A Bifunctional Enzyme For Quorum Sensing-Dependent Oxalogenesis

The structure of Glycerol Bound Structure of OBC1, A Bifunctional Enzyme For Quorum Sensing-Dependent Oxalogenesis, PDB code: 5ikz was solved by J.Oh, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.35 / 2.80
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	229.970, 229.970, 253.763, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22.7

The binding sites of Magnesium atom in the Glycerol Bound Structure of OBC1, A Bifunctional Enzyme For Quorum Sensing-Dependent Oxalogenesis (pdb code 5ikz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Glycerol Bound Structure of OBC1, A Bifunctional Enzyme For Quorum Sensing-Dependent Oxalogenesis, PDB code: 5ikz:

Magnesium binding site 1 out of 1 in the Glycerol Bound Structure of OBC1, A Bifunctional Enzyme For Quorum Sensing-Dependent Oxalogenesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glycerol Bound Structure of OBC1, A Bifunctional Enzyme For Quorum Sensing-Dependent Oxalogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:77.3 occ:1.00 O A:HOH1423 2.2 47.8 1.0 OE2 A:GLU477 2.4 51.1 1.0 NE2 A:HIS225 2.7 37.9 1.0 O A:HOH1351 2.8 43.8 1.0 NE2 A:HIS227 2.9 48.9 1.0 O A:HOH1487 3.2 61.9 1.0 CD2 A:HIS225 3.4 34.7 1.0 CD A:GLU477 3.4 50.1 1.0 OE2 A:GLU350 3.4 57.8 1.0 OE1 A:GLU477 3.6 40.0 1.0 CE1 A:HIS227 3.6 39.6 1.0 NH1 A:ARG473 3.8 34.8 1.0 CE1 A:HIS225 3.8 42.5 1.0 CD2 A:HIS227 4.0 52.6 1.0 NH2 A:ARG473 4.1 44.4 1.0 O A:HOH1402 4.1 64.0 1.0 CD A:GLU350 4.4 50.0 1.0 CZ A:ARG473 4.4 43.0 1.0 OE1 A:GLU350 4.5 42.9 1.0 O A:HOH1441 4.5 75.2 1.0 OG A:SER279 4.6 35.5 1.0 CG A:HIS225 4.6 42.6 1.0 CG A:GLU477 4.8 56.8 1.0 ND1 A:HIS225 4.8 45.5 1.0 ND1 A:HIS227 4.9 31.3 1.0 CB A:SER279 5.0 30.3 1.0

J.Oh, I.Hwang, S.Rhee. Structural Insights Into An Oxalate-Producing Serine Hydrolase with An Unusual Oxyanion Hole and Additional Lyase Activity J.Biol.Chem. V. 291 15185 2016.
ISSN: ESSN 1083-351X
PubMed: 27226606
DOI: 10.1074/JBC.M116.727180