Magnesium in PDB 6qkb: Crystal Structure of the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans

The structure of Crystal Structure of the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans, PDB code: 6qkb was solved by J.Zarzycki, L.Schada Von Borzyskowski, A.Gilardet, T.J.Erb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.03 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.598, 75.247, 157.310, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17.7

The binding sites of Magnesium atom in the Crystal Structure of the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans (pdb code 6qkb). 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 the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans, PDB code: 6qkb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans


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 the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:29.8 occ:0.73 O A:HOH513 2.1 15.9 1.0 O A:HOH792 2.1 24.4 1.0 O B:HOH502 2.1 21.6 1.0 O A:HOH608 2.3 30.4 1.0 OD1 A:ASP357 2.3 16.5 1.0 NE2 A:HIS355 2.4 13.4 1.0 CG A:ASP357 3.0 16.5 1.0 CD2 A:HIS355 3.2 16.5 1.0 OD2 A:ASP357 3.3 14.2 1.0 CE1 A:HIS355 3.4 16.8 1.0 OD1 B:ASP331 3.8 30.3 1.0 O A:HOH568 4.0 31.1 1.0 OG A:SER257 4.0 12.9 1.0 O A:HOH599 4.1 16.1 1.0 CB A:ASP357 4.1 16.8 1.0 O A:HOH818 4.2 21.6 1.0 CG A:HIS355 4.5 14.3 1.0 O2P A:PLP401 4.5 18.3 0.8 ND1 A:HIS355 4.5 13.2 1.0 CG B:ASP331 4.8 23.9 1.0 N A:ASP357 4.8 11.5 1.0 O B:HOH501 4.8 20.2 1.0 O A:HOH588 4.9 15.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans


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 the Beta-Hydroxyaspartate Aldolase of Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:34.8 occ:0.74 O A:HOH507 2.1 26.4 1.0 O B:HOH836 2.1 32.0 1.0 O B:HOH508 2.1 18.7 1.0 NE2 B:HIS355 2.3 12.8 1.0 O B:HOH719 2.3 54.8 1.0 OD1 B:ASP357 2.4 14.5 1.0 CG B:ASP357 3.1 13.1 1.0 CD2 B:HIS355 3.1 11.2 1.0 CE1 B:HIS355 3.3 14.6 1.0 OD2 B:ASP357 3.5 15.2 1.0 O B:HOH590 3.9 15.8 1.0 OD2 A:ASP331 3.9 25.9 1.0 OG B:SER257 4.0 15.3 1.0 O B:HOH845 4.1 25.1 1.0 O B:HOH622 4.1 37.6 1.0 O B:HOH503 4.2 34.9 1.0 CB B:ASP357 4.3 14.0 1.0 CG B:HIS355 4.3 13.3 1.0 ND1 B:HIS355 4.4 12.3 1.0 O2P B:PLP401 4.5 22.7 0.7 O B:HOH601 4.7 13.8 1.0 CG A:ASP331 4.8 27.0 1.0 N B:ASP357 4.9 11.5 1.0 CE1 B:HIS198 4.9 15.3 1.0 O A:HOH503 5.0 20.6 1.0 OD1 A:ASP331 5.0 28.9 1.0

L.Schada Von Borzyskowski, F.Severi, K.Kruger, L.Hermann, A.Gilardet, F.Sippel, B.Pommerenke, P.Claus, N.S.Cortina, T.Glatter, S.Zauner, J.Zarzycki, B.M.Fuchs, E.Bremer, U.G.Maier, R.I.Amann, T.J.Erb. Marine Proteobacteria Metabolize Glycolate Via the Beta-Hydroxyaspartate Cycle. Nature V. 575 500 2019.
ISSN: ESSN 1476-4687
PubMed: 31723261
DOI: 10.1038/S41586-019-1748-4