Magnesium in PDB 8adq: Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde

The structure of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde, PDB code: 8adq was solved by I.Justo, S.R.Marsden, U.Hanefeld, I.Bento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.90 / 1.60
Space group	P 42 3 2
Cell size a, b, c (Å), α, β, γ (°)	115.793, 115.793, 115.793, 90, 90, 90
R / Rfree (%)	16.8 / 20.1

The structure of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde also contains other interesting chemical elements:

Bromine	(Br)	3 atoms
Potassium	(K)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde (pdb code 8adq). 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 Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde, PDB code: 8adq:

Magnesium binding site 1 out of 1 in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde


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 Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 in Complex with Hydroxypyruvate and D- Glyceraldehyde within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg309 b:27.0 occ:1.00 O1 A:3PY301 2.0 29.8 1.0 OE1 A:GLU145 2.0 27.8 1.0 O A:HOH456 2.1 28.6 1.0 OD2 A:ASP171 2.1 31.9 1.0 O3 A:3PY301 2.2 29.0 1.0 C1 A:3PY301 2.8 33.5 1.0 C2 A:3PY301 2.8 30.9 1.0 HB2 A:ASP171 3.0 36.5 1.0 CD A:GLU145 3.1 31.3 1.0 CG A:ASP171 3.1 29.4 1.0 HH12 A:ARG69 3.3 34.1 1.0 OE2 A:GLU145 3.5 29.9 1.0 CB A:ASP171 3.5 30.4 1.0 HE2 A:MET93 3.6 38.7 1.0 HA3 A:GLY168 3.8 37.8 1.0 H A:ASP171 3.9 35.9 1.0 O1 A:3GR303 4.0 40.5 0.9 HE1 A:MET143 4.0 36.5 1.0 HE2 A:MET143 4.0 36.5 1.0 O2 A:3PY301 4.0 33.4 1.0 NH1 A:ARG69 4.0 28.5 1.0 HB3 A:GLU145 4.1 40.8 1.0 HB3 A:ASP171 4.1 36.5 1.0 OD1 A:ASP171 4.2 28.5 1.0 C3 A:3PY301 4.3 34.3 1.0 HH11 A:ARG69 4.3 34.1 1.0 OE1 A:GLN43 4.4 28.3 1.0 CG A:GLU145 4.4 31.0 1.0 HD2 A:HIS44 4.4 34.6 1.0 HH22 A:ARG69 4.4 35.6 1.0 CE A:MET143 4.5 30.4 1.0 CE A:MET93 4.5 32.2 1.0 HE22 A:GLN43 4.5 33.3 1.0 N A:ASP171 4.6 29.9 1.0 NE2 A:HIS44 4.6 29.2 1.0 HG2 A:GLU145 4.6 37.2 1.0 CA A:GLY168 4.6 31.5 1.0 C1 A:3GR303 4.7 43.8 0.9 H1 A:3GR303 4.7 52.6 0.9 CA A:ASP171 4.7 30.1 1.0 HE1 A:MET93 4.7 38.7 1.0 CB A:GLU145 4.7 34.0 1.0 HE3 A:MET93 4.8 38.7 1.0 HG1 A:THR170 4.8 40.2 1.0 HA2 A:GLY168 4.8 37.8 1.0 O4 A:3PY301 4.8 43.3 1.0 H31 A:3PY301 4.8 41.2 1.0 CD2 A:HIS44 4.9 28.8 1.0 H32 A:3PY301 4.9 41.2 1.0 CZ A:ARG69 4.9 27.2 1.0 OG1 A:THR170 5.0 33.5 1.0 NH2 A:ARG69 5.0 29.6 1.0

S.R.Marsden, H.J.Wijma, M.K.F.Mohr, I.Justo, P.L.Hagedoorn, J.Laustsen, C.M.Jeffries, D.Svergun, L.Mestrom, D.G.G.Mcmillan, I.Bento, U.Hanefeld. Substrate Induced Movement of the Metal Cofactor Between Active and Resting State. Angew.Chem.Int.Ed.Engl. V. 61 13338 2022.
ISSN: ESSN 1521-3773
PubMed: 36214476
DOI: 10.1002/ANIE.202213338