Magnesium in PDB 7obu: Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State

The structure of Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State, PDB code: 7obu was solved by J.Laustsen, 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)	35.55 / 1.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	71.094, 71.094, 222.394, 90, 90, 120
R / Rfree (%)	12.9 / 15.7

The structure of Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State (pdb code 7obu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State, PDB code: 7obu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State


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-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:10.2 occ:1.00 OD2 A:ASP171 2.0 10.6 1.0 O A:HOH461 2.0 11.0 1.0 OE1 A:GLU145 2.1 11.6 1.0 O A:HOH425 2.1 12.7 1.0 O A:HOH573 2.1 14.0 1.0 CG A:ASP171 3.0 10.7 1.0 CD A:GLU145 3.1 11.7 1.0 HE22 A:GLN43 3.4 11.9 1.0 OE2 A:GLU145 3.5 11.8 1.0 O A:HOH550 3.7 30.0 1.0 OD1 A:ASP171 3.8 10.7 1.0 CB A:ASP171 3.9 9.9 1.0 HB2 A:ASP171 3.9 11.9 1.0 HB3 A:ASP171 3.9 11.9 1.0 HE1 A:MET143 3.9 11.3 0.5 NE2 A:GLN43 4.0 9.9 1.0 HB2 A:GLU145 4.2 15.6 1.0 OE1 A:GLN43 4.2 9.5 1.0 NE2 A:HIS44 4.2 8.2 1.0 CG A:GLU145 4.4 11.7 1.0 HE2 A:MET143 4.4 11.3 0.5 O A:HOH506 4.4 16.0 1.0 O A:HOH611 4.4 20.5 1.0 CD A:GLN43 4.5 9.8 1.0 HE21 A:GLN43 4.5 11.9 1.0 HB3 A:PRO92 4.5 14.0 1.0 HG3 A:GLU145 4.6 14.1 1.0 CE A:MET143 4.6 9.4 0.5 HG2 A:MET93 4.7 18.1 1.0 CB A:GLU145 4.7 13.0 1.0 HD2 A:HIS44 4.9 9.2 1.0 HB3 A:GLU145 4.9 15.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State


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 Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:9.5 occ:0.70 MG B:MG302 0.0 9.5 0.7 O B:HOH442 2.0 12.0 1.0 O3 B:3PY301 2.0 13.5 1.0 OD2 B:ASP171 2.1 9.0 1.0 OE1 B:GLU145 2.1 7.6 0.6 O1 B:3PY301 2.1 13.8 1.0 O B:HOH471 2.1 14.0 1.0 MG B:MG302 2.4 5.1 0.3 OE1 B:GLU145 2.6 11.3 0.4 C2 B:3PY301 2.7 17.8 1.0 HE1 B:MET143 2.7 11.8 0.5 C1 B:3PY301 2.8 14.6 1.0 HB2 B:ASP171 3.0 10.7 1.0 CG B:ASP171 3.1 10.0 1.0 CD B:GLU145 3.1 8.0 0.6 HH12 B:ARG69 3.4 10.1 1.0 CB B:ASP171 3.5 8.9 1.0 OE2 B:GLU145 3.5 7.8 0.6 CE B:MET143 3.7 9.9 0.5 CD B:GLU145 3.7 9.8 0.4 HE1 B:MET143 3.7 8.8 0.5 HE2 B:MET93 3.8 17.2 0.6 HA3 B:GLY168 3.9 9.7 1.0 HE2 B:MET143 3.9 11.8 0.5 H B:ASP171 3.9 10.5 1.0 O2 B:3PY301 4.0 14.4 1.0 NH1 B:ARG69 4.0 8.4 1.0 HB2 B:GLU145 4.1 9.4 0.4 O B:HOH539 4.1 22.5 1.0 HB3 B:ASP171 4.1 10.7 1.0 C3 B:3PY301 4.1 9.8 1.0 HE3 B:MET143 4.1 11.8 0.5 O B:HOH445 4.1 8.6 0.3 HB3 B:GLU145 4.1 10.3 0.6 HE2 B:MET143 4.1 8.8 0.5 OD1 B:ASP171 4.2 10.5 1.0 OE2 B:GLU145 4.3 10.9 0.4 HH11 B:ARG69 4.3 10.1 1.0 OE1 B:GLN43 4.4 8.8 1.0 HH22 B:ARG69 4.4 9.6 1.0 CE B:MET143 4.4 7.4 0.5 H32 B:3PY301 4.4 11.7 1.0 O B:HOH566 4.4 7.5 0.3 CG B:GLU145 4.4 9.9 0.6 HE1 B:MET93 4.5 17.2 0.6 HB3 B:GLU145 4.5 9.4 0.4 HD2 B:HIS44 4.5 9.9 1.0 CE B:MET93 4.6 14.3 0.6 N B:ASP171 4.6 8.8 1.0 CB B:GLU145 4.6 7.8 0.4 HG1 B:THR170 4.6 16.8 1.0 NE2 B:HIS44 4.6 8.4 1.0 HG2 B:GLU145 4.6 11.8 0.6 H31 B:3PY301 4.7 11.7 1.0 CA B:ASP171 4.7 8.5 1.0 CA B:GLY168 4.7 8.1 1.0 HE22 B:GLN43 4.7 10.9 1.0 O4 B:3PY301 4.7 34.7 1.0 CG B:GLU145 4.7 8.2 0.4 CB B:GLU145 4.8 8.6 0.6 SD B:MET143 4.8 10.2 0.5 HA2 B:GLY168 4.8 9.7 1.0 CZ B:ARG69 4.9 7.5 1.0 CD2 B:HIS44 4.9 8.3 1.0 NH2 B:ARG69 4.9 8.0 1.0 OG1 B:THR170 5.0 14.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Holo-F210W Mutant of Hydroxy Ketone Aldolase (Swhka) From Sphingomonas Wittichii RW1, with the Active Site in the Resting and the Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:5.1 occ:0.30 MG B:MG302 0.0 5.1 0.3 HE2 B:MET93 1.8 17.2 0.6 OD2 B:ASP171 1.8 9.0 1.0 O B:HOH442 2.0 12.0 1.0 OE1 B:GLU145 2.0 11.3 0.4 O B:HOH445 2.1 8.6 0.3 O B:HOH566 2.2 7.5 0.3 MG B:MG302 2.4 9.5 0.7 CE B:MET93 2.6 14.3 0.6 HE3 B:MET93 2.8 17.2 0.6 HE1 B:MET93 2.8 17.2 0.6 CG B:ASP171 2.8 10.0 1.0 OE1 B:GLU145 2.9 7.6 0.6 CD B:GLU145 3.0 9.8 0.4 HE22 B:GLN43 3.2 10.9 1.0 OE2 B:GLU145 3.2 7.8 0.6 CD B:GLU145 3.3 8.0 0.6 O B:HOH471 3.3 14.0 1.0 OE2 B:GLU145 3.3 10.9 0.4 OD1 B:ASP171 3.6 10.5 1.0 HG2 B:MET93 3.6 19.3 0.6 HB2 B:ASP171 3.7 10.7 1.0 HG2 B:MET93 3.7 22.0 0.4 CB B:ASP171 3.8 8.9 1.0 HB3 B:ASP171 3.9 10.7 1.0 NE2 B:GLN43 3.9 9.1 1.0 SD B:MET93 4.1 17.8 0.4 SD B:MET93 4.1 15.9 0.6 HE1 B:MET143 4.1 11.8 0.5 HB3 B:GLU145 4.1 10.3 0.6 O1 B:3PY301 4.2 13.8 1.0 OE1 B:GLN43 4.2 8.8 1.0 CG B:MET93 4.2 16.1 0.6 O3 B:3PY301 4.3 13.5 1.0 NE2 B:HIS44 4.3 8.4 1.0 CG B:GLU145 4.3 8.2 0.4 CG B:MET93 4.3 18.3 0.4 HB2 B:GLU145 4.3 9.4 0.4 HB2 B:PRO92 4.4 14.7 1.0 HG3 B:MET93 4.4 19.3 0.6 CD B:GLN43 4.4 8.0 1.0 HE21 B:GLN43 4.5 10.9 1.0 HG3 B:GLU145 4.5 9.8 0.4 HG3 B:MET93 4.6 22.0 0.4 CG B:GLU145 4.6 9.9 0.6 HB2 B:GLU145 4.6 10.3 0.6 CB B:GLU145 4.7 8.6 0.6 O B:HOH614 4.7 24.4 1.0 HB3 B:PRO92 4.8 14.7 1.0 CB B:GLU145 4.8 7.8 0.4 CE B:MET143 4.9 9.9 0.5 HE2 B:MET143 4.9 11.8 0.5 O B:HOH514 5.0 27.5 1.0 HG3 B:GLU145 5.0 11.8 0.6

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