Manganese in PDB 7o5r: Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1

The structure of Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1, PDB code: 7o5r 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)	75.13 / 1.65
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	71.54, 71.54, 225.394, 90, 90, 120
R / Rfree (%)	16 / 19.3

The structure of Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 also contains other interesting chemical elements:

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

The binding sites of Manganese atom in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 (pdb code 7o5r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1, PDB code: 7o5r:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:11.4 occ:0.61 OD2 A:ASP171 1.8 14.9 1.0 O A:HOH403 1.8 16.5 1.0 OE1 A:GLU145 1.8 20.6 1.0 MN A:MN302 2.3 13.8 0.4 CD A:GLU145 2.7 15.3 1.0 CG A:ASP171 2.8 13.1 1.0 HE22 A:GLN43 3.1 9.4 0.0 OE2 A:GLU145 3.3 19.1 1.0 HE2 A:HIS44 3.3 9.4 0.0 O A:HOH432 3.3 22.4 1.0 OD1 A:ASP171 3.5 14.2 1.0 HB2 A:ASP171 3.7 13.4 1.0 CB A:ASP171 3.7 14.3 1.0 HB3 A:ASP171 3.8 13.4 1.0 HG3 A:GLU145 3.8 15.4 1.0 NE2 A:GLN43 3.9 9.4 1.0 CG A:GLU145 3.9 16.2 1.0 O A:HOH481 3.9 17.4 0.6 HG2 A:MET93 4.1 22.2 1.0 NE2 A:HIS44 4.2 9.5 1.0 OE1 A:GLN43 4.2 9.1 1.0 HE21 A:GLN43 4.4 9.4 0.0 CD A:GLN43 4.5 8.1 1.0 HG2 A:GLU145 4.5 15.4 1.0 HE1 A:MET143 4.5 14.9 1.0 O A:HOH463 4.5 40.3 1.0 SD A:MET93 4.6 23.1 1.0 HB2 A:GLU145 4.6 13.8 1.0 HB3 A:PRO92 4.6 13.7 1.0 HB2 A:PRO92 4.7 13.7 1.0 CG A:MET93 4.8 22.9 1.0 CB A:GLU145 4.9 13.6 1.0 HD2 A:HIS44 4.9 10.7 1.0 HH12 A:ARG69 4.9 7.0 0.0 CD2 A:HIS44 5.0 11.2 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:13.8 occ:0.36 O A:HOH403 1.8 16.5 1.0 O A:HOH481 1.8 17.4 0.6 OD2 A:ASP171 1.8 14.9 1.0 O A:HOH432 1.9 22.4 1.0 OE1 A:GLU145 2.0 20.6 1.0 MN A:MN301 2.3 11.4 0.6 HB2 A:ASP171 2.8 13.4 1.0 CG A:ASP171 2.9 13.1 1.0 CD A:GLU145 3.3 15.3 1.0 CB A:ASP171 3.4 14.3 1.0 HH12 A:ARG69 3.5 7.0 0.0 HE3 A:MET143 3.6 14.9 1.0 HE1 A:MET143 3.6 14.9 1.0 HB3 A:ASP171 3.9 13.4 1.0 H A:ASP171 4.0 13.7 1.0 O A:HOH585 4.0 13.1 1.0 HE2 A:HIS44 4.0 9.4 0.0 HA3 A:GLY168 4.0 10.6 1.0 OD1 A:ASP171 4.0 14.2 1.0 CE A:MET143 4.1 14.2 1.0 HB2 A:GLU145 4.1 13.8 1.0 OE2 A:GLU145 4.1 19.1 1.0 NH1 A:ARG69 4.2 7.0 1.0 O A:HOH481 4.3 15.2 0.4 CG A:GLU145 4.4 16.2 1.0 HD2 A:HIS44 4.4 10.7 1.0 HH11 A:ARG69 4.5 7.0 0.0 HG3 A:GLU145 4.5 15.4 1.0 OE1 A:GLN43 4.5 9.1 1.0 CA A:ASP171 4.6 12.1 1.0 NE2 A:HIS44 4.6 9.5 1.0 N A:ASP171 4.6 13.7 1.0 CB A:GLU145 4.6 13.6 1.0 HG1 A:THR170 4.6 19.0 0.0 HB3 A:GLU145 4.7 13.8 1.0 HE22 A:GLN43 4.7 9.4 0.0 HH21 A:ARG69 4.7 8.2 1.0 HE2 A:MET143 4.8 14.9 1.0 CD2 A:HIS44 4.8 11.2 1.0 CA A:GLY168 4.8 10.4 1.0 O A:HOH569 5.0 16.3 1.0 OG1 A:THR170 5.0 19.1 1.0 HA A:ASP171 5.0 12.5 1.0 HA2 A:GLY168 5.0 10.7 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Holo-Swhpa-Mn (Hydroxyketoacid Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:11.4 occ:0.76 OD2 B:ASP171 1.7 13.2 0.8 O B:HOH454 1.8 20.0 1.0 O B:HOH466 1.8 16.8 1.0 O B:HOH458 1.9 12.3 1.0 OE1 B:GLU145 2.2 17.1 1.0 CG B:ASP171 2.7 13.7 0.8 OD1 B:ASP171 2.8 8.3 0.2 CD B:GLU145 3.1 18.1 1.0 HE22 B:GLN43 3.3 10.6 0.0 CG B:ASP171 3.3 8.8 0.2 HE2 B:HIS44 3.4 12.7 0.0 OE2 B:GLU145 3.5 17.2 1.0 OD1 B:ASP171 3.6 11.9 0.8 HB2 B:ASP171 3.6 13.2 0.8 CB B:ASP171 3.6 13.6 0.8 HB3 B:ASP171 3.6 13.2 0.8 HB3 B:ASP171 3.6 9.3 0.2 O B:HOH423 3.9 23.3 1.0 NE2 B:GLN43 3.9 10.5 1.0 OD2 B:ASP171 4.0 9.1 0.2 CB B:ASP171 4.1 9.3 0.2 NE2 B:HIS44 4.2 12.7 1.0 OE1 B:GLN43 4.3 9.1 1.0 CG B:GLU145 4.3 18.0 1.0 HG3 B:GLU145 4.3 17.7 1.0 O B:HOH410 4.4 22.2 1.0 HB2 B:GLU145 4.5 16.4 1.0 HE21 B:GLN43 4.5 10.6 0.0 CD B:GLN43 4.5 8.3 1.0 HE1 B:MET143 4.5 15.9 1.0 HG2 B:MET93 4.5 23.2 1.0 O B:HOH498 4.5 21.6 1.0 HB2 B:ASP171 4.6 9.3 0.2 HB3 B:PRO92 4.7 12.1 1.0 HD2 B:HIS44 4.8 12.7 1.0 HE3 B:MET143 4.8 15.9 1.0 O B:HOH583 4.8 20.9 1.0 CB B:GLU145 4.9 16.7 1.0 HB2 B:PRO92 4.9 12.1 1.0 CD2 B:HIS44 5.0 13.0 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