Magnesium in PDB 6xb9: Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid

The structure of Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid, PDB code: 6xb9 was solved by P.D.Kiser, N.Khadka, W.Shi, B.S.Pierce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.26 / 2.25
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	178.219, 178.219, 75.915, 90, 90, 120
R / Rfree (%)	19.6 / 22.6

The structure of Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid also contains other interesting chemical elements:

Iron	(Fe)	12 atoms
Chlorine	(Cl)	13 atoms

The binding sites of Magnesium atom in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid (pdb code 6xb9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid, PDB code: 6xb9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:52.8 occ:1.00 O A:ARG125 2.2 49.1 1.0 OE1 A:GLN130 2.2 44.0 1.0 O B:ARG125 2.3 46.9 1.0 OE1 B:GLN130 2.4 46.1 1.0 CD A:GLN130 3.2 52.5 1.0 C A:ARG125 3.4 42.0 1.0 CD B:GLN130 3.5 44.8 1.0 C B:ARG125 3.5 42.4 1.0 NE2 A:GLN130 3.6 53.2 1.0 NE2 B:GLN130 3.8 46.1 1.0 CA A:LEU126 4.1 46.4 1.0 N A:LEU126 4.1 46.5 1.0 CA B:LEU126 4.3 46.0 1.0 OG B:SER127 4.3 52.7 1.0 N B:LEU126 4.3 42.8 1.0 OG A:SER127 4.4 43.7 1.0 N A:SER127 4.4 43.0 1.0 CA A:ARG125 4.5 46.0 1.0 C A:LEU126 4.5 39.0 1.0 N B:SER127 4.6 46.9 1.0 CA B:ARG125 4.6 44.2 1.0 CG A:GLN130 4.6 50.4 1.0 C B:LEU126 4.7 45.9 1.0 CB B:ARG125 4.7 40.7 1.0 CB A:ARG125 4.7 40.8 1.0 N A:ARG125 4.7 49.4 1.0 CG B:GLN130 4.8 45.4 1.0 N B:ARG125 4.8 43.0 1.0 CB A:GLN130 4.9 49.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg304 b:49.4 occ:1.00 O D:ARG125 1.9 44.7 1.0 O C:ARG125 2.1 62.3 1.0 O D:HOH402 2.4 35.0 1.0 OE1 C:GLN130 2.5 54.1 1.0 OE1 D:GLN130 2.5 45.6 1.0 C D:ARG125 3.2 48.0 1.0 C C:ARG125 3.4 52.0 1.0 CD D:GLN130 3.5 48.0 1.0 CD C:GLN130 3.6 62.2 1.0 NE2 D:GLN130 3.7 56.8 1.0 NE2 C:GLN130 4.0 58.8 1.0 N D:LEU126 4.0 46.8 1.0 CA D:LEU126 4.1 47.4 1.0 OG C:SER127 4.1 52.2 1.0 CA C:LEU126 4.1 51.0 1.0 CA D:ARG125 4.2 47.7 1.0 N C:LEU126 4.2 53.9 1.0 N C:SER127 4.3 42.4 1.0 CB D:ARG125 4.3 41.2 1.0 N D:ARG125 4.4 46.4 1.0 C C:LEU126 4.4 47.6 1.0 CA C:ARG125 4.4 46.6 1.0 C D:LEU126 4.5 48.1 1.0 OG D:SER127 4.5 49.7 1.0 N D:SER127 4.5 48.8 1.0 CB C:ARG125 4.6 40.0 1.0 N C:ARG125 4.8 45.2 1.0 CG C:GLN130 4.9 57.5 1.0 CG D:GLN130 4.9 47.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


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 Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg305 b:51.4 occ:1.00 O H:ARG125 2.0 40.4 1.0 OE1 H:GLN130 2.5 51.4 1.0 O H:HOH407 2.6 47.2 1.0 C H:ARG125 3.3 40.7 1.0 CD H:GLN130 3.5 54.3 1.0 NE2 H:GLN130 3.8 52.3 1.0 N H:LEU126 4.1 45.3 1.0 CA H:LEU126 4.1 40.9 1.0 CA H:ARG125 4.3 44.4 1.0 OG H:SER127 4.4 48.0 1.0 CB H:ARG125 4.4 43.8 1.0 N H:SER127 4.5 43.9 1.0 C H:LEU126 4.5 39.5 1.0 N H:ARG125 4.6 48.9 1.0 CG H:GLN130 4.9 53.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Azotobacter Vinelandii 3-Mercaptopropionic Acid Dioxygenase in Complex with 3-Hydroxypropionic Acid within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg304 b:51.2 occ:1.00 O J:ARG125 2.2 47.0 1.0 OE1 J:GLN130 2.7 57.7 1.0 C J:ARG125 3.4 46.6 1.0 CD J:GLN130 3.6 60.5 1.0 NE2 J:GLN130 3.6 61.8 1.0 CA J:ARG125 4.2 45.6 1.0 N J:ARG125 4.3 43.9 1.0 N J:LEU126 4.3 48.9 1.0 CB J:ARG125 4.3 42.5 1.0 CA J:LEU126 4.5 46.7 1.0

N.J.York, M.M.Lockart, S.Sardar, N.Khadka, W.Shi, R.E.Stenkamp, J.Zhang, P.D.Kiser, B.S.Pierce. Structure of 3-Mercaptopropionic Acid Dioxygenase with A Substrate Analog Reveals Bidentate Substrate Binding at the Iron Center J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X