Magnesium in PDB 7bug: Reduced Oxygenase of Carbazole 1,9A-Dioxygenase

The structure of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase, PDB code: 7bug was solved by J.Matsuzawa, Y.X.Wang, C.Suzuki-Minakuchi, H.Nojiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.01 / 1.60
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	91.94, 91.94, 243.46, 90, 90, 120
R / Rfree (%)	15.4 / 18.8

The structure of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase also contains other interesting chemical elements:

Iron

(Fe)

9 atoms

The binding sites of Magnesium atom in the Reduced Oxygenase of Carbazole 1,9A-Dioxygenase (pdb code 7bug). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Reduced Oxygenase of Carbazole 1,9A-Dioxygenase, PDB code: 7bug:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Reduced Oxygenase of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:18.8 occ:1.00 O A:HOH729 2.1 17.1 1.0 O A:HOH716 2.1 18.4 1.0 O A:GLU100 2.1 14.7 1.0 O A:HOH630 2.1 20.1 1.0 O A:HOH599 2.1 19.8 1.0 O A:HOH631 2.2 14.9 1.0 C A:GLU100 3.2 14.6 1.0 O A:HOH587 4.0 13.2 1.0 CA A:GLU100 4.0 15.6 1.0 OE2 A:GLU100 4.1 34.8 1.0 O A:HOH714 4.2 23.5 1.0 N A:ASP101 4.2 13.2 1.0 O A:HOH645 4.2 16.3 1.0 O A:HOH792 4.3 44.2 1.0 OG1 A:THR123 4.3 15.1 1.0 CA A:ASP101 4.3 14.4 1.0 O A:TRP99 4.4 13.0 1.0 CD A:GLU100 4.4 30.9 1.0 O2 A:CO3410 4.5 29.9 1.0 CG A:GLU100 4.6 23.4 1.0 CB A:THR123 4.6 13.1 1.0 C A:CO3410 4.9 25.2 1.0 CG2 A:THR123 4.9 17.2 1.0 CB A:GLU100 4.9 19.0 1.0 CD2 A:TYR63 4.9 12.8 1.0

Magnesium binding site 2 out of 5 in the Reduced Oxygenase of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:39.8 occ:1.00 O B:HOH540 2.0 33.8 1.0 O B:HOH782 2.0 37.3 1.0 O B:HOH632 2.1 28.1 1.0 O B:GLU100 2.1 23.7 1.0 O B:HOH738 2.2 39.3 1.0 O B:HOH752 2.3 36.2 1.0 C B:GLU100 3.3 22.4 1.0 O B:HOH613 4.1 20.8 1.0 O B:HOH694 4.1 30.4 1.0 CA B:GLU100 4.1 22.5 1.0 OG1 B:THR123 4.2 23.2 1.0 N B:ASP101 4.3 20.6 1.0 O B:TRP99 4.4 21.9 1.0 O B:HOH796 4.4 40.0 1.0 CA B:ASP101 4.4 20.2 1.0 CB B:THR123 4.5 19.0 1.0 CG B:GLU100 4.6 40.2 1.0 CG2 B:THR123 4.7 23.1 1.0 O B:HOH571 4.9 52.0 1.0 CD2 B:TYR63 5.0 20.2 1.0

Magnesium binding site 3 out of 5 in the Reduced Oxygenase of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:20.5 occ:1.00 O B:TYR253 1.9 26.6 1.0 O B:HOH737 2.0 22.8 1.0 O B:HOH608 2.1 16.8 1.0 O B:HOH503 2.1 27.0 1.0 C B:TYR253 3.2 20.9 1.0 CA B:GLY254 4.0 20.2 1.0 N B:TYR253 4.0 20.2 1.0 N B:GLY254 4.0 22.7 1.0 OD1 B:ASP197 4.1 25.4 1.0 O B:HOH735 4.1 29.8 1.0 CA B:TYR253 4.2 22.0 1.0 O B:LEU198 4.3 15.0 1.0 CA B:ASP197 4.5 19.2 1.0 O B:HOH791 4.5 24.2 1.0 O B:VAL193 4.5 16.6 1.0 C B:ALA252 4.5 17.5 1.0 O B:LYS194 4.6 24.3 1.0 CB B:ALA252 4.7 16.7 1.0 C B:ASP197 4.7 15.8 1.0 CB B:TYR253 4.8 23.7 1.0 CA B:ALA252 4.9 15.7 1.0

Magnesium binding site 4 out of 5 in the Reduced Oxygenase of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:29.3 occ:1.00 O B:HOH739 1.9 36.0 1.0 O B:HOH538 2.1 27.5 1.0 O B:HOH532 2.2 35.8 1.0 O B:HOH579 2.4 40.4 1.0 OE2 B:GLU316 3.9 33.0 0.6 OD2 B:ASP279 4.0 25.4 1.0 ND2 B:ASN277 4.2 18.2 1.0 OE1 B:GLU316 4.3 18.4 0.4 OD1 B:ASP279 4.3 23.0 1.0 OE2 B:GLU316 4.3 18.8 0.4 OE1 B:GLU316 4.3 28.8 0.6 CD B:GLU316 4.5 27.2 0.6 CG B:ASP279 4.6 22.9 1.0 CE B:LYS302 4.6 29.6 1.0 CD B:GLU316 4.7 19.5 0.4

Magnesium binding site 5 out of 5 in the Reduced Oxygenase of Carbazole 1,9A-Dioxygenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Reduced Oxygenase of Carbazole 1,9A-Dioxygenase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:21.2 occ:1.00 O C:GLU100 2.0 19.5 1.0 O C:HOH604 2.1 24.2 1.0 O C:HOH687 2.1 25.0 1.0 O C:HOH635 2.1 20.9 1.0 O C:HOH731 2.2 22.1 1.0 C C:GLU100 3.1 18.4 1.0 CA C:GLU100 3.9 20.3 1.0 O C:HOH603 4.0 15.0 1.0 N C:ASP101 4.1 18.4 1.0 OE2 C:GLU100 4.1 37.8 1.0 O C:HOH727 4.2 25.3 1.0 OG1 C:THR123 4.2 19.4 1.0 CA C:ASP101 4.2 19.1 1.0 O C:TRP99 4.3 17.7 1.0 O C:HOH664 4.4 21.3 1.0 CD C:GLU100 4.5 30.8 1.0 CB C:THR123 4.5 18.8 1.0 CG C:GLU100 4.6 25.4 1.0 CG2 C:THR123 4.8 22.1 1.0 CB C:GLU100 4.9 21.9 1.0 CD2 C:TYR63 4.9 15.1 1.0

J.Matsuzawa, Y.X.Wang, C.Suzuki-Minakuchi, H.Nojiri. Reduced Oxygenase of Carbazole 1,9A-Dioxygenase To Be Published.