Magnesium in PDB 7vws: Carbazole Prenyl Transferase LVQB4

The structure of Carbazole Prenyl Transferase LVQB4, PDB code: 7vws was solved by H.Suemune, R.Nagata, T.Kuzuyama, S.Nagano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.69 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.24, 71.394, 83.894, 90, 109.91, 90
R / Rfree (%)	17.6 / 21.3

The binding sites of Magnesium atom in the Carbazole Prenyl Transferase LVQB4 (pdb code 7vws). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Carbazole Prenyl Transferase LVQB4, PDB code: 7vws:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Carbazole Prenyl Transferase LVQB4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Carbazole Prenyl Transferase LVQB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:39.5 occ:1.00 O18 A:83B604 2.1 63.9 1.0 O A:HOH881 2.1 41.7 1.0 O15 A:83B604 2.2 50.2 1.0 O A:HOH845 2.2 36.1 1.0 OD2 A:ASP195 2.2 28.5 1.0 OD1 A:ASP191 2.2 33.4 1.0 MG A:MG602 3.1 38.2 1.0 CG A:ASP195 3.2 32.0 1.0 CG A:ASP191 3.2 31.5 1.0 P14 A:83B604 3.3 62.7 1.0 P12 A:83B604 3.4 82.3 1.0 OD1 A:ASP195 3.4 26.4 1.0 O17 A:83B604 3.5 73.0 1.0 OD2 A:ASP191 3.5 35.6 1.0 O13 A:83B604 3.8 64.2 1.0 O A:HOH791 4.0 37.4 1.0 O9 A:83B604 4.2 66.7 1.0 O A:HOH902 4.2 40.2 1.0 O16 A:83B604 4.5 69.8 1.0 CB A:ASP191 4.5 18.2 1.0 CB A:ASP195 4.6 24.5 1.0 O19 A:83B604 4.7 61.9 1.0 H081 A:83B604 4.8 75.7 1.0 O A:ASP191 4.8 21.1 1.0 O A:HOH767 4.8 37.8 1.0 C8 A:83B604 4.9 63.0 1.0 H082 A:83B604 4.9 75.7 1.0 CA A:ASP191 5.0 16.0 1.0

Magnesium binding site 2 out of 4 in the Carbazole Prenyl Transferase LVQB4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Carbazole Prenyl Transferase LVQB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:38.2 occ:1.00 OD2 A:ASP191 2.1 35.6 1.0 O A:HOH791 2.1 37.4 1.0 O15 A:83B604 2.1 50.2 1.0 OD2 A:ASP195 2.2 28.5 1.0 O A:HOH721 2.2 34.3 1.0 O A:HOH767 2.3 37.8 1.0 CG A:ASP191 3.0 31.5 1.0 MG A:MG601 3.1 39.5 1.0 CG A:ASP195 3.2 32.0 1.0 OD1 A:ASP191 3.3 33.4 1.0 P14 A:83B604 3.4 62.7 1.0 CB A:ASP195 3.7 24.5 1.0 O19 A:83B604 3.7 61.9 1.0 O A:HOH809 3.9 43.9 1.0 O17 A:83B604 4.0 73.0 1.0 O A:ASP191 4.0 21.1 1.0 O A:HOH881 4.3 41.7 1.0 OD2 A:ASP199 4.3 29.6 1.0 CB A:ASP191 4.3 18.2 1.0 OD1 A:ASP195 4.3 26.4 1.0 C A:ASP191 4.4 19.1 1.0 O18 A:83B604 4.5 63.9 1.0 O13 A:83B604 4.6 64.2 1.0 OD1 A:ASP199 4.7 31.3 1.0 O A:HOH845 4.9 36.1 1.0 CA A:ASP191 4.9 16.0 1.0 CG A:ASP199 4.9 30.4 1.0

Magnesium binding site 3 out of 4 in the Carbazole Prenyl Transferase LVQB4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Carbazole Prenyl Transferase LVQB4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:29.4 occ:1.00 O B:HOH768 1.9 33.2 1.0 O B:HOH820 2.1 32.0 1.0 O15 B:83B604 2.1 29.7 1.0 O18 B:83B604 2.1 39.9 1.0 OD1 B:ASP191 2.2 23.9 1.0 OD2 B:ASP195 2.2 23.3 1.0 MG B:MG602 3.1 28.4 1.0 CG B:ASP195 3.1 29.1 1.0 CG B:ASP191 3.1 23.2 1.0 P14 B:83B604 3.3 40.5 1.0 OD1 B:ASP195 3.3 25.6 1.0 P12 B:83B604 3.4 45.8 1.0 OD2 B:ASP191 3.4 27.0 1.0 O17 B:83B604 3.4 44.4 1.0 O13 B:83B604 3.7 42.5 1.0 O9 B:83B604 4.0 55.1 1.0 O B:HOH936 4.3 35.4 1.0 O B:HOH831 4.3 30.2 1.0 CB B:ASP191 4.5 18.2 1.0 CB B:ASP195 4.5 17.5 1.0 O16 B:83B604 4.6 55.2 1.0 O B:HOH746 4.6 31.1 1.0 O19 B:83B604 4.7 35.4 1.0 O B:ASP191 4.8 19.4 1.0 O B:HOH723 5.0 26.5 1.0 O B:HOH843 5.0 33.0 1.0 CA B:ASP191 5.0 18.8 1.0

Magnesium binding site 4 out of 4 in the Carbazole Prenyl Transferase LVQB4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Carbazole Prenyl Transferase LVQB4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:28.4 occ:1.00 OD2 B:ASP191 2.1 27.0 1.0 O15 B:83B604 2.1 29.7 1.0 O B:HOH723 2.1 26.5 1.0 OD2 B:ASP195 2.1 23.3 1.0 O B:HOH746 2.2 31.1 1.0 O B:HOH831 2.2 30.2 1.0 CG B:ASP191 3.0 23.2 1.0 MG B:MG601 3.1 29.4 1.0 CG B:ASP195 3.2 29.1 1.0 P14 B:83B604 3.3 40.5 1.0 OD1 B:ASP191 3.3 23.9 1.0 CB B:ASP195 3.6 17.5 1.0 O19 B:83B604 3.6 35.4 1.0 O B:HOH843 4.0 33.0 1.0 O B:ASP191 4.0 19.4 1.0 O17 B:83B604 4.1 44.4 1.0 O B:HOH820 4.1 32.0 1.0 OD2 B:ASP199 4.2 30.9 1.0 OD1 B:ASP195 4.3 25.6 1.0 CB B:ASP191 4.3 18.2 1.0 C B:ASP191 4.5 16.7 1.0 OD1 B:ASP199 4.5 30.6 1.0 O13 B:83B604 4.5 42.5 1.0 O18 B:83B604 4.6 39.9 1.0 O B:HOH768 4.7 33.2 1.0 CG B:ASP199 4.8 31.6 1.0 CA B:ASP191 4.9 18.8 1.0

R.Nagata, H.Suemune, M.Kobayashi, T.Shinada, K.Shin-Ya, M.Nishiyama, T.Hino, Y.Sato, T.Kuzuyama, S.Nagano. Structural Basis For the Prenylation Reaction of Carbazole-Containing Natural Products Catalyzed By Squalene Synthase-Like Enzymes. Angew.Chem.Int.Ed.Engl. V. 61 17430 2022.
ISSN: ESSN 1521-3773
PubMed: 35235232
DOI: 10.1002/ANIE.202117430