Magnesium in PDB 8kih: Phma, A Type I Diterpene Synthase Without Nst/Dte Motif

The structure of Phma, A Type I Diterpene Synthase Without Nst/Dte Motif, PDB code: 8kih was solved by B.Zhang, H.M.Ge, A.Zhu, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.88 / 2.00
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	106.549, 106.549, 55.36, 90, 90, 120
R / Rfree (%)	19.3 / 23.7

The structure of Phma, A Type I Diterpene Synthase Without Nst/Dte Motif also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Magnesium atom in the Phma, A Type I Diterpene Synthase Without Nst/Dte Motif (pdb code 8kih). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Phma, A Type I Diterpene Synthase Without Nst/Dte Motif, PDB code: 8kih:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Phma, A Type I Diterpene Synthase Without Nst/Dte Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phma, A Type I Diterpene Synthase Without Nst/Dte Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:53.9 occ:1.00 OD2 A:ASP97 2.3 44.1 1.0 O03 A:FGG401 2.7 71.0 1.0 O09 A:FGG401 2.9 67.8 1.0 CG A:ASP97 3.3 41.8 1.0 O07 A:FGG401 3.3 70.7 1.0 HB2 A:ASP97 3.3 41.7 1.0 OD2 A:ASP93 3.4 32.4 1.0 P04 A:FGG401 3.5 65.5 1.0 MG A:MG403 3.6 32.5 1.0 P02 A:FGG401 3.6 99.5 1.0 CB A:ASP97 3.7 34.7 1.0 OD1 A:ASP94 3.8 42.6 1.0 F01 A:FGG401 4.1 51.9 1.0 HA A:ASP94 4.1 43.7 1.0 O A:ASP93 4.2 24.9 1.0 OD1 A:ASP97 4.3 40.7 1.0 CG A:ASP93 4.3 29.5 1.0 O01 A:FGG401 4.4 63.9 1.0 O05 A:FGG401 4.5 46.4 1.0 O08 A:FGG401 4.6 50.0 1.0 HE2 A:LYS233 4.6 56.6 1.0 HZ2 A:LYS233 4.7 58.8 1.0 C A:ASP93 4.7 29.5 1.0 C02 A:FGG401 4.8 49.8 1.0 O A:HOH547 4.8 32.3 1.0 O06 A:FGG401 4.8 61.0 1.0 C01 A:FGG401 4.9 50.6 1.0 CA A:ASP94 5.0 36.5 1.0 CG A:ASP94 5.0 43.0 1.0 H A:ASP97 5.0 35.8 1.0 CB A:ASP93 5.0 30.5 1.0

Magnesium binding site 2 out of 2 in the Phma, A Type I Diterpene Synthase Without Nst/Dte Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phma, A Type I Diterpene Synthase Without Nst/Dte Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:32.5 occ:1.00 O A:HOH541 1.8 29.1 1.0 O A:HOH544 2.2 20.5 1.0 OD2 A:ASP93 2.3 32.4 1.0 O09 A:FGG401 2.4 67.8 1.0 O A:HOH547 2.5 32.3 1.0 OD2 A:ASP97 2.7 44.1 1.0 CG A:ASP93 3.2 29.5 1.0 O05 A:FGG401 3.2 46.4 1.0 OD1 A:ASP93 3.3 27.4 1.0 P04 A:FGG401 3.3 65.5 1.0 CG A:ASP97 3.4 41.8 1.0 OD1 A:ASP97 3.4 40.7 1.0 HZ A:PHE153 3.5 25.0 1.0 MG A:MG402 3.6 53.9 1.0 OD1 A:ASN182 3.9 22.7 1.0 O03 A:FGG401 4.0 71.0 1.0 ND2 A:ASN182 4.1 17.6 1.0 CZ A:PHE153 4.2 20.8 1.0 O A:ASN182 4.3 16.9 1.0 CG A:ASN182 4.4 24.0 1.0 C03 A:FGG401 4.5 41.9 1.0 C02 A:FGG401 4.5 49.8 1.0 F01 A:FGG401 4.6 51.9 1.0 CB A:ASP93 4.6 30.5 1.0 C04 A:FGG401 4.6 35.8 1.0 NH1 A:ARG179 4.6 22.5 1.0 O08 A:FGG401 4.7 50.0 1.0 HE2 A:PHE153 4.8 23.0 1.0 HE1 A:PHE153 4.8 24.2 1.0 CB A:ASP97 4.8 34.7 1.0 CE2 A:PHE153 4.9 19.2 1.0 CE1 A:PHE153 4.9 20.2 1.0 HB2 A:ASP97 4.9 41.7 1.0 O A:ASP93 5.0 24.9 1.0

L.Zhang, B.Zhang, A.Zhu, S.H.Liu, R.Wu, X.Zhang, Z.R.Xu, H.M.Ge. Biosynthesis of Platelet Activating Factor Antagonist Phomactins Revealing A New Class of Type I Diterpene Synthase To Be Published.