Magnesium in PDB 7xqz: Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+

The structure of Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+, PDB code: 7xqz was solved by X.M.Pan, W.Y.Du, Q.Yang, B.Zhang, L.B.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.39 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	51.53, 114.02, 180.54, 90, 90, 90
R / Rfree (%)	17.5 / 22

The structure of Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+ also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Magnesium atom in the Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+ (pdb code 7xqz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+, PDB code: 7xqz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:34.4 occ:1.00 OE1 A:GLU169 2.5 26.6 1.0 O2A A:FPF601 2.6 23.4 1.0 O3B A:FPF601 2.7 21.3 1.0 P1 A:FPF601 3.4 26.3 1.0 CD A:GLU169 3.4 25.2 1.0 CB A:PRO500 3.5 22.9 1.0 O1A A:FPF601 3.6 24.6 1.0 OE2 A:GLU169 3.7 28.9 1.0 MG A:MG603 3.7 26.4 1.0 O3A A:FPF601 3.9 24.6 1.0 CE A:MET136 3.9 24.6 1.0 P2 A:FPF601 3.9 22.4 1.0 CD1 A:LEU166 4.0 20.3 1.0 NH1 A:ARG132 4.0 20.5 1.0 CG A:PRO500 4.1 20.9 1.0 SD A:MET136 4.3 30.4 1.0 CA A:PRO500 4.5 17.6 1.0 CD A:PRO500 4.6 16.9 1.0 O2B A:FPF601 4.7 19.2 1.0 O1 A:FPF601 4.8 24.9 1.0 CG A:GLU169 4.8 20.8 1.0 NE2 A:GLN163 4.9 19.6 1.0 NE1 A:TRP165 4.9 20.6 1.0 CE A:LYS133 4.9 20.9 1.0 O1B A:FPF601 5.0 20.7 1.0

Magnesium binding site 2 out of 2 in the Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Drimenyl Diphosphate Synthase D303A From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:26.4 occ:1.00 OE2 A:GLU169 2.6 28.9 1.0 O2A A:FPF601 2.8 23.4 1.0 ND2 A:ASN208 2.8 16.5 1.0 CD A:GLU169 3.5 25.2 1.0 CE1 A:PHE248 3.6 17.6 1.0 NE1 A:TRP165 3.6 20.6 1.0 P1 A:FPF601 3.6 26.3 1.0 CD1 A:TRP165 3.7 20.9 1.0 MG A:MG602 3.7 34.4 1.0 CZ A:PHE248 3.7 18.3 1.0 CG A:ASN208 3.7 18.6 1.0 OD1 A:ASN208 3.8 17.2 1.0 H4A A:FPF601 3.8 28.3 1.0 O1A A:FPF601 3.8 24.6 1.0 OE1 A:GLU169 3.8 26.6 1.0 O1 A:FPF601 4.0 24.9 1.0 CD2 A:LEU210 4.0 18.6 1.0 CD A:PRO500 4.2 16.9 1.0 H1A A:FPF601 4.3 31.9 1.0 CG A:LEU210 4.6 15.8 1.0 CB A:LEU210 4.6 12.5 1.0 CE2 A:TRP165 4.7 22.2 1.0 C1 A:FPF601 4.7 26.5 1.0 CG A:TRP165 4.8 20.9 1.0 CG A:PRO500 4.8 20.9 1.0 N A:PRO500 4.8 16.6 1.0 C4 A:FPF601 4.8 23.5 1.0 CG A:GLU169 4.9 20.8 1.0 CD1 A:PHE248 4.9 16.5 1.0

X.Pan, W.Du, X.Zhang, X.Lin, F.R.Li, Q.Yang, H.Wang, J.D.Rudolf, B.Zhang, L.B.Dong. Discovery, Structure, and Mechanism of A Class II Sesquiterpene Cyclase. J.Am.Chem.Soc. V. 144 22067 2022.
ISSN: ESSN 1520-5126
PubMed: 36416740
DOI: 10.1021/JACS.2C09412