Magnesium in PDB 7xr7: Drimenyl Diphosphate Synthase D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (Fpp) and MG2+

The structure of Drimenyl Diphosphate Synthase D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (Fpp) and MG2+, PDB code: 7xr7 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)	35.43 / 1.63
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	51.64, 114.21, 180.67, 90, 90, 90
R / Rfree (%)	18.8 / 21.8

The binding sites of Magnesium atom in the Drimenyl Diphosphate Synthase D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (Fpp) and MG2+ (pdb code 7xr7). 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 D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (Fpp) and MG2+, PDB code: 7xr7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Drimenyl Diphosphate Synthase D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (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 D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (Fpp) and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:28.9 occ:1.00 OE2 A:GLU169 2.5 26.5 1.0 O1A A:FPP601 2.6 28.3 1.0 ND2 A:ASN208 3.0 17.6 1.0 H12A A:FPP601 3.3 37.8 1.0 CD A:GLU169 3.5 26.1 1.0 CE1 A:PHE248 3.6 15.7 1.0 MG A:MG603 3.6 32.9 1.0 CD1 A:TRP165 3.6 24.8 1.0 NE1 A:TRP165 3.7 25.6 1.0 CZ A:PHE248 3.7 16.8 1.0 PA A:FPP601 3.7 26.0 1.0 OE1 A:GLU169 3.8 27.6 1.0 CG A:ASN208 3.9 15.9 1.0 OD1 A:ASN208 3.9 14.0 1.0 CD2 A:LEU210 4.0 16.2 1.0 C1 A:FPP601 4.1 31.5 1.0 CG A:PRO500 4.1 19.6 1.0 O2A A:FPP601 4.1 30.1 1.0 O1 A:FPP601 4.3 30.9 1.0 CD A:PRO500 4.3 17.5 1.0 H11 A:FPP601 4.3 37.8 1.0 CG A:LEU210 4.6 13.8 1.0 CB A:LEU210 4.6 13.7 1.0 N A:PRO500 4.7 16.1 1.0 H42 A:FPP601 4.7 32.0 1.0 CG A:TRP165 4.8 25.6 1.0 CG A:GLU169 4.8 20.7 1.0 CE2 A:TRP165 4.8 27.4 1.0 CD1 A:PHE248 4.9 12.5 1.0

Magnesium binding site 2 out of 2 in the Drimenyl Diphosphate Synthase D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (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 D303E From Streptomyces Showdoensis in Complex with Farnesyl Diphosphate (Fpp) and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:32.9 occ:1.00 OE1 A:GLU169 2.5 27.6 1.0 O3B A:FPP601 2.7 25.6 1.0 O1A A:FPP601 2.8 28.3 1.0 CD A:GLU169 3.3 26.1 1.0 OE2 A:GLU169 3.5 26.5 1.0 PA A:FPP601 3.6 26.0 1.0 MG A:MG602 3.6 28.9 1.0 CG A:PRO500 3.6 19.6 1.0 CB A:PRO500 3.7 19.0 1.0 CD1 A:LEU166 3.7 25.1 1.0 O2A A:FPP601 3.9 30.1 1.0 PB A:FPP601 3.9 26.5 1.0 O3A A:FPP601 3.9 26.8 1.0 NH1 A:ARG132 4.0 27.8 1.0 CE A:MET136 4.1 22.9 1.0 SD A:MET136 4.4 30.1 1.0 CA A:PRO500 4.4 16.8 1.0 O1B A:FPP601 4.7 27.2 1.0 CG A:GLU169 4.7 20.7 1.0 CD A:PRO500 4.8 17.5 1.0 CG A:LEU166 4.8 30.3 1.0 CB A:LEU166 4.8 30.8 1.0 NE2 A:GLN163 4.9 24.4 1.0 CE A:LYS133 5.0 25.8 1.0 CB A:GLU169 5.0 20.4 1.0 CD1 A:TRP165 5.0 24.8 1.0 O2B A:FPP601 5.0 18.4 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