Magnesium in PDB 7xru: Drimenyl Diphosphate Synthase D303E From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+

The structure of Drimenyl Diphosphate Synthase D303E From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+, PDB code: 7xru 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)	30.51 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	51.35, 113.78, 179.81, 90, 90, 90
R / Rfree (%)	18.6 / 23.1

The structure of Drimenyl Diphosphate Synthase D303E 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 D303E From Streptomyces Showdoensis in Complex with 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+ (pdb code 7xru). 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 2-Fluorofarnesyl Diphosphate (2F-Fpp) and MG2+, PDB code: 7xru:
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 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 D303E 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:52.2 occ:1.00 O A:HOH703 2.3 64.4 1.0 OE2 A:GLU169 2.6 36.7 1.0 O3A A:2CF601 2.6 47.8 1.0 ND2 A:ASN208 3.2 28.9 1.0 CD A:GLU169 3.5 36.7 1.0 CE1 A:PHE248 3.7 25.1 1.0 PA A:2CF601 3.7 48.4 1.0 OE1 A:GLU169 3.7 39.9 1.0 OD1 A:ASN208 3.7 27.6 1.0 MG A:MG603 3.8 44.7 1.0 O1A A:2CF601 3.8 47.9 1.0 CZ A:PHE248 3.8 28.9 1.0 CD1 A:TRP165 3.9 37.6 1.0 CD2 A:LEU210 3.9 31.0 1.0 CG A:ASN208 3.9 25.9 1.0 H4 A:2CF601 3.9 54.2 1.0 CD A:PRO500 4.2 32.7 1.0 NE1 A:TRP165 4.4 42.5 1.0 O2A A:2CF601 4.4 46.5 1.0 CB A:LEU210 4.6 23.6 1.0 CG A:LEU210 4.6 31.3 1.0 CG A:PRO500 4.6 32.5 1.0 N A:PRO500 4.7 29.4 1.0 CB A:PRO500 4.7 38.2 1.0 CG A:TRP165 4.8 31.6 1.0 C4 A:2CF601 4.9 45.2 1.0 CG A:GLU169 4.9 29.5 1.0 CD1 A:PHE248 4.9 26.6 1.0 C15 A:2CF601 4.9 49.0 1.0 H15A A:2CF601 5.0 58.8 1.0 OB4 A:2CF601 5.0 46.8 1.0

Magnesium binding site 2 out of 2 in the Drimenyl Diphosphate Synthase D303E 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 D303E 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:44.7 occ:1.00 O3A A:2CF601 2.3 47.8 1.0 OB3 A:2CF601 2.5 55.7 1.0 OE1 A:GLU169 2.6 39.9 1.0 PA A:2CF601 3.4 48.4 1.0 CB A:PRO500 3.5 38.2 1.0 PB A:2CF601 3.6 53.8 1.0 CD A:GLU169 3.6 36.7 1.0 OB4 A:2CF601 3.7 46.8 1.0 MG A:MG602 3.8 52.2 1.0 CE A:MET136 3.8 33.5 1.0 CD1 A:LEU166 3.9 40.6 1.0 OE2 A:GLU169 4.0 36.7 1.0 NH1 A:ARG132 4.0 44.9 1.0 O2A A:2CF601 4.0 46.5 1.0 SD A:MET136 4.1 52.6 1.0 O A:HOH703 4.2 64.4 1.0 CG A:PRO500 4.2 32.5 1.0 OB1 A:2CF601 4.3 52.3 1.0 CA A:PRO500 4.6 37.6 1.0 O1A A:2CF601 4.7 47.9 1.0 CE A:LYS133 4.8 40.1 1.0 OB2 A:2CF601 4.9 40.9 1.0 NE2 A:GLN163 4.9 33.1 1.0 CD A:PRO500 5.0 32.7 1.0 CG A:GLU169 5.0 29.5 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