Magnesium in PDB 6wkd: Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate:
4.2.3.7;

The structure of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate, PDB code: 6wkd was solved by R.Prem Kumar, J.O.Matos, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	182.467, 182.467, 56.212, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 22

The structure of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate (pdb code 6wkd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate, PDB code: 6wkd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:69.3 occ:1.00 O A:HOH641 2.5 65.9 1.0 OD2 A:ASP80 2.5 54.4 1.0 O A:HOH504 2.9 60.7 1.0 OD1 A:ASP84 3.1 64.4 1.0 NH2 A:ARG314 3.5 69.5 1.0 OD2 A:ASP84 3.6 66.7 1.0 CG A:ASP80 3.7 46.7 1.0 O3A A:FDF401 3.7 74.1 1.0 CG A:ASP84 3.7 59.9 1.0 O A:HOH502 3.8 50.8 1.0 O A:HOH526 4.0 53.8 1.0 O1B A:FDF401 4.1 75.6 1.0 O A:HOH614 4.2 61.9 1.0 O A:ASP80 4.4 39.8 1.0 OD2 A:ASP81 4.4 58.7 1.0 OD1 A:ASP80 4.4 48.0 1.0 O2A A:FDF401 4.5 70.5 1.0 CB A:ASP80 4.6 36.7 1.0 PB A:FDF401 4.6 82.7 1.0 C A:ASP80 4.7 40.3 1.0 PA A:FDF401 4.7 74.3 1.0 CZ A:ARG314 4.8 68.4 1.0 O A:HOH647 4.9 65.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:74.7 occ:1.00 O1A A:FDF401 2.5 64.1 1.0 OD1 A:ASN219 2.5 60.1 1.0 OG A:SER223 2.8 69.2 1.0 CB A:SER223 3.0 67.0 1.0 O3B A:FDF401 3.1 73.8 1.0 O A:HOH632 3.4 71.8 1.0 CG A:ASN219 3.6 58.6 1.0 PA A:FDF401 3.8 74.3 1.0 OD1 A:ASP220 3.8 56.1 1.0 O1 A:FDF401 4.0 69.7 1.0 ND2 A:ASN219 4.1 62.1 1.0 O A:ASN219 4.1 54.7 1.0 NH2 A:ARG173 4.3 54.2 1.0 PB A:FDF401 4.4 82.7 1.0 C A:ASN219 4.4 57.0 1.0 O3A A:FDF401 4.5 74.1 1.0 CA A:ASP220 4.5 55.5 1.0 CA A:SER223 4.6 68.7 1.0 N A:ASP220 4.6 49.4 1.0 CB A:ASN219 4.7 51.2 1.0 ND2 A:ASN235 4.8 61.0 1.0 CG A:ASP220 4.9 56.1 1.0 O2A A:FDF401 4.9 70.5 1.0

J.O.Matos, R.P.Kumar, A.C.Ma, M.Patterson, I.J.Krauss, D.D.Oprian. Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase. Biochemistry V. 59 3271 2020.
ISSN: ISSN 0006-2960
PubMed: 32786410
DOI: 10.1021/ACS.BIOCHEM.0C00518