Magnesium in PDB 5gul: Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190

The structure of Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190, PDB code: 5gul was solved by T.Tomita, M.Kobayashi, M.Nishiyama, T.Kuzuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.04 / 1.73
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.851, 61.661, 82.242, 74.00, 84.54, 86.04
R / Rfree (%)	21.6 / 27.8

The binding sites of Magnesium atom in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 (pdb code 5gul). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190, PDB code: 5gul:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


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 Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:30.1 occ:1.00 O2 A:POP301 2.0 25.5 1.0 O2 A:POP302 2.0 26.1 1.0 O4 A:POP302 2.1 33.4 1.0 O A:HOH421 2.1 30.5 1.0 OD1 A:ASP9 2.2 27.7 1.0 O A:HOH401 2.4 26.1 1.0 P1 A:POP302 3.1 26.2 1.0 P2 A:POP302 3.2 29.4 1.0 CG A:ASP9 3.2 29.3 1.0 O6 A:POP302 3.4 30.2 1.0 P1 A:POP301 3.4 29.1 1.0 O A:POP302 3.5 26.1 1.0 OD2 A:ASP9 3.6 29.8 1.0 O3 A:POP302 3.7 25.5 1.0 O3 A:TRS304 3.8 28.3 1.0 O5 A:POP301 3.8 30.3 1.0 O3 A:POP301 3.9 30.9 1.0 NH2 A:ARG60 4.0 29.2 1.0 O B:HOH425 4.0 26.9 1.0 NH2 A:ARG13 4.1 28.6 1.0 O A:POP301 4.2 27.2 1.0 C3 A:TRS304 4.4 26.9 1.0 NE B:ARG211 4.4 34.4 1.0 N A:GLY10 4.4 27.3 1.0 NH2 B:ARG211 4.4 35.3 1.0 O1 A:POP302 4.5 26.6 1.0 O1 A:POP301 4.5 32.4 1.0 CB A:ASP9 4.5 29.7 1.0 P2 A:POP301 4.5 27.7 1.0 O5 A:POP302 4.6 31.0 1.0 O4 A:POP301 4.9 25.4 1.0 CZ B:ARG211 4.9 36.8 1.0 NH2 A:ARG163 4.9 27.6 1.0 CA A:ASP9 4.9 28.8 1.0 CA A:GLY10 5.0 27.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


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 Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:28.6 occ:1.00 O4 B:POP302 2.0 27.8 1.0 O5 B:POP301 2.0 30.0 1.0 OD1 B:ASP9 2.1 30.5 1.0 O2 B:POP302 2.1 34.3 1.0 O B:HOH406 2.1 28.5 1.0 O B:HOH419 2.2 27.4 1.0 CG B:ASP9 3.1 28.4 1.0 P2 B:POP302 3.2 30.6 1.0 P1 B:POP302 3.2 31.7 1.0 P2 B:POP301 3.4 28.8 1.0 OD2 B:ASP9 3.4 30.2 1.0 O1 B:POP302 3.6 26.5 1.0 O B:POP302 3.6 32.6 1.0 O3 B:TRS304 3.7 28.0 1.0 O5 B:POP302 3.8 27.9 1.0 O6 B:POP301 3.8 28.3 1.0 NH2 B:ARG60 3.8 26.2 1.0 O B:HOH408 3.9 28.8 1.0 O2 B:POP301 4.0 29.1 1.0 O B:POP301 4.1 30.6 1.0 NH2 B:ARG13 4.1 30.5 1.0 N B:GLY10 4.4 27.5 1.0 O4 B:POP301 4.4 29.2 1.0 C3 B:TRS304 4.4 28.3 1.0 CB B:ASP9 4.4 28.5 1.0 O6 B:POP302 4.5 26.7 1.0 O3 B:POP302 4.5 30.5 1.0 P1 B:POP301 4.5 28.3 1.0 NE A:ARG211 4.6 32.2 1.0 NH2 A:ARG211 4.6 32.9 1.0 NH2 B:ARG163 4.8 35.0 1.0 CA B:ASP9 4.9 28.8 1.0 O1 B:POP301 4.9 27.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:32.5 occ:1.00 O C:HOH402 1.9 34.0 1.0 O6 C:POP301 2.1 30.2 1.0 O2 C:POP301 2.1 32.8 1.0 O4 C:POP302 2.1 29.8 1.0 OD1 C:ASP9 2.2 33.1 1.0 O C:HOH416 2.3 35.1 1.0 CG C:ASP9 3.1 29.7 1.0 P1 C:POP301 3.2 35.5 1.0 P2 C:POP301 3.3 31.9 1.0 P2 C:POP302 3.5 30.1 1.0 OD2 C:ASP9 3.5 33.1 1.0 O3 C:POP301 3.6 36.4 1.0 O C:POP301 3.6 32.1 1.0 O5 C:POP301 3.8 29.2 1.0 O5 C:POP302 3.8 31.7 1.0 O1 C:POP302 3.8 35.6 1.0 O1 C:TRS304 3.8 32.1 1.0 O C:HOH405 4.0 27.8 1.0 NH2 C:ARG60 4.1 33.1 1.0 O C:POP302 4.2 32.8 1.0 NH2 C:ARG13 4.3 36.2 1.0 N C:GLY10 4.3 35.2 1.0 C1 C:TRS304 4.4 32.2 1.0 NE D:ARG211 4.4 35.6 1.0 NH2 D:ARG211 4.5 31.4 1.0 CB C:ASP9 4.5 32.7 1.0 O1 C:POP301 4.5 39.1 1.0 O6 C:POP302 4.5 31.8 1.0 O4 C:POP301 4.6 27.4 1.0 P1 C:POP302 4.6 32.3 1.0 O3 C:POP302 4.8 29.4 1.0 CA C:ASP9 4.9 34.2 1.0 CZ D:ARG211 4.9 34.7 1.0 NH2 C:ARG163 4.9 31.4 1.0 CA C:GLY10 5.0 33.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:42.9 occ:1.00 O C:HOH413 2.0 46.2 1.0 O6 D:POP302 2.0 44.7 1.0 O6 D:POP301 2.1 43.1 1.0 O D:HOH407 2.2 41.7 1.0 OD1 D:ASP9 2.2 37.2 1.0 O1 D:POP301 2.3 51.7 1.0 O2 D:POP301 3.0 41.0 1.0 P1 D:POP301 3.1 50.8 1.0 CG D:ASP9 3.3 43.6 1.0 P2 D:POP301 3.4 43.7 1.0 P2 D:POP302 3.5 43.9 1.0 O D:POP301 3.6 44.6 1.0 NH2 D:ARG60 3.7 44.1 1.0 OD2 D:ASP9 3.7 46.5 1.0 O3 D:POP302 3.7 50.4 1.0 O1 D:TRS304 4.0 39.9 1.0 O4 D:POP302 4.0 35.6 1.0 NE C:ARG211 4.0 43.2 1.0 O D:POP302 4.2 44.3 1.0 O4 D:POP301 4.2 36.2 1.0 NH2 D:ARG13 4.2 58.8 1.0 NH2 C:ARG211 4.4 41.3 1.0 O5 D:POP301 4.5 47.1 1.0 O3 D:POP301 4.5 61.5 1.0 O5 D:POP302 4.5 42.6 1.0 P1 D:POP302 4.6 41.8 1.0 C1 D:TRS304 4.6 43.0 1.0 CB D:ASP9 4.7 41.7 1.0 CZ C:ARG211 4.7 47.8 1.0 O2 D:POP302 4.8 40.5 1.0 N D:GLY10 4.9 51.4 1.0 CZ D:ARG60 4.9 43.6 1.0 CD C:ARG211 4.9 43.4 1.0

T.Tomita, M.Kobayashi, Y.Karita, Y.Yasuno, T.Shinada, M.Nishiyama, T.Kuzuyama. Structure and Mechanism of the Monoterpene Cyclolavandulyl Diphosphate Synthase That Catalyzes Consecutive Condensation and Cyclization. Angew. Chem. Int. Ed. Engl. V. 56 14913 2017.
ISSN: ESSN 1521-3773
PubMed: 28922556
DOI: 10.1002/ANIE.201708474