Magnesium in PDB 5xk7: Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp

The structure of Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp, PDB code: 5xk7 was solved by T.P.Ko, R.T.Guo, W.Liu, C.C.Chen, J.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.73 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.924, 120.653, 126.327, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp (pdb code 5xk7). 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 Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp, PDB code: 5xk7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp


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 Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:65.9 occ:1.00 OD1 A:ASP9 2.5 40.9 1.0 O1 A:POP303 2.7 49.1 1.0 O6 A:POP302 2.8 80.4 1.0 O4 A:POP303 3.1 50.3 0.5 OD2 A:ASP9 3.2 40.7 1.0 CG A:ASP9 3.2 39.0 1.0 O3 A:POP303 3.3 55.7 1.0 O2 A:POP302 3.4 82.9 1.0 P1 A:POP303 3.6 48.5 1.0 CD2 A:HIS167 3.9 43.6 1.0 NE2 A:HIS167 4.0 43.8 1.0 P2 A:POP302 4.1 79.3 1.0 NH2 A:ARG163 4.2 29.0 1.0 P2 A:POP303 4.2 50.4 0.5 NH2 A:ARG169 4.2 40.1 1.0 O5 A:POP302 4.2 80.4 1.0 O A:POP303 4.4 51.5 1.0 NH1 A:ARG13 4.5 46.1 1.0 O6 A:POP303 4.5 48.9 0.5 P1 A:POP302 4.6 82.0 1.0 CB A:ASP9 4.7 35.6 1.0 O2 A:POP303 4.7 49.8 1.0 O A:POP302 4.7 81.9 1.0 O3 A:POP302 4.9 80.8 1.0 CG A:HIS167 5.0 40.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp


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 Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:32.6 occ:1.00 O1A B:DMA303 2.0 34.9 1.0 O2 B:POP302 2.1 30.6 1.0 O B:HOH411 2.1 31.8 1.0 OD2 B:ASP9 2.1 27.4 1.0 O4 B:POP302 2.2 33.2 1.0 O B:HOH489 2.2 33.0 1.0 CG B:ASP9 3.2 28.3 1.0 P1 B:POP302 3.3 34.6 1.0 P2 B:POP302 3.3 34.3 1.0 PA B:DMA303 3.5 34.4 1.0 OD1 B:ASP9 3.5 26.9 1.0 O5 B:POP302 3.7 32.4 1.0 O B:POP302 3.7 35.9 1.0 O1 B:POP302 3.8 33.3 1.0 O1B B:DMA303 3.9 35.2 1.0 NH2 B:ARG60 4.0 34.3 1.0 C1 B:DMA303 4.0 40.6 1.0 O B:HOH445 4.1 27.9 1.0 O1 B:DMA303 4.1 39.3 1.0 O B:HOH429 4.2 37.9 1.0 NH2 A:ARG211 4.3 33.2 1.0 NH1 B:ARG13 4.4 32.0 1.0 O2A B:DMA303 4.4 35.7 1.0 O3A B:DMA303 4.4 36.6 1.0 N B:GLY10 4.4 29.3 1.0 CB B:ASP9 4.5 29.8 1.0 O3 B:POP302 4.5 34.2 1.0 O6 B:POP302 4.6 27.1 1.0 PB B:DMA303 4.6 34.6 1.0 NE A:ARG211 4.7 34.7 1.0 NH2 B:ARG163 4.7 23.8 1.0 CA B:ASP9 4.8 30.6 1.0 C2 B:DMA303 4.8 39.4 1.0 O3B B:DMA303 4.8 36.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp


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 Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:56.5 occ:1.00 O C:HOH513 2.1 50.9 1.0 O2 C:POP302 2.1 56.0 1.0 O6 C:POP302 2.2 56.6 1.0 O C:HOH528 2.3 44.7 1.0 O2A C:DMA303 2.4 62.1 1.0 OD1 C:ASP9 2.4 39.6 1.0 P2 C:POP302 3.3 56.6 1.0 P1 C:POP302 3.3 59.3 1.0 CG C:ASP9 3.4 37.4 1.0 O C:POP302 3.6 57.7 1.0 OD2 C:ASP9 3.7 38.0 1.0 O4 C:POP302 3.7 59.4 1.0 PA C:DMA303 3.8 62.1 1.0 O3 C:POP302 3.9 59.0 1.0 O1B C:DMA303 4.2 51.9 1.0 O C:HOH459 4.2 63.2 1.0 O C:HOH452 4.2 46.8 1.0 O3A C:DMA303 4.3 54.6 1.0 C1 C:DMA303 4.3 60.8 1.0 O3B C:DMA303 4.3 50.7 1.0 O1 C:POP302 4.5 62.3 1.0 PB C:DMA303 4.5 50.6 1.0 O5 C:POP302 4.6 55.0 1.0 N C:GLY10 4.6 35.7 1.0 O1 C:DMA303 4.6 63.3 1.0 NH1 C:ARG13 4.7 43.4 1.0 CB C:ASP9 4.8 36.5 1.0 O C:HOH470 4.8 55.2 1.0 O1A C:DMA303 4.8 63.4 1.0 C2 C:DMA303 4.9 58.2 1.0 NH2 C:ARG60 4.9 63.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp


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 Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:26.8 occ:1.00 O1 D:POP302 2.0 28.9 1.0 O2A D:DMA303 2.0 29.2 1.0 OD1 D:ASP9 2.1 26.2 1.0 O D:HOH432 2.1 29.3 1.0 O4 D:POP302 2.1 26.3 1.0 O D:HOH405 2.2 24.5 1.0 CG D:ASP9 3.1 25.4 1.0 P2 D:POP302 3.2 27.8 1.0 P1 D:POP302 3.2 27.8 1.0 PA D:DMA303 3.5 30.9 1.0 OD2 D:ASP9 3.5 26.5 1.0 O5 D:POP302 3.6 27.1 1.0 O D:POP302 3.6 29.5 1.0 O2 D:POP302 3.8 26.9 1.0 O2B D:DMA303 3.8 30.9 1.0 NH1 D:ARG60 4.0 31.8 1.0 C1 D:DMA303 4.1 35.5 1.0 O C:HOH442 4.1 29.0 1.0 O1 D:DMA303 4.2 33.4 1.0 NH1 C:ARG211 4.2 34.3 1.0 NH1 D:ARG13 4.3 26.2 1.0 O3A D:DMA303 4.4 33.1 1.0 N D:GLY10 4.4 26.6 1.0 O3 D:POP302 4.4 29.0 1.0 O1A D:DMA303 4.5 29.3 1.0 CB D:ASP9 4.5 25.2 1.0 O D:HOH471 4.5 43.4 1.0 O6 D:POP302 4.5 28.2 1.0 PB D:DMA303 4.6 29.2 1.0 NE C:ARG211 4.6 34.1 1.0 CA D:ASP9 4.8 26.0 1.0 NH2 D:ARG163 4.8 22.4 1.0 C2 D:DMA303 4.8 36.6 1.0 O3B D:DMA303 4.8 29.6 1.0 CZ C:ARG211 4.9 33.5 1.0

J.Gao, T.P.Ko, L.Chen, S.R.Malwal, J.Zhang, X.Hu, F.Qu, W.Liu, J.W.Huang, Y.S.Cheng, C.C.Chen, Y.Yang, Y.Zhang, E.Oldfield, R.T.Guo. "Head-to-Middle" and "Head-to-Tail" Cis-Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase. Angew. Chem. Int. Ed. Engl. V. 57 683 2018.
ISSN: ESSN 1521-3773
PubMed: 29215779
DOI: 10.1002/ANIE.201710185