Magnesium in PDB 5xk9: Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp

The structure of Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp, PDB code: 5xk9 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)	24.78 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	120.955, 68.774, 129.465, 90.00, 90.08, 90.00
R / Rfree (%)	23.3 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp (pdb code 5xk9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp, PDB code: 5xk9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and 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 Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:41.0 occ:1.00 O2A A:DMA502 1.9 40.7 0.5 O1A A:GST501 2.1 39.7 1.0 O1A A:DMA502 2.1 40.7 0.5 OD1 A:ASP9 2.1 38.5 1.0 O3B A:GST501 2.2 37.0 1.0 CG A:ASP9 3.1 36.8 1.0 PA A:GST501 3.1 38.4 1.0 PB A:GST501 3.2 38.6 1.0 PA A:DMA502 3.4 41.5 0.5 OD2 A:ASP9 3.4 37.2 1.0 PA A:DMA502 3.5 40.3 0.5 O1B A:GST501 3.5 38.9 1.0 O3A A:GST501 3.6 38.1 1.0 S1 A:GST501 3.9 40.0 1.0 O1A A:DMA502 4.0 41.0 0.5 C1 A:GST501 4.0 41.6 1.0 O1 A:DMA502 4.0 42.0 1.0 NH2 A:ARG13 4.2 36.9 1.0 N A:GLY10 4.3 32.6 1.0 O3A A:DMA502 4.3 41.0 0.5 O2A A:GST501 4.4 37.1 1.0 O3A A:DMA502 4.4 41.0 0.5 CB A:ASP9 4.5 34.8 1.0 O2A A:DMA502 4.5 41.1 0.5 O2B A:GST501 4.6 38.7 1.0 NH1 A:ARG12 4.6 47.1 1.0 CA A:ASP9 4.8 33.0 1.0 NH2 A:ARG60 4.8 47.3 1.0 C2 A:GST501 4.9 42.3 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and 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 Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:40.5 occ:1.00 O A:HOH613 2.0 39.1 1.0 O2A B:GST501 2.1 39.5 1.0 O2B B:GST501 2.2 42.5 1.0 OD1 B:ASP9 2.2 28.9 1.0 O1A B:DMA502 2.4 50.4 1.0 O A:HOH626 2.6 47.5 1.0 CG B:ASP9 3.1 29.9 1.0 PA B:GST501 3.3 38.5 1.0 OD2 B:ASP9 3.3 29.5 1.0 PB B:GST501 3.4 43.2 1.0 NH1 A:ARG211 3.6 51.1 1.0 O1A B:GST501 3.6 39.7 1.0 O1B B:DMA502 3.7 48.3 1.0 O B:HOH655 3.7 35.5 1.0 O1B B:GST501 3.7 40.3 1.0 PA B:DMA502 3.8 52.1 1.0 C1 B:DMA502 4.2 53.4 1.0 S1 B:GST501 4.2 45.2 1.0 NH1 B:ARG13 4.2 32.7 1.0 C1 B:GST501 4.4 46.9 1.0 O1 B:DMA502 4.4 52.8 1.0 N B:GLY10 4.5 28.0 1.0 CB B:ASP9 4.5 30.9 1.0 O3A B:GST501 4.5 36.9 1.0 CZ A:ARG211 4.5 51.0 1.0 NE A:ARG211 4.6 50.9 1.0 PB B:DMA502 4.6 49.9 1.0 O3B B:GST501 4.6 45.4 1.0 C2 B:GST501 4.6 47.5 1.0 O3A B:DMA502 4.6 50.8 1.0 NH2 B:ARG163 4.7 25.6 1.0 O2A B:DMA502 4.8 52.8 1.0 O2B B:DMA502 4.8 49.5 1.0 NH2 B:ARG60 4.9 41.2 1.0 CA B:ASP9 5.0 30.3 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and 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 Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg500 b:31.4 occ:1.00 O3B C:DMA502 2.4 41.4 0.5 OD1 C:ASP9 2.7 33.0 1.0 O1A C:GST501 2.8 38.4 1.0 OD2 C:ASP9 2.9 33.8 1.0 O C:HOH702 3.0 52.4 1.0 CG C:ASP9 3.2 32.5 1.0 O3B C:GST501 3.3 40.2 1.0 ND1 C:HIS167 3.6 32.8 1.0 CE1 C:HIS167 3.7 32.6 1.0 PB C:DMA502 3.8 41.1 0.5 PA C:GST501 4.1 37.4 1.0 NH2 C:ARG163 4.1 21.7 1.0 O2B C:DMA502 4.2 42.1 0.5 NH2 C:ARG13 4.2 28.2 1.0 O1 C:DMA502 4.2 41.3 1.0 NH2 C:ARG169 4.2 28.2 1.0 O2A C:DMA502 4.3 41.7 0.5 O3B C:DMA502 4.4 42.5 0.5 O2A C:GST501 4.4 37.4 1.0 PB C:GST501 4.6 38.4 1.0 O1B C:DMA502 4.7 41.2 0.5 CB C:ASP9 4.7 31.1 1.0 O3A C:DMA502 4.8 41.8 0.5 CG C:HIS167 4.8 31.4 1.0 PA C:DMA502 4.8 42.7 0.5 O1B C:GST501 4.8 40.0 1.0 NE2 C:HIS167 4.9 32.6 1.0 O2B C:DMA502 4.9 41.7 0.5 O C:HOH602 4.9 32.8 1.0 PA C:DMA502 5.0 42.2 0.5

Magnesium binding site 4 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and 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 Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg500 b:32.1 occ:1.00 O2B D:GST501 2.0 32.4 1.0 O2A D:GST501 2.1 31.1 1.0 O2A D:DMA502 2.1 30.2 1.0 OD1 D:ASP9 2.2 30.4 1.0 O D:HOH602 2.3 20.8 1.0 O D:HOH609 2.5 32.7 1.0 PA D:GST501 3.1 31.6 1.0 PB D:GST501 3.2 34.5 1.0 CG D:ASP9 3.3 31.9 1.0 O3A D:GST501 3.4 33.7 1.0 O1B D:GST501 3.6 33.0 1.0 PA D:DMA502 3.6 29.2 1.0 OD2 D:ASP9 3.6 32.2 1.0 NH1 C:ARG211 3.9 28.7 1.0 O3B D:DMA502 4.0 26.5 1.0 S1 D:GST501 4.0 36.6 1.0 NH2 D:ARG60 4.2 26.6 1.0 C1 D:DMA502 4.2 33.4 1.0 O D:HOH611 4.2 28.9 1.0 O1 D:DMA502 4.3 31.4 1.0 N D:GLY10 4.4 28.3 1.0 O3A D:DMA502 4.4 28.9 1.0 O1A D:GST501 4.4 30.5 1.0 O3B D:GST501 4.5 34.8 1.0 O1A D:DMA502 4.5 28.8 1.0 NH1 D:ARG13 4.5 28.8 1.0 NE C:ARG211 4.5 30.9 1.0 PB D:DMA502 4.6 27.4 1.0 CB D:ASP9 4.6 31.1 1.0 CZ C:ARG211 4.7 30.3 1.0 O2B D:DMA502 4.7 28.2 1.0 C2 D:GST501 4.7 38.6 1.0 C1 D:GST501 4.8 38.9 1.0 CA D:ASP9 4.9 30.6 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg500 b:40.8 occ:1.00 O2A E:DMA502 2.0 41.2 0.5 O1A E:DMA502 2.1 40.5 0.5 OD1 E:ASP9 2.1 38.9 1.0 O E:HOH662 2.2 40.5 1.0 O3B E:GST501 2.3 36.6 1.0 O1A E:GST501 2.6 36.5 1.0 CG E:ASP9 3.0 37.9 1.0 OD2 E:ASP9 3.2 38.4 1.0 PA E:DMA502 3.4 41.3 0.5 PA E:DMA502 3.5 41.5 0.5 PB E:GST501 3.5 38.0 1.0 PA E:GST501 3.6 37.7 1.0 O3A E:DMA502 3.9 41.2 0.5 O3A E:GST501 4.0 38.5 1.0 O1B E:GST501 4.0 38.7 1.0 O3A E:DMA502 4.0 41.1 0.5 O1A E:DMA502 4.1 41.1 0.5 C1 E:GST501 4.3 41.0 1.0 O2A E:DMA502 4.3 40.4 0.5 S1 E:GST501 4.3 39.3 1.0 CB E:ASP9 4.4 35.8 1.0 NH2 E:ARG13 4.5 37.2 1.0 C1 E:DMA502 4.5 41.1 1.0 N E:GLY10 4.5 35.1 1.0 O1 E:DMA502 4.6 41.2 1.0 C2 E:DMA502 4.7 41.0 1.0 O2B E:GST501 4.7 38.8 1.0 NH1 E:ARG12 4.8 42.0 1.0 CA E:ASP9 4.8 35.5 1.0 NH2 E:ARG60 4.8 50.3 1.0 NH2 E:ARG163 4.8 29.1 1.0 C2 E:GST501 4.9 41.5 1.0 O2A E:GST501 5.0 36.8 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg500 b:38.8 occ:1.00 O F:HOH619 2.1 39.4 1.0 O F:HOH610 2.2 33.5 1.0 OD1 F:ASP9 2.2 35.4 1.0 O2B F:GST501 2.3 46.1 1.0 O1A F:DMA502 2.3 47.4 1.0 O2A F:GST501 2.3 41.9 1.0 CG F:ASP9 3.1 35.0 1.0 OD2 F:ASP9 3.3 35.1 1.0 PA F:GST501 3.3 42.8 1.0 PB F:GST501 3.4 46.5 1.0 O1A F:GST501 3.5 44.6 1.0 NH1 E:ARG211 3.7 48.7 1.0 PA F:DMA502 3.7 47.5 1.0 O1B F:GST501 3.8 44.8 1.0 O1B F:DMA502 3.8 45.4 1.0 O F:HOH634 3.8 32.5 1.0 C1 F:DMA502 4.0 45.5 1.0 S1 F:GST501 4.2 49.3 1.0 NH1 F:ARG13 4.3 28.6 1.0 O1 F:DMA502 4.3 46.9 1.0 NH1 F:ARG12 4.4 58.3 1.0 O3A F:DMA502 4.4 46.6 1.0 CB F:ASP9 4.5 34.2 1.0 PB F:DMA502 4.5 46.0 1.0 N F:GLY10 4.5 34.1 1.0 CZ E:ARG211 4.6 48.9 1.0 C1 F:GST501 4.6 50.5 1.0 O3B F:GST501 4.7 48.9 1.0 O3A F:GST501 4.7 42.0 1.0 NE E:ARG211 4.7 49.3 1.0 O2B F:DMA502 4.7 45.7 1.0 O2A F:DMA502 4.7 46.0 1.0 C2 F:GST501 4.8 50.7 1.0 NH2 F:ARG60 4.8 37.5 1.0 NH2 F:ARG163 4.8 30.9 1.0 CA F:ASP9 4.9 32.9 1.0 ND1 F:HIS167 5.0 39.2 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg500 b:84.4 occ:1.00 OD1 G:ASP9 2.4 39.1 1.0 O G:HOH652 2.5 34.1 1.0 O3B G:GST501 2.5 39.0 1.0 O3B G:DMA502 2.6 42.4 0.5 O1A G:GST501 2.8 34.5 1.0 CG G:ASP9 3.2 37.4 1.0 OD2 G:ASP9 3.3 38.5 1.0 O1 G:DMA502 3.5 45.0 1.0 PA G:GST501 3.8 33.8 1.0 PB G:GST501 3.9 37.7 1.0 O2A G:GST501 4.0 33.2 1.0 PB G:DMA502 4.0 41.2 0.5 O1B G:GST501 4.3 37.1 1.0 PA G:DMA502 4.4 44.9 0.5 O2A G:DMA502 4.4 43.1 0.5 NH2 G:ARG163 4.4 19.4 1.0 NH2 G:ARG13 4.4 29.4 1.0 O3A G:DMA502 4.5 43.5 0.5 C1 G:DMA502 4.5 44.8 1.0 ND1 G:HIS167 4.5 36.9 1.0 PA G:DMA502 4.5 44.5 0.5 O2B G:DMA502 4.5 42.6 0.5 O1A G:DMA502 4.5 43.5 0.5 CE1 G:HIS167 4.5 36.9 1.0 O3B G:DMA502 4.6 42.9 0.5 C1 G:GST501 4.6 37.0 1.0 C2 G:DMA502 4.6 44.8 1.0 O2B G:DMA502 4.6 42.8 0.5 CB G:ASP9 4.7 34.9 1.0 O3A G:DMA502 4.8 43.4 0.5 PB G:DMA502 4.8 43.7 0.5 S1 G:GST501 4.8 35.9 1.0 N G:GLY10 4.9 29.0 1.0 O2B G:GST501 5.0 40.0 1.0 NH2 G:ARG169 5.0 30.6 1.0 O1B G:DMA502 5.0 36.9 0.5

Magnesium binding site 8 out of 8 in the Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Isosesquilavandulyl Diphosphate Synthase From Streptomyces Sp. Strain Cnh-189 in Complex with Gspp and Dmapp within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg500 b:35.4 occ:1.00 O2B H:GST501 2.1 36.3 1.0 O H:HOH613 2.1 33.9 1.0 O2A H:GST501 2.2 32.2 1.0 O2A H:DMA502 2.2 31.7 1.0 O H:HOH624 2.4 31.7 1.0 OD1 H:ASP9 2.4 27.8 1.0 PA H:GST501 3.2 32.2 1.0 PB H:GST501 3.3 36.8 1.0 O3A H:GST501 3.4 33.4 1.0 CG H:ASP9 3.4 28.4 1.0 PA H:DMA502 3.7 32.2 1.0 OD2 H:ASP9 3.7 28.6 1.0 NH1 G:ARG211 3.7 36.7 1.0 O1B H:GST501 3.7 34.9 1.0 O3B H:DMA502 3.8 29.2 1.0 O H:HOH607 3.9 20.4 1.0 NH2 H:ARG60 4.1 23.0 1.0 C1 H:DMA502 4.2 35.3 1.0 S1 H:GST501 4.2 39.3 1.0 O3A H:DMA502 4.3 31.7 1.0 NE G:ARG211 4.4 34.2 1.0 O1 H:DMA502 4.4 34.4 1.0 NH1 H:ARG13 4.4 26.8 1.0 PB H:DMA502 4.5 28.8 1.0 CZ G:ARG211 4.5 36.4 1.0 O1A H:GST501 4.5 33.0 1.0 O3B H:GST501 4.5 37.9 1.0 O2B H:DMA502 4.6 28.3 1.0 N H:GLY10 4.6 29.7 1.0 O1A H:DMA502 4.7 32.6 1.0 CB H:ASP9 4.8 28.9 1.0 C2 H:GST501 4.9 40.8 1.0 C1 H:GST501 5.0 40.8 1.0 NH2 H:ARG163 5.0 25.7 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