Magnesium in PDB 5xk6: Structure of A Prenyltransferase Soaked with Ipp

The structure of Structure of A Prenyltransferase Soaked with Ipp, PDB code: 5xk6 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)	24.56 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.552, 120.634, 130.077, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.3

The binding sites of Magnesium atom in the Structure of A Prenyltransferase Soaked with Ipp (pdb code 5xk6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of A Prenyltransferase Soaked with Ipp, PDB code: 5xk6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of A Prenyltransferase Soaked with Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Prenyltransferase Soaked with Ipp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:48.2 occ:1.00 O A:HOH621 1.8 48.3 1.0 O2 A:POP501 2.1 47.2 1.0 O A:HOH606 2.2 49.6 1.0 OD1 A:ASP9 2.2 28.0 1.0 O6 A:POP501 2.6 36.1 1.0 CG A:ASP9 3.2 27.4 1.0 O2 A:SO4502 3.3 46.6 1.0 P1 A:POP501 3.4 42.1 1.0 OD2 A:ASP9 3.5 25.7 1.0 P2 A:POP501 3.5 33.1 1.0 O5 A:POP501 3.6 37.9 1.0 O A:POP501 3.9 37.4 1.0 O3 A:POP501 4.0 35.1 1.0 O1 A:SO4502 4.2 40.4 1.0 O A:HOH761 4.3 37.0 1.0 O A:HOH800 4.3 41.0 1.0 S A:SO4502 4.4 42.6 1.0 N A:GLY10 4.5 21.6 1.0 CB A:ASP9 4.5 24.4 1.0 O1 A:POP501 4.6 44.3 1.0 NH1 A:ARG13 4.6 27.0 1.0 CD2 A:HIS167 4.8 23.0 1.0 NE2 A:HIS167 4.8 23.6 1.0 CA A:ASP9 4.8 22.7 1.0 NH2 A:ARG60 4.9 51.1 1.0 O4 A:POP501 4.9 30.4 1.0 NH2 A:ARG163 4.9 17.6 1.0

Magnesium binding site 2 out of 4 in the Structure of A Prenyltransferase Soaked with Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Prenyltransferase Soaked with Ipp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:17.1 occ:1.00 O B:HOH615 2.1 15.3 1.0 O4 B:POP501 2.1 18.2 1.0 OD1 B:ASP9 2.1 15.7 1.0 O2 B:POP501 2.1 18.8 1.0 O B:HOH622 2.1 17.7 1.0 O6 B:POP502 2.2 37.0 1.0 CG B:ASP9 3.1 14.4 1.0 P2 B:POP501 3.2 17.5 1.0 P1 B:POP501 3.2 17.3 1.0 OD2 B:ASP9 3.5 14.6 1.0 O5 B:POP501 3.5 19.1 1.0 O B:POP501 3.6 16.5 1.0 P2 B:POP502 3.7 42.1 1.0 O1 B:POP501 3.8 16.3 1.0 O1 B:POP502 3.9 18.4 1.0 O4 B:POP502 4.1 54.5 1.0 NH2 B:ARG60 4.1 15.4 1.0 NH1 B:ARG13 4.1 17.8 1.0 O B:HOH680 4.1 15.2 1.0 NH2 A:ARG211 4.2 20.9 1.0 O B:HOH613 4.2 40.8 1.0 O B:POP502 4.3 19.1 1.0 N B:GLY10 4.4 15.1 1.0 O6 B:POP501 4.4 17.1 1.0 CB B:ASP9 4.5 15.0 1.0 NE A:ARG211 4.5 20.4 1.0 O3 B:POP501 4.5 19.8 1.0 P1 B:POP502 4.6 13.8 1.0 O B:HOH743 4.7 34.5 1.0 CA B:ASP9 4.8 14.6 1.0 NH2 B:ARG163 4.8 14.1 1.0 O5 B:POP502 4.8 28.1 1.0 CZ A:ARG211 4.8 20.8 1.0 O3 B:POP502 5.0 17.3 1.0

Magnesium binding site 3 out of 4 in the Structure of A Prenyltransferase Soaked with Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Prenyltransferase Soaked with Ipp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg500 b:41.8 occ:1.00 OD1 C:ASP9 2.4 28.1 1.0 O C:HOH612 2.6 43.8 1.0 O2 C:POP501 2.8 44.3 1.0 O6 C:POP501 2.9 28.8 1.0 OD2 C:ASP9 3.0 26.2 1.0 CG C:ASP9 3.1 25.0 1.0 O3 C:SO4502 3.1 46.0 1.0 O C:HOH713 3.6 32.6 1.0 CD2 C:HIS167 3.9 17.1 1.0 P2 C:POP501 3.9 25.6 1.0 O4 C:POP501 4.0 34.3 1.0 O C:HOH615 4.0 39.7 1.0 NE2 C:HIS167 4.0 17.9 1.0 S C:SO4502 4.1 36.0 1.0 O4 C:SO4502 4.1 32.0 1.0 P1 C:POP501 4.1 40.3 1.0 O C:HOH833 4.2 40.0 1.0 NH1 C:ARG12 4.2 60.9 1.0 O2 C:SO4502 4.3 41.3 1.0 NH1 C:ARG13 4.4 23.5 1.0 NH2 C:ARG163 4.4 17.7 1.0 O C:POP501 4.5 29.9 1.0 CB C:ASP9 4.6 19.9 1.0 O C:HOH842 4.7 30.9 1.0 O3 C:POP501 4.8 34.8 1.0 NH1 C:ARG169 4.9 17.6 1.0 N C:GLY10 4.9 18.8 1.0

Magnesium binding site 4 out of 4 in the Structure of A Prenyltransferase Soaked with Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Prenyltransferase Soaked with Ipp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg500 b:15.7 occ:1.00 O4 D:POP501 2.0 16.5 1.0 O1 D:POP501 2.0 16.1 1.0 OD1 D:ASP9 2.1 14.8 1.0 O D:HOH627 2.1 17.1 1.0 O D:HOH615 2.1 14.6 1.0 O6 D:POP502 2.2 21.7 1.0 CG D:ASP9 3.1 14.2 1.0 P2 D:POP501 3.1 16.8 1.0 P1 D:POP501 3.2 15.8 1.0 OD2 D:ASP9 3.5 14.6 1.0 O5 D:POP501 3.5 17.5 1.0 O D:POP501 3.5 17.1 1.0 P2 D:POP502 3.7 30.5 1.0 O2 D:POP501 3.7 14.4 1.0 O3 D:POP502 3.9 18.8 1.0 O D:HOH626 3.9 36.3 1.0 NH1 D:ARG60 4.1 15.2 1.0 O D:HOH652 4.1 14.6 1.0 O5 D:POP502 4.1 40.9 1.0 NH1 C:ARG211 4.2 18.8 1.0 NH1 D:ARG13 4.2 15.2 1.0 O D:POP502 4.3 17.7 1.0 N D:GLY10 4.4 14.6 1.0 O6 D:POP501 4.4 17.5 1.0 CB D:ASP9 4.5 12.8 1.0 O3 D:POP501 4.5 18.3 1.0 NE C:ARG211 4.5 19.2 1.0 P1 D:POP502 4.6 13.1 1.0 O D:HOH713 4.7 43.8 1.0 CA D:ASP9 4.7 13.6 1.0 NH2 D:ARG163 4.8 14.5 1.0 O4 D:POP502 4.8 18.3 1.0 CZ C:ARG211 4.9 19.0 1.0 O2 D:POP502 4.9 15.5 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