Magnesium in PDB 7vq9: Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate

The structure of Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate, PDB code: 7vq9 was solved by L.L.Zhang, C.C.Chen, W.D.Liu, J.W.Huang, X.W.Zhang, B.B.Liu, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.88 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.899, 81.308, 60.023, 90, 103.46, 90
R / Rfree (%)	14.2 / 18.5

The binding sites of Magnesium atom in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate (pdb code 7vq9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate, PDB code: 7vq9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:17.1 occ:1.00 O7 A:ISY301 1.9 19.8 1.0 O A:HOH447 2.0 17.1 1.0 O2A A:FPS302 2.1 16.5 1.0 O1B A:FPS302 2.1 15.7 1.0 O A:HOH426 2.1 13.9 1.0 OD1 A:ASP23 2.1 14.5 1.0 CG A:ASP23 3.1 14.7 1.0 PB A:FPS302 3.2 16.7 1.0 PA A:FPS302 3.3 16.6 1.0 P3 A:ISY301 3.4 23.3 1.0 OD2 A:ASP23 3.4 15.1 1.0 O3A A:FPS302 3.6 15.5 1.0 O2B A:FPS302 3.6 16.2 1.0 S9 A:ISY301 4.0 30.1 1.0 O6 A:ISY301 4.0 27.6 1.0 NH2 A:ARG74 4.0 22.2 1.0 O A:HOH540 4.1 30.2 1.0 NH2 A:ARG27 4.2 18.7 1.0 S1 A:FPS302 4.2 17.1 1.0 O2 A:ISY301 4.3 27.9 1.0 O8 A:ISY301 4.4 28.2 1.0 O3B A:FPS302 4.5 14.8 1.0 CB A:ASP23 4.5 13.3 1.0 O1A A:FPS302 4.5 15.4 1.0 C1 A:FPS302 4.5 26.1 1.0 N A:GLY24 4.5 13.1 1.0 O A:HOH503 4.6 37.6 1.0 P1 A:ISY301 4.7 24.9 1.0 O5 A:ISY301 4.9 31.3 1.0 NH2 A:ARG26 5.0 21.1 1.0 CA A:ASP23 5.0 12.9 1.0

Magnesium binding site 2 out of 2 in the Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of MA1831 From Methanosarcina Acetivorans in Complex with Farnesyl Thiopyrophosphate and Isopentyl S-Thiolodiphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:18.9 occ:1.00 O7 B:ISY301 2.0 21.6 1.0 O2A B:FPS302 2.1 19.3 1.0 O B:HOH460 2.1 17.4 1.0 O2B B:FPS302 2.1 16.2 1.0 OD1 B:ASP23 2.1 14.8 1.0 O B:HOH407 2.2 16.3 1.0 CG B:ASP23 3.1 15.9 1.0 PB B:FPS302 3.2 18.5 1.0 PA B:FPS302 3.3 19.5 1.0 P3 B:ISY301 3.4 23.2 1.0 OD2 B:ASP23 3.4 16.2 1.0 O3A B:FPS302 3.5 19.3 1.0 O3B B:FPS302 3.6 18.6 1.0 S9 B:ISY301 4.0 31.9 1.0 O B:HOH408 4.0 35.3 1.0 O4 B:ISY301 4.1 30.4 1.0 NH2 B:ARG74 4.1 22.9 1.0 O B:HOH498 4.1 30.1 1.0 NH2 B:ARG27 4.2 18.3 1.0 S1 B:FPS302 4.2 20.3 1.0 O2 B:ISY301 4.3 24.9 1.0 C1 B:FPS302 4.4 28.6 1.0 O B:HOH437 4.4 46.2 1.0 CB B:ASP23 4.5 15.4 1.0 O1A B:FPS302 4.5 17.0 1.0 O8 B:ISY301 4.5 26.2 1.0 O1B B:FPS302 4.5 18.1 1.0 N B:GLY24 4.6 16.8 1.0 P1 B:ISY301 4.7 25.3 1.0 CA B:ASP23 5.0 15.6 1.0 NH2 B:ARG26 5.0 24.9 1.0

L.Zhang, X.Zhang, J.Min, B.Liu, J.W.Huang, Y.Yang, W.Liu, L.Dai, Y.Yang, C.C.Chen, R.T.Guo. Structural Insights to A Bi-Functional Isoprenyl Diphosphate Synthase That Can Catalyze Head-to-Tail and Head-to-Middle Condensation. Int.J.Biol.Macromol. V. 214 492 2022.
ISSN: ISSN 0141-8130
PubMed: 35764165
DOI: 10.1016/J.IJBIOMAC.2022.06.146