Magnesium in PDB 2z7i: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742:
2.5.1.1; 2.5.1.10; 2.5.1.29; 2.5.1.30;

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742, PDB code: 2z7i was solved by R.T.Guo, C.K.-M.Chen, T.-P.Ko, R.Cao, M.Hudock, E.Oldfield, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.44 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.111, 116.337, 129.434, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 24.4

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742 (pdb code 2z7i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742, PDB code: 2z7i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:26.3 occ:1.00 OAE A:7421302 1.9 25.6 1.0 O A:HOH469 2.0 19.1 1.0 OAF A:7421302 2.0 22.7 1.0 OD2 A:ASP80 2.1 27.1 1.0 OD2 A:ASP84 2.1 26.7 1.0 O A:HOH379 2.2 23.2 1.0 CG A:ASP80 3.1 29.6 1.0 PAX A:7421302 3.2 31.4 1.0 PAW A:7421302 3.3 30.6 1.0 CG A:ASP84 3.3 29.8 1.0 O A:HOH507 3.4 37.3 1.0 OD1 A:ASP80 3.4 32.7 1.0 CAV A:7421302 3.6 29.8 1.0 O A:HOH581 3.8 38.1 1.0 NH2 A:ARG89 4.0 24.0 1.0 OAG A:7421302 4.0 30.9 1.0 O A:HOH383 4.1 29.6 1.0 O A:HOH538 4.1 44.1 1.0 CB A:ASP84 4.1 25.8 1.0 OAH A:7421302 4.1 33.4 1.0 OD1 A:ASP84 4.2 31.3 1.0 O A:HOH486 4.3 34.2 1.0 OE2 A:GLU236 4.4 39.3 1.0 OAI A:7421302 4.4 30.7 1.0 CB A:ASP80 4.4 24.0 1.0 OAD A:7421302 4.5 30.2 1.0 O A:ASP80 4.5 17.5 1.0 OD1 A:ASP81 4.6 28.5 1.0 C A:ASP80 4.8 22.1 1.0 NZ A:LYS238 4.9 38.7 1.0 O A:HOH484 5.0 33.0 1.0

Magnesium binding site 2 out of 2 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Inhibitor Bph-742 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1302 b:33.2 occ:1.00 O B:HOH616 2.0 36.2 1.0 OAE B:7421303 2.1 25.1 1.0 OD2 B:ASP84 2.1 32.5 1.0 OAF B:7421303 2.1 27.3 1.0 OD1 B:ASP80 2.1 25.3 1.0 CG B:ASP80 3.1 30.3 1.0 PAX B:7421303 3.3 32.8 1.0 CG B:ASP84 3.3 33.1 1.0 PAW B:7421303 3.4 33.0 1.0 OD2 B:ASP80 3.4 30.7 1.0 O B:HOH603 3.7 44.7 1.0 CAV B:7421303 3.7 32.3 1.0 O B:HOH428 3.9 35.6 1.0 OAG B:7421303 4.0 31.0 1.0 CB B:ASP84 4.0 27.4 1.0 OAH B:7421303 4.2 33.4 1.0 NH2 B:ARG89 4.2 31.8 1.0 OD1 B:ASP84 4.2 32.7 1.0 O B:HOH535 4.3 39.2 1.0 O B:ASP80 4.3 24.8 1.0 CB B:ASP80 4.4 25.9 1.0 OE1 B:GLU236 4.5 39.2 1.0 NZ B:LYS238 4.5 37.4 1.0 OAD B:7421303 4.5 31.1 1.0 OAI B:7421303 4.5 33.6 1.0 OD1 B:ASP81 4.7 25.1 1.0 C B:ASP80 4.7 25.8 1.0

C.K.-M.Chen, M.P.Hudock, Y.Zhang, R.-T.Guo, R.Cao, J.H.No, P.-H.Liang, T.-P.Ko, T.-H.Chang, S.-C.Chang, Y.Song, J.Axelson, A.Kumar, A.H.-J.Wang, E.Oldfield. Inhibition of Geranylgeranyl Diphosphate Synthase By Bisphosphonates: A Crystallographic and Computational Investigation J.Med.Chem. V. 51 5594 2008.
ISSN: ISSN 0022-2623
PubMed: 18800762
DOI: 10.1021/JM800325Y