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Magnesium in PDB 2z4y: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252:
2.5.1.1; 2.5.1.10; 2.5.1.29; 2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252, PDB code: 2z4y was solved by C.K.-M.Chen, R.T.Guo, M.Hudock, R.Cao, 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) 30.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.952, 116.208, 126.020, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252 (pdb code 2z4y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252, PDB code: 2z4y:

Magnesium binding site 1 out of 1 in 2z4y

Go back to Magnesium Binding Sites List in 2z4y
Magnesium binding site 1 out of 1 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-252


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 Magnesium and Bph-252 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1301

b:42.0
occ:1.00
 OAB B:2521203 1.9 48.4 1.0
OAH B:2521203 2.0 44.0 1.0
O B:HOH1356 2.0 44.1 1.0
O B:HOH1411 2.0 42.0 1.0
OD2 B:ASP214 2.2 38.8 1.0
O B:HOH1438 2.3 34.3 1.0
P1P B:2521203 3.0 47.7 1.0
P1R B:2521203 3.2 44.9 1.0
CG B:ASP214 3.3 37.8 1.0
CAP B:2521203 3.5 45.6 1.0
NZ B:LYS238 3.7 46.5 1.0
OD1 B:ASP214 3.7 38.0 1.0
OAD B:2521203 3.8 48.1 1.0
OAF B:2521203 3.8 43.4 1.0
OAC B:2521203 3.9 41.7 1.0
NE2 B:GLN211 4.1 30.0 1.0
OD1 B:ASP233 4.3 34.6 1.0
OAE B:2521203 4.4 47.3 1.0
OD2 B:ASP233 4.4 31.9 1.0
OAG B:2521203 4.5 46.0 1.0
CB B:ASP214 4.6 33.9 1.0
OD1 B:ASP215 4.7 27.3 1.0
CG B:ASP233 4.8 30.7 1.0
CE B:LYS238 4.8 39.3 1.0
O B:HOH1465 4.9 38.3 1.0
CAO B:2521203 5.0 45.7 1.0
O B:HOH1439 5.0 64.0 1.0

Reference:

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
Page generated: Sun Aug 10 16:52:59 2025

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