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Magnesium in PDB 2e92: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261:
2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261, PDB code: 2e92 was solved by R.T.Guo, T.P.Ko, R.Cao, W.Y.Jeng, C.K.-M.Chen, T.H.Chang, P.H.Liang, 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 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.871, 116.051, 127.733, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261 (pdb code 2e92). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261, PDB code: 2e92:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2e92

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Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


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-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:42.8
occ:1.00
 OD2 A:ASP84 2.1 36.1 1.0
O5 A:M0N901 2.2 38.9 1.0
OD1 A:ASP80 2.3 39.9 1.0
CG A:ASP84 3.0 35.0 1.0
CG A:ASP80 3.1 36.4 1.0
OD1 A:ASP84 3.2 34.5 1.0
OD2 A:ASP80 3.2 40.6 1.0
P2 A:M0N901 3.3 40.9 1.0
O4 A:M0N901 3.3 39.7 1.0
MG A:MG1302 3.4 53.9 1.0
NE2 A:GLN147 3.8 38.8 1.0
O6 A:M0N901 4.3 42.6 1.0
O A:HOH406 4.3 36.9 1.0
CB A:ASP84 4.4 35.4 1.0
CB A:ASP80 4.4 35.4 1.0
C8 A:M0N901 4.6 48.7 1.0
CD A:GLN147 4.6 39.6 1.0
C9 A:M0N901 4.6 44.3 1.0
OD2 A:ASP150 4.6 46.9 1.0
O A:ASP80 4.6 28.3 1.0
NZ A:LYS238 4.7 40.2 1.0
OE1 A:GLN147 4.8 39.6 1.0
O1 A:M0N901 4.8 42.8 1.0
C2 A:M0N901 4.8 53.9 1.0
CA A:ASP80 5.0 33.0 1.0

Magnesium binding site 2 out of 4 in 2e92

Go back to Magnesium Binding Sites List in 2e92
Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


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 Magnesium and Bph-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:53.9
occ:1.00
 OD2 A:ASP80 2.1 40.6 1.0
O5 A:M0N901 2.2 38.9 1.0
OD2 A:ASP84 2.3 36.1 1.0
O1 A:M0N901 2.3 42.8 1.0
CG A:ASP80 3.2 36.4 1.0
CG A:ASP84 3.3 35.0 1.0
MG A:MG1301 3.4 42.8 1.0
CB A:ASP84 3.6 35.4 1.0
P2 A:M0N901 3.6 40.9 1.0
P1 A:M0N901 3.7 44.0 1.0
OD1 A:ASP80 3.7 39.9 1.0
NH2 A:ARG89 4.0 41.1 1.0
O6 A:M0N901 4.0 42.6 1.0
OE2 A:GLU236 4.1 58.5 1.0
C9 A:M0N901 4.1 44.3 1.0
O A:ASP80 4.3 28.3 1.0
O2 A:M0N901 4.3 42.0 1.0
OD1 A:ASP81 4.3 37.5 1.0
C8 A:M0N901 4.4 48.7 1.0
OD1 A:ASP84 4.4 34.5 1.0
CB A:ASP80 4.4 35.4 1.0
OE1 A:GLU236 4.6 60.6 1.0
C A:ASP80 4.6 32.7 1.0
O A:HOH722 4.6 37.3 1.0
CD A:GLU236 4.7 59.8 1.0
O4 A:M0N901 4.8 39.7 1.0
O A:HOH406 4.8 36.9 1.0
O3 A:M0N901 4.9 49.0 1.0
O A:HOH566 4.9 41.8 1.0

Magnesium binding site 3 out of 4 in 2e92

Go back to Magnesium Binding Sites List in 2e92
Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:44.9
occ:1.00
 O1 B:M0N902 1.9 48.5 1.0
OD1 B:ASP80 2.0 44.6 1.0
O5 B:M0N902 2.1 48.0 1.0
OD2 B:ASP84 2.3 36.8 1.0
O B:HOH708 2.5 29.7 1.0
CG B:ASP80 3.1 46.3 1.0
P2 B:M0N902 3.1 48.9 1.0
MG B:MG1304 3.2 45.1 1.0
P1 B:M0N902 3.2 49.6 1.0
O6 B:M0N902 3.3 50.7 1.0
OD2 B:ASP80 3.4 47.6 1.0
CG B:ASP84 3.5 37.9 1.0
C9 B:M0N902 3.6 50.8 1.0
O2 B:M0N902 3.9 49.8 1.0
C8 B:M0N902 3.9 54.9 1.0
CB B:ASP84 4.2 34.9 1.0
NH2 B:ARG89 4.3 54.6 1.0
O3 B:M0N902 4.4 51.8 1.0
CB B:ASP80 4.4 42.9 1.0
O4 B:M0N902 4.5 46.4 1.0
OD1 B:ASP84 4.5 37.2 1.0
OE1 B:GLU236 4.5 52.8 1.0
O B:HOH707 4.5 38.5 1.0
O B:ASP80 4.6 42.9 1.0
NZ B:LYS238 4.6 43.1 1.0
O B:HOH595 4.8 47.0 1.0
OD1 B:ASP81 4.9 40.3 1.0
C B:ASP80 4.9 41.2 1.0
O B:M0N902 4.9 47.1 1.0

Magnesium binding site 4 out of 4 in 2e92

Go back to Magnesium Binding Sites List in 2e92
Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Bph-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:45.1
occ:1.00
 OD2 B:ASP80 2.1 47.6 1.0
O5 B:M0N902 2.1 48.0 1.0
O B:HOH707 2.2 38.5 1.0
OD2 B:ASP84 2.3 36.8 1.0
CG B:ASP80 3.0 46.3 1.0
CG B:ASP84 3.1 37.9 1.0
OD1 B:ASP84 3.1 37.2 1.0
MG B:MG1303 3.2 44.9 1.0
OD1 B:ASP80 3.2 44.6 1.0
P2 B:M0N902 3.5 48.9 1.0
OE1 B:GLN147 3.6 54.2 1.0
O4 B:M0N902 3.9 46.4 1.0
OD2 B:ASP150 4.0 48.8 1.0
CD B:GLN147 4.3 50.1 1.0
CB B:ASP80 4.3 42.9 1.0
OE2 B:GLU236 4.4 49.4 1.0
O6 B:M0N902 4.4 50.7 1.0
NE2 B:GLN147 4.5 50.6 1.0
CB B:ASP84 4.5 34.9 1.0
O B:ASP80 4.6 42.9 1.0
NZ B:LYS238 4.6 43.1 1.0
O1 B:M0N902 4.7 48.5 1.0
C8 B:M0N902 4.8 54.9 1.0
C9 B:M0N902 4.8 50.8 1.0
CA B:ASP80 4.8 40.6 1.0
O B:HOH708 4.9 29.7 1.0

Reference:

R.T.Guo, R.Cao, P.H.Liang, T.P.Ko, T.H.Chang, M.P.Hudock, W.Y.Jeng, C.K.-M.Chen, Y.Zhang, Y.Song, C.J.Kuo, F.Yin, E.Oldfield, A.H.-J.Wang. Bisphosphonates Target Multiple Sites in Both Cis- and Trans-Prenyltransferases Proc.Natl.Acad.Sci.Usa V. 104 10022 2007.
ISSN: ISSN 0027-8424
PubMed: 17535895
DOI: 10.1073/PNAS.0702254104
Page generated: Sun Aug 10 10:35:44 2025

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