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Magnesium in PDB 2z4v: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site)

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site)

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site):
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 Ggpp (Inhibitory Site), PDB code: 2z4v 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 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.164, 115.944, 128.404, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site) (pdb code 2z4v). 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 Ggpp (Inhibitory Site), PDB code: 2z4v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2z4v

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Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site)


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 Ggpp (Inhibitory Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1501

b:15.7
occ:1.00
 OD2 A:ASP84 2.1 11.8 1.0
O1A A:GRG1401 2.1 14.6 1.0
OD1 A:ASP80 2.1 12.4 1.0
O A:HOH1507 2.1 15.7 1.0
O A:HOH1511 2.2 13.9 1.0
O A:HOH1540 2.2 17.7 1.0
CG A:ASP84 2.9 15.0 1.0
CG A:ASP80 3.0 12.7 1.0
MG A:MG1502 3.0 12.9 1.0
OD1 A:ASP84 3.1 15.8 1.0
OD2 A:ASP80 3.2 13.3 1.0
PA A:GRG1401 3.3 16.8 1.0
O1 A:GRG1401 3.6 20.1 1.0
O2A A:GRG1401 3.9 17.1 1.0
O A:HOH1771 4.0 14.8 1.0
OD2 A:ASP150 4.0 15.7 1.0
C1 A:GRG1401 4.0 24.3 1.0
NE2 A:GLN147 4.1 19.0 1.0
OE1 A:GLU236 4.2 17.8 1.0
OE1 A:GLN147 4.2 18.4 1.0
CB A:ASP80 4.3 10.8 1.0
CB A:ASP84 4.4 14.2 1.0
CD A:GLN147 4.4 22.8 1.0
O3A A:GRG1401 4.6 18.6 1.0
O A:ASP80 4.6 11.4 1.0
O2B A:GRG1401 4.7 15.2 1.0
NZ A:LYS238 4.7 22.3 1.0
O A:HOH1505 4.8 13.7 1.0
CA A:ASP80 4.9 11.1 1.0

Magnesium binding site 2 out of 4 in 2z4v

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Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site)


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 Ggpp (Inhibitory Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1502

b:12.9
occ:1.00
 OD2 A:ASP80 2.0 13.3 1.0
O1A A:GRG1401 2.0 14.6 1.0
O2B A:GRG1401 2.1 15.2 1.0
OD2 A:ASP84 2.1 11.8 1.0
O A:HOH1505 2.1 13.7 1.0
O A:HOH1771 2.1 14.8 1.0
CG A:ASP80 3.0 12.7 1.0
MG A:MG1501 3.0 15.7 1.0
CG A:ASP84 3.2 15.0 1.0
PB A:GRG1401 3.3 16.4 1.0
OD1 A:ASP80 3.4 12.4 1.0
PA A:GRG1401 3.4 16.8 1.0
O3A A:GRG1401 3.6 18.6 1.0
CB A:ASP84 3.7 14.2 1.0
O A:HOH1511 4.0 13.9 1.0
NH2 A:ARG89 4.0 16.4 1.0
O3B A:GRG1401 4.1 20.4 1.0
O A:HOH1599 4.2 18.2 1.0
O A:HOH1590 4.2 26.1 1.0
OD1 A:ASP84 4.3 15.8 1.0
O A:ASP80 4.3 11.4 1.0
OE2 A:GLU236 4.3 17.2 1.0
O A:HOH1697 4.3 27.5 1.0
CB A:ASP80 4.3 10.8 1.0
O1 A:GRG1401 4.4 20.1 1.0
O2A A:GRG1401 4.4 17.1 1.0
OD1 A:ASP81 4.5 16.6 1.0
O1B A:GRG1401 4.5 19.2 1.0
C1 A:GRG1401 4.6 24.3 1.0
NZ A:LYS238 4.6 22.3 1.0
C A:ASP80 4.6 11.8 1.0
O A:HOH1507 4.8 15.7 1.0
OE1 A:GLU236 4.9 17.8 1.0
O A:HOH1540 4.9 17.7 1.0
CD A:GLU236 5.0 16.6 1.0

Magnesium binding site 3 out of 4 in 2z4v

Go back to Magnesium Binding Sites List in 2z4v
Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site)


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 Ggpp (Inhibitory Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1503

b:14.8
occ:1.00
 OD1 B:ASP80 1.9 15.4 1.0
O2B B:GRG1402 2.0 17.9 1.0
O B:HOH1549 2.0 17.4 1.0
O1A B:GRG1402 2.1 17.2 1.0
O B:HOH1610 2.1 17.0 1.0
OD2 B:ASP84 2.2 12.5 1.0
CG B:ASP80 3.0 15.2 1.0
MG B:MG1504 3.1 17.6 1.0
PB B:GRG1402 3.2 20.4 1.0
CG B:ASP84 3.2 15.9 1.0
PA B:GRG1402 3.4 19.6 1.0
OD2 B:ASP80 3.4 14.0 1.0
O3A B:GRG1402 3.6 20.6 1.0
CB B:ASP84 3.7 13.9 1.0
NH2 B:ARG89 4.0 20.6 1.0
O3B B:GRG1402 4.0 21.9 1.0
O B:HOH1525 4.1 16.8 1.0
O B:HOH1550 4.1 25.1 1.0
O B:HOH1757 4.2 29.7 1.0
O B:HOH1516 4.3 21.5 1.0
O B:ASP80 4.3 12.9 1.0
OD1 B:ASP84 4.3 14.2 1.0
CB B:ASP80 4.3 14.8 1.0
OE1 B:GLU236 4.3 19.9 1.0
O1B B:GRG1402 4.4 21.2 1.0
O2A B:GRG1402 4.4 19.8 1.0
O1 B:GRG1402 4.4 23.9 1.0
OD1 B:ASP81 4.4 16.0 1.0
NZ B:LYS238 4.5 28.2 1.0
C1 B:GRG1402 4.6 28.5 1.0
C B:ASP80 4.7 15.2 1.0
O B:HOH1614 4.7 16.4 1.0
O B:HOH1539 4.9 17.9 1.0

Magnesium binding site 4 out of 4 in 2z4v

Go back to Magnesium Binding Sites List in 2z4v
Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ggpp (Inhibitory Site)


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 Ggpp (Inhibitory Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1504

b:17.6
occ:1.00
 O1A B:GRG1402 2.0 17.2 1.0
O B:HOH1614 2.1 16.4 1.0
OD2 B:ASP80 2.1 14.0 1.0
OD2 B:ASP84 2.1 12.5 1.0
O B:HOH1539 2.2 17.9 1.0
O B:HOH1525 2.3 16.8 1.0
CG B:ASP80 2.9 15.2 1.0
CG B:ASP84 3.0 15.9 1.0
MG B:MG1503 3.1 14.8 1.0
OD1 B:ASP84 3.1 14.2 1.0
OD1 B:ASP80 3.2 15.4 1.0
PA B:GRG1402 3.3 19.6 1.0
O1 B:GRG1402 3.6 23.9 1.0
O2A B:GRG1402 4.0 19.8 1.0
O B:HOH1610 4.0 17.0 1.0
C1 B:GRG1402 4.0 28.5 1.0
OE1 B:GLN147 4.0 24.6 1.0
OD2 B:ASP150 4.0 17.6 1.0
NE2 B:GLN147 4.1 17.0 1.0
CD B:GLN147 4.3 25.9 1.0
OE2 B:GLU236 4.3 18.6 1.0
CB B:ASP80 4.3 14.8 1.0
CB B:ASP84 4.4 13.9 1.0
O B:ASP80 4.5 12.9 1.0
O3A B:GRG1402 4.6 20.6 1.0
NZ B:LYS238 4.6 28.2 1.0
O2B B:GRG1402 4.7 17.9 1.0
O B:HOH1549 4.8 17.4 1.0
CA B:ASP80 4.9 14.5 1.0
OE2 B:GLU83 5.0 18.6 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: Wed Aug 14 07:45:36 2024

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