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Magnesium in PDB 2e8u: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21)

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21)

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21):
2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21), PDB code: 2e8u was solved by R.T.Guo, C.K.-M.Chen, T.P.Ko, W.Y.Jeng, 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) 40.54 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.236, 47.707, 91.831, 90.00, 110.71, 90.00
R / Rfree (%) 19.8 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21) (pdb code 2e8u). 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 Ipp (P21), PDB code: 2e8u:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2e8u

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Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21)


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 Ipp (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:26.4
occ:1.00
 O1A A:IPE1102 1.9 29.7 1.0
OD2 A:ASP80 2.0 27.3 1.0
O A:HOH763 2.0 26.7 1.0
O2B A:IPE1102 2.0 29.6 1.0
O A:HOH612 2.1 24.2 1.0
OD2 A:ASP84 2.2 23.6 1.0
MG A:MG1302 2.9 20.6 1.0
CG A:ASP80 3.0 27.2 1.0
CG A:ASP84 3.3 22.8 1.0
PA A:IPE1102 3.3 33.9 1.0
PB A:IPE1102 3.3 30.9 1.0
OD1 A:ASP80 3.3 24.2 1.0
O3A A:IPE1102 3.5 34.3 1.0
CB A:ASP84 3.8 24.7 1.0
NH2 A:ARG89 4.0 28.8 1.0
O A:HOH569 4.1 25.1 1.0
O3B A:IPE1102 4.1 35.5 1.0
O1 A:IPE1102 4.2 38.4 1.0
O A:HOH415 4.2 31.8 1.0
O A:ASP80 4.3 25.4 1.0
OD1 A:ASP84 4.3 25.0 1.0
CB A:ASP80 4.3 25.2 1.0
O2A A:IPE1102 4.4 33.5 1.0
OE2 A:GLU236 4.4 33.4 1.0
O1B A:IPE1102 4.5 32.0 1.0
OD1 A:ASP81 4.5 27.9 1.0
C A:ASP80 4.6 25.6 1.0
O A:HOH765 4.6 25.1 1.0
O A:HOH416 4.6 41.3 1.0
C1 A:IPE1102 4.7 42.5 1.0
O A:HOH564 4.8 30.5 1.0
OE1 A:GLU236 4.9 29.5 1.0
NZ A:LYS238 5.0 38.5 1.0
CD A:GLU236 5.0 30.6 1.0

Magnesium binding site 2 out of 4 in 2e8u

Go back to Magnesium Binding Sites List in 2e8u
Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21)


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 Ipp (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:20.6
occ:1.00
 O A:HOH765 2.0 25.1 1.0
O1A A:IPE1102 2.0 29.7 1.0
OD1 A:ASP80 2.1 24.2 1.0
OD2 A:ASP84 2.1 23.6 1.0
O A:HOH569 2.2 25.1 1.0
O A:HOH564 2.2 30.5 1.0
MG A:MG1301 2.9 26.4 1.0
CG A:ASP80 3.0 27.2 1.0
CG A:ASP84 3.0 22.8 1.0
OD2 A:ASP80 3.2 27.3 1.0
PA A:IPE1102 3.2 33.9 1.0
OD1 A:ASP84 3.2 25.0 1.0
O1 A:IPE1102 3.3 38.4 1.0
O A:HOH612 3.8 24.2 1.0
O2A A:IPE1102 3.9 33.5 1.0
OE1 A:GLU236 4.1 29.5 1.0
OD2 A:ASP150 4.1 33.4 1.0
NE2 A:GLN147 4.1 28.0 1.0
OE1 A:GLN147 4.2 30.1 1.0
C1 A:IPE1102 4.3 42.5 1.0
CD A:GLN147 4.3 33.0 1.0
CB A:ASP80 4.4 25.2 1.0
CB A:ASP84 4.4 24.7 1.0
O3A A:IPE1102 4.5 34.3 1.0
O2B A:IPE1102 4.6 29.6 1.0
O A:ASP80 4.6 25.4 1.0
O A:HOH763 4.7 26.7 1.0
NZ A:LYS238 4.9 38.5 1.0
CE A:LYS238 4.9 35.2 1.0
CD A:GLU236 5.0 30.6 1.0
CA A:ASP80 5.0 25.6 1.0

Magnesium binding site 3 out of 4 in 2e8u

Go back to Magnesium Binding Sites List in 2e8u
Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21)


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 Ipp (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:23.1
occ:1.00
 O1A B:IPE1104 1.9 28.9 1.0
OD1 B:ASP80 1.9 22.6 1.0
O B:HOH788 2.0 22.1 1.0
O B:HOH692 2.1 26.7 1.0
OD2 B:ASP84 2.2 24.7 1.0
O2B B:IPE1104 2.2 27.5 1.0
CG B:ASP80 2.9 25.7 1.0
MG B:MG1304 3.0 17.9 1.0
CG B:ASP84 3.2 27.4 1.0
OD2 B:ASP80 3.2 23.9 1.0
PA B:IPE1104 3.3 32.4 1.0
PB B:IPE1104 3.4 26.9 1.0
O3A B:IPE1104 3.7 31.5 1.0
CB B:ASP84 3.7 24.1 1.0
O B:HOH589 3.8 19.1 1.0
NH2 B:ARG89 4.1 28.9 1.0
O3B B:IPE1104 4.1 27.1 1.0
O1 B:IPE1104 4.2 33.5 1.0
OE1 B:GLU236 4.2 32.6 1.0
O B:HOH548 4.2 39.0 1.0
O B:ASP80 4.3 25.2 1.0
CB B:ASP80 4.3 21.9 1.0
OD1 B:ASP84 4.3 24.7 1.0
O2A B:IPE1104 4.3 32.3 1.0
NZ B:LYS238 4.5 34.5 1.0
C B:ASP80 4.6 22.4 1.0
OD1 B:ASP81 4.6 25.5 1.0
O1B B:IPE1104 4.6 30.6 1.0
O B:HOH558 4.8 25.7 1.0
O B:HOH768 4.9 27.4 1.0
CD B:GLU236 5.0 32.2 1.0
OE2 B:GLU236 5.0 31.8 1.0

Magnesium binding site 4 out of 4 in 2e8u

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Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (P21)


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 Ipp (P21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:17.9
occ:1.00
 OD2 B:ASP80 1.9 23.9 1.0
O B:HOH589 1.9 19.1 1.0
OD2 B:ASP84 2.1 24.7 1.0
O1A B:IPE1104 2.2 28.9 1.0
O B:HOH768 2.2 27.4 1.0
O B:HOH558 2.2 25.7 1.0
CG B:ASP80 2.9 25.7 1.0
MG B:MG1303 3.0 23.1 1.0
CG B:ASP84 3.1 27.4 1.0
OD1 B:ASP80 3.2 22.6 1.0
PA B:IPE1104 3.2 32.4 1.0
OD1 B:ASP84 3.3 24.7 1.0
O1 B:IPE1104 3.4 33.5 1.0
O2A B:IPE1104 3.8 32.3 1.0
O B:HOH788 3.9 22.1 1.0
OE1 B:GLN147 3.9 34.8 1.0
OD2 B:ASP150 4.0 25.0 1.0
NE2 B:GLN147 4.2 29.0 1.0
CB B:ASP80 4.3 21.9 1.0
CD B:GLN147 4.4 32.5 1.0
OE2 B:GLU236 4.4 31.8 1.0
CB B:ASP84 4.5 24.1 1.0
O3A B:IPE1104 4.6 31.5 1.0
NZ B:LYS238 4.6 34.5 1.0
O B:ASP80 4.6 25.2 1.0
O2B B:IPE1104 4.7 27.5 1.0
C1 B:IPE1104 4.8 37.9 1.0
CA B:ASP80 4.9 22.8 1.0
O B:HOH692 4.9 26.7 1.0
CE B:LYS238 5.0 33.4 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: Tue Aug 13 22:41:39 2024

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