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Magnesium in PDB 2zev: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715

Enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715:
2.5.1.30;

Protein crystallography data

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715, PDB code: 2zev was solved by R.T.Guo, C.K.-M.Chen, 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) 41.81 / 2.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.822, 115.879, 128.336, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715 (pdb code 2zev). 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, Ipp and Bph-715, PDB code: 2zev:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2zev

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Magnesium binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715


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, Ipp and Bph-715 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:41.3
occ:1.00
 OD1 A:ASP80 2.2 37.1 1.0
OAE A:B711201 2.2 51.5 1.0
OD2 A:ASP84 2.3 35.8 1.0
CG A:ASP84 3.2 36.3 1.0
CG A:ASP80 3.2 37.3 1.0
MG A:MG1302 3.3 48.0 1.0
OD1 A:ASP84 3.3 37.2 1.0
PAZ A:B711201 3.3 52.9 1.0
OAB A:B711201 3.4 51.7 1.0
OD2 A:ASP80 3.5 40.8 1.0
CAJ A:B711201 4.0 62.9 1.0
OE1 A:GLN147 4.0 49.9 1.0
NE2 A:GLN147 4.2 44.8 1.0
OD2 A:ASP150 4.3 33.3 1.0
OE1 A:GLU236 4.3 37.8 1.0
OAD A:B711201 4.3 55.3 1.0
CD A:GLN147 4.3 44.7 1.0
NZ A:LYS238 4.4 44.0 1.0
CAU A:B711201 4.5 58.2 1.0
CB A:ASP80 4.5 34.6 1.0
CB A:ASP84 4.6 34.5 1.0
CAX A:B711201 4.6 53.4 1.0
NAY A:B711201 4.7 62.3 1.0
CE A:LYS238 4.7 40.3 1.0
O A:ASP80 4.7 31.1 1.0
OAF A:B711201 4.8 47.8 1.0
CAH A:B711201 4.9 63.7 1.0

Magnesium binding site 2 out of 4 in 2zev

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Magnesium binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715


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, Ipp and Bph-715 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:48.0
occ:1.00
 OD2 A:ASP80 2.0 40.8 1.0
OAE A:B711201 2.1 51.5 1.0
OAF A:B711201 2.2 47.8 1.0
OD2 A:ASP84 2.3 35.8 1.0
CG A:ASP80 3.0 37.3 1.0
MG A:MG1301 3.3 41.3 1.0
OD1 A:ASP80 3.3 37.1 1.0
CG A:ASP84 3.3 36.3 1.0
PBA A:B711201 3.5 50.8 1.0
PAZ A:B711201 3.6 52.9 1.0
CB A:ASP84 3.8 34.5 1.0
CAX A:B711201 3.9 53.4 1.0
OAG A:B711201 4.0 50.4 1.0
CAU A:B711201 4.0 58.2 1.0
O A:HOH1373 4.0 43.3 1.0
NH2 A:ARG89 4.0 39.8 1.0
OAD A:B711201 4.2 55.3 1.0
O A:ASP80 4.3 31.1 1.0
NZ A:LYS238 4.3 44.0 1.0
CB A:ASP80 4.4 34.6 1.0
OE2 A:GLU236 4.4 42.5 1.0
OD1 A:ASP84 4.4 37.2 1.0
O A:HOH1497 4.5 38.7 1.0
OD1 A:ASP81 4.6 38.0 1.0
C A:ASP80 4.7 33.1 1.0
OAC A:B711201 4.7 52.5 1.0
OAB A:B711201 4.7 51.7 1.0
OE1 A:GLU236 4.9 37.8 1.0

Magnesium binding site 3 out of 4 in 2zev

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Magnesium binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715


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, Ipp and Bph-715 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1303

b:51.0
occ:1.00
 OD1 B:ASP80 1.8 43.7 1.0
OAE B:B711202 2.1 55.6 1.0
OAF B:B711202 2.2 48.4 1.0
OD2 B:ASP84 2.2 42.8 1.0
CG B:ASP80 2.8 42.7 1.0
OD2 B:ASP80 3.2 43.6 1.0
CG B:ASP84 3.3 41.9 1.0
MG B:MG1304 3.5 46.5 1.0
PBA B:B711202 3.5 51.3 1.0
PAZ B:B711202 3.6 56.4 1.0
CB B:ASP84 3.7 39.9 1.0
CAX B:B711202 3.9 55.3 1.0
NH2 B:ARG89 4.0 43.3 1.0
CAU B:B711202 4.0 61.1 1.0
CB B:ASP80 4.2 38.7 1.0
OAG B:B711202 4.2 51.0 1.0
O B:HOH1433 4.2 43.8 1.0
O B:ASP80 4.3 37.1 1.0
OAD B:B711202 4.3 58.0 1.0
OD1 B:ASP81 4.3 38.3 1.0
OD1 B:ASP84 4.4 43.7 1.0
OE1 B:GLU236 4.4 40.9 1.0
C B:ASP80 4.5 37.0 1.0
O B:HOH1470 4.5 40.9 1.0
OAB B:B711202 4.7 57.1 1.0
OAC B:B711202 4.7 51.5 1.0
O B:HOH1394 4.9 35.5 1.0
N B:ASP81 4.9 35.6 1.0
CA B:ASP80 4.9 37.1 1.0

Magnesium binding site 4 out of 4 in 2zev

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Magnesium binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, Ipp and Bph-715


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, Ipp and Bph-715 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1304

b:46.5
occ:1.00
 OD2 B:ASP80 2.0 43.6 1.0
OAE B:B711202 2.2 55.6 1.0
O B:HOH1470 2.3 40.9 1.0
OD2 B:ASP84 2.4 42.8 1.0
OAB B:B711202 2.9 57.1 1.0
PAZ B:B711202 3.1 56.4 1.0
CG B:ASP80 3.1 42.7 1.0
CG B:ASP84 3.3 41.9 1.0
OD1 B:ASP84 3.4 43.7 1.0
MG B:MG1303 3.5 51.0 1.0
OD1 B:ASP80 3.5 43.7 1.0
OE1 B:GLN147 3.6 48.3 1.0
CAJ B:B711202 3.8 66.7 1.0
OD2 B:ASP150 4.1 45.0 1.0
OAD B:B711202 4.1 58.0 1.0
CD B:GLN147 4.3 45.4 1.0
NE2 B:GLN147 4.3 45.3 1.0
OE2 B:GLU236 4.5 39.1 1.0
CAX B:B711202 4.5 55.3 1.0
CB B:ASP80 4.5 38.7 1.0
CAU B:B711202 4.5 61.1 1.0
NAY B:B711202 4.6 65.3 1.0
CAH B:B711202 4.6 67.7 1.0
CB B:ASP84 4.8 39.9 1.0
NZ B:LYS174 4.8 47.3 1.0
NZ B:LYS238 4.9 49.4 1.0
O B:ASP80 4.9 37.1 1.0
OE1 B:GLU236 4.9 40.9 1.0
OAF B:B711202 5.0 48.4 1.0
CE B:LYS238 5.0 46.0 1.0

Reference:

Y.Zhang, R.Cao, F.Yin, M.P.Hudock, R.T.Guo, K.Krysiak, S.Mukherjee, Y.-G.Gao, H.Robinson, Y.Song, J.H.No, K.Bergan, A.Leon, L.Cass, A.Goddard, T.-K.Chang, F.-Y.Lin, E.Van Beek, S.Papapoulos, A.H.-J.Wang, T.Kubo, M.Ochi, D.Mukkamala, E.Oldfield. Lipophilic Bisphosphonates As Dual Farnesyl/Geranylgeranyl Diphosphate Synthase Inhibitors: An X-Ray and uc(Nmr) Investigation J.Am.Chem.Soc. V. 131 5153 2009.
ISSN: ISSN 0002-7863
PubMed: 19309137
DOI: 10.1021/JA808285E
Page generated: Wed Aug 14 07:51:16 2024

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