Magnesium in PDB 2e8w: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp

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

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp, PDB code: 2e8w was solved by R.T.Guo, T.P.Ko, C.K.-M.Chen, 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)	43.11 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.662, 116.064, 128.826, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.6

The binding sites of Magnesium atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium and Ipp (pdb code 2e8w). 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, PDB code: 2e8w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:21.2 occ:1.00 O1A A:IPE1001 2.0 32.1 1.0 O A:HOH539 2.1 17.2 1.0 OD1 A:ASP80 2.1 21.9 1.0 OD2 A:ASP84 2.2 17.2 1.0 O A:HOH540 2.2 20.1 1.0 CG A:ASP84 2.9 18.5 1.0 OD1 A:ASP84 3.0 20.7 1.0 CG A:ASP80 3.1 20.1 1.0 MG A:MG1202 3.3 20.6 1.0 PA A:IPE1001 3.4 32.2 1.0 OD2 A:ASP80 3.4 20.1 1.0 NE2 A:GLN147 3.8 22.3 1.0 O2A A:IPE1001 3.9 31.7 1.0 O1 A:IPE1001 4.0 35.1 1.0 O A:HOH677 4.0 16.4 1.0 C1 A:IPE1001 4.1 35.9 1.0 OE1 A:GLU236 4.2 25.1 1.0 OE1 A:GLN147 4.2 23.9 1.0 OD2 A:ASP150 4.2 28.4 1.0 CD A:GLN147 4.3 24.4 1.0 CB A:ASP80 4.4 19.2 1.0 CB A:ASP84 4.4 17.3 1.0 O A:ASP80 4.6 16.9 1.0 O3A A:IPE1001 4.6 37.1 1.0 O A:HOH538 4.9 18.1 1.0 CA A:ASP80 4.9 19.7 1.0 NZ A:LYS238 4.9 26.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:20.6 occ:1.00 O A:HOH677 2.1 16.4 1.0 OD2 A:ASP80 2.1 20.1 1.0 O1A A:IPE1001 2.2 32.1 1.0 OD2 A:ASP84 2.2 17.2 1.0 O A:HOH538 2.2 18.1 1.0 O3B A:IPE1001 2.2 33.1 1.0 O3A A:IPE1001 3.1 37.1 1.0 CG A:ASP80 3.1 20.1 1.0 PB A:IPE1001 3.1 31.5 1.0 PA A:IPE1001 3.2 32.2 1.0 MG A:MG1201 3.3 21.2 1.0 CG A:ASP84 3.3 18.5 1.0 OD1 A:ASP80 3.4 21.9 1.0 O A:HOH459 3.7 40.2 1.0 O1 A:IPE1001 3.8 35.1 1.0 CB A:ASP84 3.9 17.3 1.0 O A:HOH665 3.9 29.0 1.0 NH2 A:ARG89 4.0 26.7 1.0 O A:HOH540 4.1 20.1 1.0 O2B A:IPE1001 4.2 36.9 1.0 OD1 A:ASP84 4.4 20.7 1.0 OE2 A:GLU236 4.4 27.6 1.0 O1B A:IPE1001 4.4 36.8 1.0 O2A A:IPE1001 4.5 31.7 1.0 CB A:ASP80 4.5 19.2 1.0 O A:ASP80 4.5 16.9 1.0 OD1 A:ASP81 4.7 24.6 1.0 NZ A:LYS238 4.8 26.2 1.0 C1 A:IPE1001 4.8 35.9 1.0 OE1 A:GLU236 4.9 25.1 1.0 O A:HOH539 4.9 17.2 1.0 C A:ASP80 4.9 17.6 1.0 CD A:GLU236 5.0 26.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1203 b:27.6 occ:1.00 OD1 B:ASP80 2.0 22.9 1.0 O3A B:IPE1002 2.2 36.6 1.0 OD2 B:ASP84 2.4 26.4 1.0 O3B B:IPE1002 2.6 31.4 1.0 PB B:IPE1002 3.0 28.9 1.0 CG B:ASP80 3.0 23.3 1.0 MG B:MG1204 3.2 22.0 1.0 O1A B:IPE1002 3.4 40.2 1.0 OD2 B:ASP80 3.4 26.3 1.0 PA B:IPE1002 3.4 31.5 1.0 CG B:ASP84 3.5 22.4 1.0 NH2 B:ARG89 4.0 25.7 1.0 CB B:ASP84 4.0 22.0 1.0 O1B B:IPE1002 4.1 32.6 1.0 O1 B:IPE1002 4.1 39.4 1.0 O B:HOH785 4.1 51.0 1.0 O2B B:IPE1002 4.1 32.7 1.0 O B:HOH734 4.2 26.3 1.0 O B:HOH526 4.3 32.1 1.0 O B:HOH401 4.3 11.0 1.0 OE1 B:GLU236 4.4 27.4 1.0 CB B:ASP80 4.4 20.8 1.0 O B:ASP80 4.4 20.2 1.0 NZ B:LYS238 4.5 30.6 1.0 OD1 B:ASP84 4.5 25.9 1.0 OD1 B:ASP81 4.6 23.9 1.0 O2A B:IPE1002 4.6 36.0 1.0 C B:ASP80 4.7 20.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1204 b:22.0 occ:1.00 O1A B:IPE1002 1.8 40.2 1.0 OD2 B:ASP80 2.1 26.3 1.0 OD2 B:ASP84 2.2 26.4 1.0 O B:HOH401 2.3 11.0 1.0 CG B:ASP80 3.0 23.3 1.0 CG B:ASP84 3.1 22.4 1.0 MG B:MG1203 3.2 27.6 1.0 OD1 B:ASP84 3.2 25.9 1.0 PA B:IPE1002 3.2 31.5 1.0 OD1 B:ASP80 3.2 22.9 1.0 O3A B:IPE1002 3.5 36.6 1.0 OE1 B:GLN147 3.8 34.7 1.0 O1 B:IPE1002 4.1 39.4 1.0 OD2 B:ASP150 4.2 31.0 1.0 O2A B:IPE1002 4.2 36.0 1.0 C1 B:IPE1002 4.3 38.2 1.0 OE2 B:GLU236 4.3 21.5 1.0 CB B:ASP80 4.4 20.8 1.0 CD B:GLN147 4.4 31.9 1.0 NE2 B:GLN147 4.4 27.9 1.0 CB B:ASP84 4.5 22.0 1.0 NZ B:LYS238 4.5 30.6 1.0 O B:ASP80 4.6 20.2 1.0 OE1 B:GLU236 4.9 27.4 1.0 NZ B:LYS174 4.9 27.4 1.0 CA B:ASP80 4.9 19.4 1.0

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