Magnesium in PDB 2dh4: Geranylgeranyl Pyrophosphate Synthase

All present enzymatic activity of Geranylgeranyl Pyrophosphate Synthase:
2.5.1.29;

The structure of Geranylgeranyl Pyrophosphate Synthase, PDB code: 2dh4 was solved by T.-H.Chang, R.-T.Guo, T.-P.Ko, A.H.Wang, P.-H.Liang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.747, 116.331, 129.768, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.3

The binding sites of Magnesium atom in the Geranylgeranyl Pyrophosphate Synthase (pdb code 2dh4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Geranylgeranyl Pyrophosphate Synthase, PDB code: 2dh4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Geranylgeranyl Pyrophosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Geranylgeranyl Pyrophosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg341 b:24.5 occ:1.00 OD2 A:ASP84 2.0 40.4 1.0 OD2 A:ASP80 2.1 39.1 1.0 O A:HOH373 2.1 33.5 1.0 O A:HOH370 2.5 32.8 1.0 O A:HOH371 3.1 36.8 1.0 O A:HOH368 3.1 17.8 1.0 CG A:ASP80 3.1 36.4 1.0 CG A:ASP84 3.2 37.9 1.0 O A:HOH369 3.5 39.9 1.0 OD1 A:ASP80 3.5 40.3 1.0 NH2 A:ARG89 4.0 36.0 1.0 CB A:ASP84 4.1 35.2 1.0 OD1 A:ASP84 4.1 40.3 1.0 O A:HOH372 4.2 38.3 1.0 CB A:ASP80 4.4 32.7 1.0 O A:ASP80 4.5 24.4 1.0 OE2 A:GLU236 4.5 44.1 1.0 OD1 A:ASP81 4.6 27.6 1.0 NZ A:LYS238 4.6 36.9 1.0 C A:ASP80 4.8 28.1 1.0 O A:HOH428 5.0 34.5 1.0

Magnesium binding site 2 out of 2 in the Geranylgeranyl Pyrophosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Geranylgeranyl Pyrophosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg341 b:29.7 occ:1.00 OD1 B:ASP80 2.0 40.0 1.0 OD2 B:ASP84 2.1 50.5 1.0 O B:HOH471 2.3 37.9 1.0 O B:HOH440 2.3 32.3 1.0 O B:HOH386 2.8 43.0 1.0 O B:HOH385 3.0 23.6 1.0 CG B:ASP80 3.1 41.3 1.0 CG B:ASP84 3.3 46.7 1.0 OD2 B:ASP80 3.4 40.2 1.0 O B:HOH387 3.4 45.7 1.0 NZ B:LYS238 4.0 39.4 1.0 O B:HOH469 4.0 46.4 1.0 OD1 B:ASP84 4.2 48.1 1.0 CB B:ASP84 4.2 42.1 1.0 OE1 B:GLU236 4.3 45.2 1.0 CB B:ASP80 4.4 34.8 1.0 NH2 B:ARG89 4.6 43.5 1.0 O B:ASP80 4.7 34.2 1.0 O B:HOH581 4.7 59.5 1.0 C B:ASP80 5.0 32.8 1.0 O B:HOH441 5.0 50.2 1.0

T.-H.Chang, R.-T.Guo, T.-P.Ko, A.H.Wang, P.-H.Liang. Crystal Structure of Type-III Geranylgeranyl Pyrophosphate Synthase From Saccharomyces Cerevisiae and the Mechanism of Product Chain Length Determination. J.Biol.Chem. V. 281 14991 2006.
ISSN: ISSN 0021-9258
PubMed: 16554305
DOI: 10.1074/JBC.M512886200