Magnesium in PDB 6kd7: Crystal Structure of Geranylgeranyl Pyrophosphate Synthase

The structure of Crystal Structure of Geranylgeranyl Pyrophosphate Synthase, PDB code: 6kd7 was solved by S.Kim, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.43 / 2.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	194.718, 194.718, 107.544, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase (pdb code 6kd7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Geranylgeranyl Pyrophosphate Synthase, PDB code: 6kd7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of 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 Crystal Structure of Geranylgeranyl Pyrophosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:48.3 occ:1.00 NH1 A:ARG88 3.3 32.1 1.0 NH2 A:ARG88 3.8 28.1 1.0 CZ A:ARG88 4.0 28.3 1.0 O12 A:PPV401 4.1 0.3 1.0 O11 A:PPV401 4.2 86.5 1.0 CD2 A:LEU76 4.3 25.9 1.0 O A:HOH602 4.7 52.3 1.0 OPP A:PPV401 4.9 89.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 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 Crystal Structure of Geranylgeranyl Pyrophosphate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:57.2 occ:1.00 O A:HOH570 3.2 37.6 1.0 NZ A:LYS168 3.9 72.0 1.0 OE1 A:GLN206 3.9 32.3 1.0 O A:HOH536 4.4 30.4 1.0 CD A:GLN206 4.5 30.3 1.0 CD A:LYS168 4.5 50.8 1.0 OD2 A:ASP147 4.6 35.8 1.0 NE2 A:GLN206 4.7 28.2 1.0 CE A:LYS168 4.7 66.8 1.0

S.Kim, E.J.Kim, J.B.Park, S.W.Kim, K.J.Kim. Crystal Structure of Geranylgeranyl Pyrophosphate Synthase (Crte) From Nonlabens Dokdonensis Dsw-6. Biochem.Biophys.Res.Commun. V. 518 479 2019.
ISSN: ESSN 1090-2104
PubMed: 31427080
DOI: 10.1016/J.BBRC.2019.08.071