Magnesium in PDB 1zw5: X-Ray Structure of Farnesyl Diphosphate Synthase Protein

All present enzymatic activity of X-Ray Structure of Farnesyl Diphosphate Synthase Protein:
2.5.1.10;

The structure of X-Ray Structure of Farnesyl Diphosphate Synthase Protein, PDB code: 1zw5 was solved by K.L.Kavanagh, K.Guo, X.Wu, F.Von Delft, C.Arrowsmith, M.Sundstrom, A.Edwards, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.255, 112.255, 63.245, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.3

The binding sites of Magnesium atom in the X-Ray Structure of Farnesyl Diphosphate Synthase Protein (pdb code 1zw5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Structure of Farnesyl Diphosphate Synthase Protein, PDB code: 1zw5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Structure of Farnesyl Diphosphate Synthase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Farnesyl Diphosphate Synthase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg907 b:26.1 occ:1.00 O A:HOH911 1.9 22.8 1.0 OD2 A:ASP117 2.1 36.1 1.0 OD2 A:ASP121 2.2 46.3 1.0 O17 A:ZOL901 2.2 33.4 1.0 O11 A:ZOL901 2.2 35.2 1.0 O A:HOH913 2.3 24.4 1.0 MG A:MG909 2.7 26.6 1.0 CG A:ASP117 3.1 45.6 1.0 CG A:ASP121 3.2 52.5 1.0 OD1 A:ASP117 3.4 42.9 1.0 P14 A:ZOL901 3.5 44.3 1.0 P9 A:ZOL901 3.5 40.9 1.0 CB A:ASP121 3.6 50.3 1.0 C8 A:ZOL901 3.9 36.8 1.0 O16 A:ZOL901 4.0 34.1 1.0 O A:HOH910 4.0 30.2 1.0 O A:HOH961 4.2 28.0 1.0 O A:HOH912 4.2 22.4 1.0 C7 A:ZOL901 4.2 41.2 1.0 O12 A:ZOL901 4.3 35.6 1.0 OD1 A:ASP121 4.3 55.3 1.0 O A:ASP117 4.4 46.9 1.0 O A:HOH914 4.4 22.4 1.0 O A:HOH917 4.4 36.4 1.0 O A:HOH916 4.4 24.1 1.0 CB A:ASP117 4.5 38.7 1.0 OG A:SER123 4.5 42.9 1.0 O15 A:ZOL901 4.6 30.3 1.0 O10 A:ZOL901 4.6 26.4 1.0 C A:ASP117 4.7 40.7 1.0 NH2 A:ARG126 4.8 36.2 1.0 OD1 A:ASP118 4.9 39.0 1.0

Magnesium binding site 2 out of 3 in the X-Ray Structure of Farnesyl Diphosphate Synthase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Farnesyl Diphosphate Synthase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg908 b:25.9 occ:1.00 O A:HOH915 2.0 27.4 1.0 O A:HOH917 2.1 36.4 1.0 O A:HOH960 2.1 30.2 1.0 O12 A:ZOL901 2.1 35.6 1.0 OD2 A:ASP257 2.2 42.1 1.0 O16 A:ZOL901 2.2 34.1 1.0 CG A:ASP257 3.0 48.5 1.0 OD1 A:ASP257 3.3 42.8 1.0 P9 A:ZOL901 3.4 40.9 1.0 P14 A:ZOL901 3.5 44.3 1.0 O13 A:ZOL901 3.6 44.0 1.0 C8 A:ZOL901 3.6 36.8 1.0 O A:ASP257 4.0 45.5 1.0 O11 A:ZOL901 4.1 35.2 1.0 OD1 A:ASP261 4.2 45.8 1.0 NZ A:LYS271 4.2 37.1 1.0 CB A:ASP257 4.3 44.4 1.0 NE2 A:GLN254 4.3 41.3 1.0 C A:ASP257 4.3 46.9 1.0 OD2 A:ASP275 4.3 45.0 1.0 O17 A:ZOL901 4.3 33.4 1.0 OD1 A:ASP258 4.4 39.6 1.0 O A:HOH911 4.4 22.8 1.0 O10 A:ZOL901 4.5 26.4 1.0 CB A:ASP261 4.5 43.2 1.0 CE A:LYS271 4.5 44.9 1.0 O A:HOH940 4.5 30.8 1.0 OD1 A:ASP275 4.6 44.9 1.0 O15 A:ZOL901 4.6 30.3 1.0 CG A:ASP261 4.6 49.4 1.0 N A:ASP258 4.9 44.4 1.0 CG A:ASP275 4.9 43.1 1.0 CA A:ASP257 4.9 46.8 1.0 O A:HOH961 4.9 28.0 1.0 CA A:ASP258 5.0 44.3 1.0

Magnesium binding site 3 out of 3 in the X-Ray Structure of Farnesyl Diphosphate Synthase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Farnesyl Diphosphate Synthase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg909 b:26.6 occ:1.00 O A:HOH916 2.0 24.1 1.0 O A:HOH914 2.0 22.4 1.0 OD2 A:ASP121 2.1 46.3 1.0 O17 A:ZOL901 2.2 33.4 1.0 OD1 A:ASP117 2.2 42.9 1.0 O A:HOH912 2.3 22.4 1.0 MG A:MG907 2.7 26.1 1.0 CG A:ASP117 3.0 45.6 1.0 OD2 A:ASP117 3.1 36.1 1.0 CG A:ASP121 3.1 52.5 1.0 P14 A:ZOL901 3.4 44.3 1.0 O15 A:ZOL901 3.5 30.3 1.0 OD1 A:ASP121 3.5 55.3 1.0 OD1 A:ASP188 3.6 43.9 1.0 NZ A:LYS280 3.9 55.7 1.0 OE1 A:GLN185 4.2 41.5 1.0 O A:HOH911 4.2 22.8 1.0 O16 A:ZOL901 4.4 34.1 1.0 O11 A:ZOL901 4.4 35.2 1.0 CB A:ASP121 4.4 50.3 1.0 CB A:ASP117 4.5 38.7 1.0 C8 A:ZOL901 4.5 36.8 1.0 C7 A:ZOL901 4.5 41.2 1.0 CG A:ASP188 4.6 65.0 1.0 O A:HOH940 4.6 30.8 1.0 NE2 A:GLN185 4.6 39.8 1.0 C19 A:ZOL901 4.7 32.6 1.0 N15 A:ZOL901 4.7 38.3 1.0 O A:HOH913 4.8 24.4 1.0 CD A:GLN185 4.8 55.9 1.0 O A:HOH910 4.9 30.2 1.0 O A:ASP117 4.9 46.9 1.0 OD2 A:ASP188 5.0 58.4 1.0

K.L.Kavanagh, K.Guo, J.E.Dunford, X.Wu, S.Knapp, F.H.Ebetino, M.J.Rogers, R.G.Russell, U.Oppermann. The Molecular Mechanism of Nitrogen-Containing Bisphosphonates As Antiosteoporosis Drugs. Proc.Natl.Acad.Sci.Usa V. 103 7829 2006.
ISSN: ISSN 0027-8424
PubMed: 16684881
DOI: 10.1073/PNAS.0601643103