Magnesium in PDB 1yv5: Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate

All present enzymatic activity of Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate:
2.5.1.10;

The structure of Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate, PDB code: 1yv5 was solved by K.L.Kavanagh, K.Guo, 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)	52.34 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.946, 110.946, 70.264, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.9

The binding sites of Magnesium atom in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate (pdb code 1yv5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate, PDB code: 1yv5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg907 b:7.7 occ:1.00 O A:HOH1009 1.8 12.1 1.0 OD2 A:ASP117 2.1 16.7 1.0 O15 A:RIS901 2.2 11.4 1.0 O12 A:RIS901 2.2 12.7 1.0 OD2 A:ASP121 2.2 20.8 1.0 O A:HOH1017 2.3 2.0 1.0 MG A:MG909 2.8 8.8 1.0 CG A:ASP117 3.2 21.7 1.0 CG A:ASP121 3.2 29.6 1.0 P9 A:RIS901 3.5 15.7 1.0 P14 A:RIS901 3.5 16.5 1.0 OD1 A:ASP117 3.6 24.5 1.0 CB A:ASP121 3.6 28.5 1.0 C8 A:RIS901 3.9 12.3 1.0 C7 A:RIS901 4.0 14.5 1.0 O16 A:RIS901 4.1 12.2 1.0 O A:HOH1012 4.1 8.5 1.0 O A:HOH1044 4.1 6.2 1.0 O A:ASP117 4.3 15.0 1.0 O A:HOH1004 4.3 15.8 1.0 O11 A:RIS901 4.3 11.9 1.0 OD1 A:ASP121 4.3 27.9 1.0 OG A:SER123 4.3 28.3 1.0 CB A:ASP117 4.4 19.4 1.0 O A:HOH1034 4.4 14.0 1.0 NH2 A:ARG126 4.4 22.6 1.0 OD1 A:ASP118 4.5 9.4 1.0 O10 A:RIS901 4.5 12.6 1.0 C A:ASP117 4.6 18.2 1.0 O17 A:RIS901 4.6 12.7 1.0 O A:HOH1049 4.6 12.0 1.0 O A:HOH1010 4.7 15.5 1.0 O A:HOH1073 4.7 20.2 1.0 O A:HOH1080 4.9 18.2 1.0 C2 A:RIS901 5.0 20.5 1.0

Magnesium binding site 2 out of 3 in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg908 b:10.6 occ:1.00 O A:HOH1080 2.0 18.2 1.0 O A:HOH1046 2.1 13.8 1.0 O11 A:RIS901 2.1 11.9 1.0 O16 A:RIS901 2.1 12.2 1.0 OD2 A:ASP257 2.2 30.8 1.0 O A:HOH1045 2.2 5.9 1.0 CG A:ASP257 3.2 25.6 1.0 P9 A:RIS901 3.3 15.7 1.0 P14 A:RIS901 3.4 16.5 1.0 OD1 A:ASP257 3.6 31.4 1.0 C8 A:RIS901 3.6 12.3 1.0 O13 A:RIS901 3.7 15.7 1.0 O A:HOH1010 3.8 15.5 1.0 OD1 A:ASP261 4.0 29.1 1.0 O A:ASP257 4.0 20.4 1.0 O12 A:RIS901 4.1 12.7 1.0 O15 A:RIS901 4.1 11.4 1.0 NE2 A:GLN254 4.2 30.5 1.0 OD1 A:ASP275 4.2 19.4 1.0 NZ A:LYS271 4.2 29.7 1.0 OD2 A:ASP275 4.2 23.0 1.0 C A:ASP257 4.4 21.7 1.0 CB A:ASP257 4.4 24.1 1.0 O A:HOH1009 4.4 12.1 1.0 OD1 A:ASP258 4.5 7.5 1.0 O17 A:RIS901 4.5 12.7 1.0 O10 A:RIS901 4.5 12.6 1.0 CB A:ASP261 4.6 24.1 1.0 CG A:ASP261 4.6 37.2 1.0 CG A:ASP275 4.7 26.2 1.0 O A:HOH1044 4.8 6.2 1.0 CE A:LYS271 4.8 28.6 1.0 N A:ASP258 4.9 20.6 1.0 CA A:ASP257 5.0 21.8 1.0

Magnesium binding site 3 out of 3 in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Farnesyl Diphosphate Synthase Complexed with Mg and Risedronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg909 b:8.8 occ:1.00 O A:HOH1034 2.0 14.0 1.0 O A:HOH1049 2.1 12.0 1.0 OD2 A:ASP121 2.1 20.8 1.0 OD1 A:ASP117 2.1 24.5 1.0 O15 A:RIS901 2.1 11.4 1.0 O A:HOH1012 2.2 8.5 1.0 CG A:ASP117 2.8 21.7 1.0 MG A:MG907 2.8 7.7 1.0 OD2 A:ASP117 2.8 16.7 1.0 CG A:ASP121 3.1 29.6 1.0 P14 A:RIS901 3.3 16.5 1.0 O17 A:RIS901 3.4 12.7 1.0 OD1 A:ASP121 3.4 27.9 1.0 O A:HOH1009 4.0 12.1 1.0 O A:HOH1010 4.2 15.5 1.0 CB A:ASP117 4.2 19.4 1.0 OD1 A:ASP188 4.2 43.0 1.0 O16 A:RIS901 4.2 12.2 1.0 OE1 A:GLN185 4.3 35.0 1.0 NE2 A:GLN185 4.3 23.8 1.0 C7 A:RIS901 4.4 14.5 1.0 CB A:ASP121 4.4 28.5 1.0 O12 A:RIS901 4.4 12.7 1.0 C8 A:RIS901 4.4 12.3 1.0 C2 A:RIS901 4.5 20.5 1.0 C1 A:RIS901 4.5 14.9 1.0 NZ A:LYS280 4.7 34.4 1.0 CD A:GLN185 4.7 36.8 1.0 NZ A:LYS214 4.8 19.5 1.0 O A:ASP117 4.8 15.0 1.0 CG A:ASP188 4.8 37.5 1.0 O A:HOH1017 4.8 2.0 1.0 OD2 A:ASP188 4.8 36.0 1.0 CA A:ASP117 4.9 19.3 1.0 CE A:LYS280 4.9 29.3 1.0 O A:HOH1004 5.0 15.8 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