Magnesium in PDB 1yhl: Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2

The structure of Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2, PDB code: 1yhl was solved by S.B.Gabelli, J.S.Mclellan, A.Montalvetti, E.Oldfield, R.Docampo, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.55 / 1.95
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.152, 58.152, 389.512, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 23.2

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

Magnesium binding site 1 out of 3 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:18.6 occ:1.00 OD2 A:ASP98 2.0 17.2 1.0 O A:HOH1407 2.1 18.4 1.0 O15 A:RIS1400 2.1 18.5 1.0 OD2 A:ASP102 2.1 17.9 1.0 O12 A:RIS1400 2.1 20.6 1.0 O A:HOH1408 2.2 13.9 1.0 CG A:ASP98 3.0 19.8 1.0 MG A:MG1403 3.1 13.3 1.0 CG A:ASP102 3.2 19.4 1.0 OD1 A:ASP98 3.3 15.7 1.0 P9 A:RIS1400 3.4 18.0 1.0 P14 A:RIS1400 3.4 18.1 1.0 CB A:ASP102 3.7 19.9 1.0 C8 A:RIS1400 3.8 18.5 1.0 C7 A:RIS1400 3.9 13.6 1.0 O A:HOH1455 4.0 21.9 1.0 O16 A:RIS1400 4.0 15.0 1.0 O A:HOH1406 4.2 18.4 1.0 NH2 A:ARG107 4.2 16.8 1.0 O11 A:RIS1400 4.2 19.1 1.0 OD1 A:ASP102 4.3 17.6 1.0 CB A:ASP98 4.4 16.4 1.0 O A:ASP98 4.4 16.5 1.0 OG A:SER104 4.4 24.5 1.0 O A:HOH1411 4.4 18.1 1.0 O10 A:RIS1400 4.5 22.5 1.0 O17 A:RIS1400 4.5 18.1 1.0 OD1 A:ASP99 4.5 20.5 1.0 O A:HOH1458 4.5 23.9 1.0 C A:ASP98 4.6 19.0 1.0 O A:HOH1409 4.7 18.7 1.0 O A:HOH1532 4.8 18.2 1.0 C2 A:RIS1400 4.9 20.3 1.0 O A:HOH1447 4.9 19.6 1.0 MG A:MG1402 5.0 16.3 1.0

Magnesium binding site 2 out of 3 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:16.3 occ:1.00 O16 A:RIS1400 2.0 15.0 1.0 O A:HOH1410 2.0 18.9 1.0 O A:HOH1411 2.0 18.1 1.0 O A:HOH1533 2.0 20.9 1.0 OD2 A:ASP250 2.2 18.7 1.0 O11 A:RIS1400 2.2 19.1 1.0 CG A:ASP250 3.1 22.0 1.0 P14 A:RIS1400 3.2 18.1 1.0 P9 A:RIS1400 3.3 18.0 1.0 C8 A:RIS1400 3.6 18.5 1.0 O13 A:RIS1400 3.6 16.6 1.0 OD1 A:ASP250 3.6 25.2 1.0 O A:HOH1569 3.9 26.9 1.0 O A:HOH1440 4.0 17.0 1.0 O15 A:RIS1400 4.0 18.5 1.0 O12 A:RIS1400 4.0 20.6 1.0 OD1 A:ASP254 4.2 24.5 1.0 O A:HOH1408 4.2 13.9 1.0 O A:ASP250 4.2 18.4 1.0 OD2 A:ASP268 4.3 17.8 1.0 OD1 A:ASP268 4.3 17.8 1.0 CB A:ASP250 4.3 19.9 1.0 NE2 A:GLN247 4.3 16.4 1.0 O17 A:RIS1400 4.4 18.1 1.0 OD1 A:ASP251 4.5 20.2 1.0 NZ A:LYS264 4.5 23.6 1.0 C A:ASP250 4.5 20.6 1.0 O10 A:RIS1400 4.6 22.5 1.0 O A:HOH1455 4.6 21.9 1.0 CB A:ASP254 4.6 22.7 1.0 CE A:LYS264 4.7 24.4 1.0 CG A:ASP268 4.7 18.9 1.0 CG A:ASP254 4.7 21.7 1.0 N A:ASP251 5.0 20.5 1.0 MG A:MG1401 5.0 18.6 1.0 CA A:ASP250 5.0 20.2 1.0

Magnesium binding site 3 out of 3 in the Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Complex of Trypanosoma Cruzi Farnesyl Diphosphate Synthase with Risedronate, Dmapp and Mg+2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1403 b:13.3 occ:1.00 O A:HOH1409 2.0 18.7 1.0 OD1 A:ASP98 2.0 15.7 1.0 OD2 A:ASP102 2.1 17.9 1.0 O A:HOH1532 2.1 18.2 1.0 O A:HOH1406 2.2 18.4 1.0 O15 A:RIS1400 2.4 18.5 1.0 CG A:ASP98 3.0 19.8 1.0 CG A:ASP102 3.0 19.4 1.0 MG A:MG1401 3.1 18.6 1.0 OD1 A:ASP102 3.2 17.6 1.0 OD2 A:ASP98 3.3 17.2 1.0 O17 A:RIS1400 3.4 18.1 1.0 P14 A:RIS1400 3.4 18.1 1.0 OD2 A:ASP170 3.8 22.0 1.0 NE2 A:GLN167 4.2 19.5 1.0 O A:HOH1408 4.2 13.9 1.0 OE1 A:GLN167 4.2 15.8 1.0 O A:HOH1440 4.3 17.0 1.0 CG A:ASP170 4.3 17.2 1.0 O16 A:RIS1400 4.4 15.0 1.0 CB A:ASP98 4.4 16.4 1.0 NZ A:LYS273 4.4 27.5 1.0 OD1 A:ASP170 4.5 20.7 1.0 CB A:ASP102 4.5 19.9 1.0 C7 A:RIS1400 4.6 13.6 1.0 C1 A:RIS1400 4.6 16.4 1.0 C2 A:RIS1400 4.6 20.3 1.0 C8 A:RIS1400 4.6 18.5 1.0 CD A:GLN167 4.7 20.9 1.0 O12 A:RIS1400 4.7 20.6 1.0 O A:HOH1407 4.8 18.4 1.0 NZ A:LYS207 4.9 17.9 1.0 O A:ASP98 4.9 16.5 1.0 O A:HOH1458 5.0 23.9 1.0 CA A:ASP98 5.0 16.9 1.0

S.B.Gabelli, J.S.Mclellan, A.Montalvetti, E.Oldfield, R.Docampo, L.M.Amzel. Structure and Mechanism of the Farnesyl Diphosphate Synthase From Trypanosoma Cruzi: Implications For Drug Design. Proteins V. 62 80 2005.
ISSN: ISSN 0887-3585
PubMed: 16288456
DOI: 10.1002/PROT.20754