Magnesium in PDB 5cg5: Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate

All present enzymatic activity of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate:
2.5.1.1; 2.5.1.10;

The structure of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate, PDB code: 5cg5 was solved by T.Yokoyama, M.Mizuguchi, A.Ostermann, K.Kusaka, N.Niimura, T.E.Schrader, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.966, 111.966, 72.754, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.9

The binding sites of Magnesium atom in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate (pdb code 5cg5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate, PDB code: 5cg5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:6.8 occ:1.00 O A:DOD503 2.0 7.8 1.0 O A:DOD501 2.1 8.0 1.0 OD1 A:ASP103 2.1 7.2 1.0 O A:DOD502 2.1 7.8 1.0 OD2 A:ASP107 2.1 6.5 1.0 O17 A:RIS400 2.1 6.1 1.0 D2 A:DOD501 2.4 6.7 1.0 D2 A:DOD502 2.6 11.2 1.0 D2 A:DOD503 2.7 11.7 1.0 D1 A:DOD503 2.7 11.8 1.0 D1 A:DOD502 2.8 9.5 1.0 D1 A:DOD501 2.9 11.7 1.0 CG A:ASP107 3.0 7.6 1.0 CG A:ASP103 3.1 6.2 1.0 MG A:MG402 3.1 7.3 1.0 OD1 A:ASP107 3.2 7.3 1.0 P14 A:RIS400 3.3 7.8 1.0 HE21 A:GLN171 3.3 8.2 0.1 DE21 A:GLN171 3.3 8.2 0.9 OD2 A:ASP103 3.4 5.9 1.0 O16 A:RIS400 3.5 8.6 1.0 HZ2 A:LYS266 3.8 16.3 0.4 DZ2 A:LYS266 3.8 16.3 0.6 D1 A:DOD504 3.9 8.9 1.0 OD1 A:ASP174 4.0 12.4 1.0 HZ1 A:LYS266 4.1 18.3 0.2 DZ1 A:LYS266 4.1 18.3 0.8 HE3 A:LYS266 4.1 19.5 1.0 HC72 A:RIS400 4.1 7.8 1.0 NE2 A:GLN171 4.1 7.9 1.0 O A:DOD504 4.2 8.3 1.0 DZ2 A:LYS200 4.2 11.3 1.0 HZ2 A:LYS200 4.2 11.3 0.0 OE1 A:GLN171 4.2 10.5 1.0 D2 A:DOD529 4.2 14.2 1.0 O15 A:RIS400 4.3 8.0 1.0 DZ3 A:LYS200 4.3 12.3 0.9 HZ3 A:LYS200 4.3 12.3 0.1 NZ A:LYS266 4.3 19.6 1.0 O A:DOD529 4.4 10.4 1.0 OD2 A:ASP174 4.4 11.2 1.0 CG A:ASP174 4.4 12.7 1.0 CB A:ASP103 4.4 5.8 1.0 CB A:ASP107 4.5 9.1 1.0 HC1 A:RIS400 4.5 10.3 1.0 HB2 A:ASP103 4.6 8.5 1.0 D1 A:DOD529 4.6 9.4 1.0 C1 A:RIS400 4.6 8.9 1.0 CD A:GLN171 4.6 9.9 1.0 C8 A:RIS400 4.6 8.1 1.0 HB2 A:ASP107 4.7 8.0 1.0 C2 A:RIS400 4.7 7.1 1.0 C7 A:RIS400 4.7 7.7 1.0 NZ A:LYS200 4.7 10.1 1.0 HA A:ASP103 4.7 6.7 1.0 D2 A:DOD504 4.7 12.2 1.0 CE A:LYS266 4.8 9.3 1.0 O12 A:RIS400 4.8 7.0 1.0 HB3 A:ASP107 4.8 11.5 1.0 HD2 A:LYS200 4.8 9.2 1.0 DE22 A:GLN171 4.8 10.0 1.0 HE22 A:GLN171 4.8 10.0 0.0 O A:DOD505 4.9 7.5 1.0 O A:ASP103 4.9 5.4 1.0 O A:DOD528 5.0 10.0 1.0

Magnesium binding site 2 out of 3 in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:7.3 occ:1.00 O12 A:RIS400 2.0 7.0 1.0 O17 A:RIS400 2.1 6.1 1.0 O A:DOD504 2.1 8.3 1.0 OD2 A:ASP103 2.1 5.9 1.0 O A:DOD505 2.1 7.5 1.0 OD2 A:ASP107 2.2 6.5 1.0 D1 A:DOD504 2.6 8.9 1.0 D2 A:DOD504 2.7 12.2 1.0 D2 A:DOD505 2.8 5.6 1.0 D1 A:DOD505 2.8 9.3 1.0 CG A:ASP103 3.1 6.2 1.0 MG A:MG401 3.1 6.8 1.0 D2 A:DOD523 3.2 11.1 1.0 HC72 A:RIS400 3.3 7.8 1.0 P14 A:RIS400 3.3 7.8 1.0 CG A:ASP107 3.3 7.6 1.0 P9 A:RIS400 3.4 8.2 1.0 OD1 A:ASP103 3.4 7.2 1.0 HB2 A:ASP107 3.5 8.0 1.0 HH22 A:ARG112 3.6 9.1 0.2 DH22 A:ARG112 3.6 9.1 0.8 C8 A:RIS400 3.7 8.1 1.0 CB A:ASP107 3.8 9.1 1.0 HB3 A:ASP107 3.8 11.5 1.0 O A:DOD523 3.9 10.7 1.0 O15 A:RIS400 3.9 8.0 1.0 C7 A:RIS400 4.0 7.7 1.0 O10 A:RIS400 4.1 7.4 1.0 DH21 A:ARG112 4.1 9.9 0.8 HH21 A:ARG112 4.1 9.9 0.2 D1 A:DOD503 4.2 11.8 1.0 O A:DOD503 4.2 7.8 1.0 NH2 A:ARG112 4.2 9.3 1.0 D2 A:DOD524 4.3 17.0 1.0 O A:DOD508 4.3 10.0 1.0 D1 A:DOD523 4.4 13.3 1.0 CB A:ASP103 4.4 5.8 1.0 OD1 A:ASP107 4.4 7.3 1.0 O A:DOD528 4.4 10.0 1.0 O A:ASP103 4.4 5.4 1.0 D2 A:DOD501 4.5 6.7 1.0 OG A:SER109 4.5 10.4 1.0 D1 A:DOD528 4.5 14.3 1.0 HG A:SER109 4.5 10.8 0.3 DG A:SER109 4.5 10.8 0.7 HB3 A:ASP103 4.5 7.0 1.0 O11 A:RIS400 4.5 9.2 1.0 OD1 A:ASP104 4.6 8.6 1.0 HA A:ASP104 4.6 6.1 1.0 O16 A:RIS400 4.6 8.6 1.0 C A:ASP103 4.7 5.2 1.0 D2 A:DOD529 4.7 14.2 1.0 HC71 A:RIS400 4.7 8.2 1.0 HC1 A:RIS400 4.7 10.3 1.0 O A:DOD501 4.8 8.0 1.0 D1 A:DOD529 4.8 9.4 1.0 D1 A:DOD508 4.9 8.8 1.0 MG A:MG403 4.9 8.0 1.0 C2 A:RIS400 4.9 7.1 1.0 D2 A:DOD508 4.9 11.1 1.0 O A:DOD524 4.9 10.8 1.0 D2 A:DOD528 4.9 13.3 1.0 O A:DOD502 5.0 7.8 1.0

Magnesium binding site 3 out of 3 in the Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Neutron Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with Risedronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:8.0 occ:1.00 O10 A:RIS400 1.9 7.4 1.0 O A:DOD506 2.0 8.5 1.0 O15 A:RIS400 2.0 8.0 1.0 O A:DOD508 2.2 10.0 1.0 O A:DOD507 2.2 9.8 1.0 OD2 A:ASP243 2.2 9.1 1.0 D1 A:DOD507 2.6 11.8 1.0 D2 A:DOD507 2.6 15.1 1.0 D1 A:DOD508 2.7 8.8 1.0 D2 A:DOD506 2.7 9.3 1.0 D2 A:DOD508 2.7 11.1 1.0 D1 A:DOD506 2.7 12.7 1.0 D13 A:RIS400 2.8 10.4 1.0 CG A:ASP243 3.2 10.2 1.0 D2 A:DOD529 3.2 14.2 1.0 P9 A:RIS400 3.2 8.2 1.0 D2 A:DOD504 3.3 12.2 1.0 P14 A:RIS400 3.4 7.8 1.0 DE22 A:GLN240 3.5 11.0 0.9 HE22 A:GLN240 3.5 11.0 0.1 HZ3 A:LYS257 3.6 17.1 0.3 DZ3 A:LYS257 3.6 17.1 0.7 O13 A:RIS400 3.6 7.2 1.0 C8 A:RIS400 3.6 8.1 1.0 OD1 A:ASP243 3.6 13.3 1.0 HZ1 A:LYS257 3.8 21.9 0.0 DZ1 A:LYS257 3.8 21.9 1.0 D1 A:DOD529 3.8 9.4 1.0 O A:DOD529 4.0 10.4 1.0 OD1 A:ASP247 4.0 14.3 1.0 NZ A:LYS257 4.0 22.1 1.0 O12 A:RIS400 4.0 7.0 1.0 HB2 A:ASP247 4.1 10.4 1.0 HZ2 A:LYS257 4.1 19.1 0.7 DZ2 A:LYS257 4.1 19.1 0.3 O A:DOD504 4.2 8.3 1.0 O A:ASP243 4.2 10.7 1.0 O17 A:RIS400 4.2 6.1 1.0 NE2 A:GLN240 4.2 11.9 1.0 OD2 A:ASP261 4.3 12.8 1.0 HE21 A:GLN240 4.3 9.9 0.2 DE21 A:GLN240 4.3 9.9 0.8 OD1 A:ASP261 4.3 11.7 1.0 HA A:ASP244 4.4 12.5 1.0 O A:DOD526 4.4 24.6 1.0 D2 A:DOD523 4.4 11.1 1.0 D1 A:DOD526 4.4 22.9 1.0 CB A:ASP243 4.5 11.2 1.0 O16 A:RIS400 4.5 8.6 1.0 OD1 A:ASP244 4.5 11.3 1.0 HB3 A:ASP243 4.5 9.4 1.0 O11 A:RIS400 4.5 9.2 1.0 C A:ASP243 4.5 8.0 1.0 D1 A:DOD504 4.5 8.9 1.0 CG A:ASP247 4.6 12.5 1.0 CG A:ASP261 4.7 12.9 1.0 O A:DOD523 4.8 10.7 1.0 CB A:ASP247 4.8 9.5 1.0 MG A:MG402 4.9 7.3 1.0 D2 A:DOD509 4.9 31.8 1.0 N A:ASP244 5.0 10.3 1.0

T.Yokoyama, M.Mizuguchi, A.Ostermann, K.Kusaka, N.Niimura, T.E.Schrader, I.Tanaka. Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase J.Med.Chem. V. 58 7549 2015.
ISSN: ISSN 0022-2623
PubMed: 26314394
DOI: 10.1021/ACS.JMEDCHEM.5B01147