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Magnesium in PDB 4pvy: Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid)

Enzymatic activity of Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid)

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid):
2.5.1.1; 2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid), PDB code: 4pvy was solved by D.Rodionov, J.Park, J.W.De Schutter, Y.S.Tsantrizos, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 111.06 / 2.05
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.060, 111.060, 67.030, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) (pdb code 4pvy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid), PDB code: 4pvy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4pvy

Go back to Magnesium Binding Sites List in 4pvy
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid)


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 Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:19.2
occ:1.00
 O F:HOH515 2.0 17.3 1.0
O F:HOH541 2.0 16.8 1.0
OAJ F:JD1404 2.1 17.9 1.0
O F:HOH517 2.2 18.4 1.0
OD1 F:ASP103 2.2 20.4 1.0
OD2 F:ASP107 2.2 21.1 1.0
CG F:ASP103 3.1 18.5 1.0
CG F:ASP107 3.1 22.1 1.0
MG F:MG402 3.2 20.2 1.0
OD1 F:ASP107 3.2 21.6 1.0
OD2 F:ASP103 3.3 17.7 1.0
PAI F:JD1404 3.4 20.4 1.0
OAL F:JD1404 3.5 20.0 1.0
NE2 F:GLN171 3.9 22.5 1.0
NZ F:LYS266 4.0 31.1 1.0
OE1 F:GLN171 4.1 22.9 1.0
OD1 F:ASP174 4.2 29.4 1.0
O F:HOH534 4.3 24.5 1.0
O F:HOH505 4.3 16.6 1.0
OAK F:JD1404 4.4 21.4 1.0
OD2 F:ASP174 4.4 28.2 1.0
NAG F:JD1404 4.4 21.3 1.0
CD F:GLN171 4.4 22.9 1.0
CB F:ASP103 4.4 17.6 1.0
CAE F:JD1404 4.5 19.4 1.0
O F:HOH683 4.5 42.9 1.0
CB F:ASP107 4.5 20.0 1.0
CG F:ASP174 4.6 26.8 1.0
CAD F:JD1404 4.6 20.9 1.0
CAH F:JD1404 4.6 20.3 1.0
OAN F:JD1404 4.8 19.3 1.0
NZ F:LYS200 4.8 20.3 1.0
O F:HOH530 4.9 21.1 1.0
O F:ASP103 4.9 16.9 1.0
O F:HOH537 4.9 15.5 1.0

Magnesium binding site 2 out of 3 in 4pvy

Go back to Magnesium Binding Sites List in 4pvy
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid)


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 Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:20.2
occ:1.00
 O F:HOH505 2.1 16.6 1.0
OD2 F:ASP103 2.1 17.7 1.0
OAN F:JD1404 2.1 19.3 1.0
OD2 F:ASP107 2.2 21.1 1.0
O F:HOH537 2.2 15.5 1.0
OAJ F:JD1404 2.2 17.9 1.0
CG F:ASP103 3.1 18.5 1.0
MG F:MG401 3.2 19.2 1.0
CG F:ASP107 3.3 22.1 1.0
PAM F:JD1404 3.4 19.9 1.0
PAI F:JD1404 3.4 20.4 1.0
OD1 F:ASP103 3.5 20.4 1.0
CAH F:JD1404 3.7 20.3 1.0
CB F:ASP107 3.8 20.0 1.0
NAG F:JD1404 3.8 21.3 1.0
OAK F:JD1404 3.9 21.4 1.0
O F:HOH509 4.0 20.5 1.0
OAP F:JD1404 4.0 19.1 1.0
O F:HOH517 4.2 18.4 1.0
O F:HOH520 4.3 18.1 1.0
O F:HOH530 4.3 21.1 1.0
NH2 F:ARG112 4.3 19.5 1.0
OD1 F:ASP107 4.3 21.6 1.0
O F:ASP103 4.4 16.9 1.0
CB F:ASP103 4.4 17.6 1.0
OAO F:JD1404 4.4 18.4 1.0
OAL F:JD1404 4.5 20.0 1.0
OG F:SER109 4.5 21.3 1.0
OD1 F:ASP104 4.6 19.6 1.0
O F:HOH541 4.7 16.8 1.0
C F:ASP103 4.7 17.2 1.0
CAD F:JD1404 4.8 20.9 1.0
O F:HOH515 4.8 17.3 1.0
MG F:MG403 4.8 22.7 1.0
O F:HOH534 4.9 24.5 1.0
O F:HOH526 4.9 21.9 1.0

Magnesium binding site 3 out of 3 in 4pvy

Go back to Magnesium Binding Sites List in 4pvy
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Fpps in Complex with [({5-[4-(Propan-2- Yloxy)Phenyl]Pyridin-3-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:22.7
occ:1.00
 OAK F:JD1404 2.0 21.4 1.0
OD2 F:ASP243 2.0 20.6 1.0
OAP F:JD1404 2.1 19.1 1.0
O F:HOH520 2.1 18.1 1.0
O F:HOH508 2.2 18.6 1.0
O F:HOH540 2.3 21.2 1.0
CG F:ASP243 3.1 23.0 1.0
PAI F:JD1404 3.2 20.4 1.0
PAM F:JD1404 3.3 19.9 1.0
CAH F:JD1404 3.5 20.3 1.0
OD1 F:ASP243 3.5 22.8 1.0
O F:HOH534 3.9 24.5 1.0
OD1 F:ASP247 4.0 27.1 1.0
OAN F:JD1404 4.0 19.3 1.0
NZ F:LYS257 4.0 21.1 0.5
O F:HOH617 4.1 40.9 1.0
OAJ F:JD1404 4.2 17.9 1.0
O F:HOH505 4.2 16.6 1.0
NE2 F:GLN240 4.2 21.7 1.0
O F:ASP243 4.2 22.8 1.0
OD1 F:ASP261 4.3 21.9 1.0
OD2 F:ASP261 4.3 22.7 1.0
CB F:ASP243 4.3 22.4 1.0
OAL F:JD1404 4.4 20.0 1.0
OAO F:JD1404 4.5 18.4 1.0
OD1 F:ASP244 4.5 21.9 1.0
C F:ASP243 4.5 22.4 1.0
NZ F:LYS257 4.6 24.7 0.5
CG F:ASP247 4.7 24.7 1.0
CG F:ASP261 4.7 23.0 1.0
O F:HOH509 4.8 20.5 1.0
MG F:MG402 4.8 20.2 1.0
CB F:ASP247 4.9 24.3 1.0
O F:HOH637 4.9 40.7 1.0
N F:ASP244 4.9 22.3 1.0
NAG F:JD1404 5.0 21.3 1.0

Reference:

J.Park, D.Rodionov, J.W.De Schutter, Y.-S.Lin, Y.S.Tsantrizos, A.M.Berghuis. Binding of Novel Phenylaminopyridine Bisphosphonate Inhibitors of Human Farnesyl Pyrophosphate Synthase to the Target Enzyme Involves Unexpected Conformational Flexibility To Be Published.
Page generated: Mon Aug 11 22:10:35 2025

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