Atomistry » Magnesium » PDB 4pjk-4pyk » 4pvy
Atomistry »
  Magnesium »
    PDB 4pjk-4pyk »
      4pvy »

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: Tue Aug 20 01:41:19 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy