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

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

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-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 [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-Yl}Amino)Methanediyl]Bis(Phosphonic Acid), PDB code: 4pvx was solved by D.Rodionov, J.Park, Y.-S.Lin, 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) 69.34 / 2.18
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.260, 111.260, 69.340, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) (pdb code 4pvx). 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 [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-Yl}Amino)Methanediyl]Bis(Phosphonic Acid), PDB code: 4pvx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4pvx

Go back to Magnesium Binding Sites List in 4pvx
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-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 [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:26.9
occ:1.00
OAK F:YS1404 2.1 32.5 1.0
O F:HOH502 2.1 25.2 1.0
O F:HOH501 2.1 25.2 1.0
OD1 F:ASP103 2.1 25.2 1.0
OD2 F:ASP107 2.1 25.5 1.0
O F:HOH503 2.2 25.6 1.0
CG F:ASP107 3.0 26.5 1.0
CG F:ASP103 3.1 26.0 1.0
OD1 F:ASP107 3.1 27.2 1.0
MG F:MG402 3.2 26.8 1.0
PAI F:YS1404 3.3 27.6 1.0
OD2 F:ASP103 3.3 23.7 1.0
OAJ F:YS1404 3.5 28.1 1.0
O F:HOH505 4.1 24.2 1.0
NE2 F:GLN171 4.1 37.8 1.0
OD1 F:ASP174 4.1 34.7 1.0
OE1 F:GLN171 4.2 31.9 1.0
OD2 F:ASP174 4.2 30.7 1.0
O F:HOH507 4.3 27.1 1.0
OAL F:YS1404 4.3 26.7 1.0
CB F:ASP107 4.4 24.7 1.0
CG F:ASP174 4.5 32.3 1.0
CB F:ASP103 4.5 23.3 1.0
NAG F:YS1404 4.5 31.0 1.0
CAE F:YS1404 4.5 27.3 1.0
CD F:GLN171 4.6 32.5 1.0
CAH F:YS1404 4.6 27.3 1.0
CE F:LYS266 4.6 33.0 1.0
O F:HOH506 4.7 28.4 1.0
CAD F:YS1404 4.7 29.7 1.0
NZ F:LYS266 4.8 40.4 1.0
OAP F:YS1404 4.8 24.4 1.0
NZ F:LYS200 4.9 30.3 1.0
O F:HOH504 4.9 24.9 1.0
O F:ASP103 4.9 27.1 1.0
CAR F:YS1404 5.0 40.9 1.0

Magnesium binding site 2 out of 3 in 4pvx

Go back to Magnesium Binding Sites List in 4pvx
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-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 [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:26.8
occ:1.00
OD2 F:ASP103 2.0 23.7 1.0
O F:HOH505 2.1 24.2 1.0
OAP F:YS1404 2.1 24.4 1.0
O F:HOH504 2.1 24.9 1.0
OD2 F:ASP107 2.2 25.5 1.0
OAK F:YS1404 2.2 32.5 1.0
CG F:ASP103 3.0 26.0 1.0
MG F:MG401 3.2 26.9 1.0
CG F:ASP107 3.3 26.5 1.0
PAM F:YS1404 3.3 28.8 1.0
OD1 F:ASP103 3.4 25.2 1.0
PAI F:YS1404 3.4 27.6 1.0
CAH F:YS1404 3.7 27.3 1.0
CB F:ASP107 3.8 24.7 1.0
NAG F:YS1404 3.8 31.0 1.0
O F:HOH511 3.9 26.7 1.0
OAL F:YS1404 4.0 26.7 1.0
OAO F:YS1404 4.1 29.1 1.0
NH2 F:ARG112 4.1 23.5 1.0
O F:HOH522 4.2 23.5 1.0
CB F:ASP103 4.3 23.3 1.0
OD1 F:ASP107 4.4 27.2 1.0
OG F:SER109 4.4 31.1 1.0
O F:HOH506 4.4 28.4 1.0
OAN F:YS1404 4.5 26.3 1.0
O F:HOH503 4.5 25.6 1.0
O F:ASP103 4.5 27.1 1.0
OD1 F:ASP104 4.5 27.4 1.0
OAJ F:YS1404 4.7 28.1 1.0
C F:ASP103 4.7 25.3 1.0
O F:HOH502 4.7 25.2 1.0
O F:HOH512 4.8 31.5 1.0
CAD F:YS1404 4.8 29.7 1.0
MG F:MG403 4.9 27.4 1.0
O F:HOH501 5.0 25.2 1.0

Magnesium binding site 3 out of 3 in 4pvx

Go back to Magnesium Binding Sites List in 4pvx
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-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 [({4-[4- (Cyclopropyloxy)Phenyl]Pyridin-2-Yl}Amino)Methanediyl]Bis(Phosphonic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:27.4
occ:1.00
OAO F:YS1404 1.9 29.1 1.0
OAL F:YS1404 2.0 26.7 1.0
OD2 F:ASP243 2.1 28.0 1.0
O F:HOH522 2.1 23.5 1.0
O F:HOH523 2.2 28.0 1.0
O F:HOH524 2.2 22.3 1.0
CG F:ASP243 3.1 27.3 1.0
PAM F:YS1404 3.2 28.8 1.0
PAI F:YS1404 3.3 27.6 1.0
OD1 F:ASP243 3.5 28.3 1.0
CAH F:YS1404 3.5 27.3 1.0
O F:HOH507 4.0 27.1 1.0
OAP F:YS1404 4.0 24.4 1.0
OD1 F:ASP247 4.1 32.4 1.0
O F:HOH579 4.1 40.4 1.0
O F:HOH505 4.2 24.2 1.0
O F:ASP243 4.2 28.8 1.0
OAK F:YS1404 4.2 32.5 1.0
NE2 F:GLN240 4.3 30.3 1.0
OD1 F:ASP261 4.3 27.9 1.0
NZ F:LYS257 4.3 42.8 1.0
OAN F:YS1404 4.3 26.3 1.0
OD2 F:ASP261 4.4 30.6 1.0
CB F:ASP243 4.4 27.0 1.0
OAJ F:YS1404 4.4 28.1 1.0
OD1 F:ASP244 4.4 23.9 1.0
C F:ASP243 4.5 29.3 1.0
CG F:ASP247 4.7 32.0 1.0
CG F:ASP261 4.8 32.2 1.0
CB F:ASP247 4.8 30.3 1.0
O F:HOH511 4.9 26.7 1.0
MG F:MG402 4.9 26.8 1.0
NAG F:YS1404 5.0 31.0 1.0
N F:ASP244 5.0 27.0 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 01:41:17 2024

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