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
|