Magnesium in PDB 4lfv: Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate
Enzymatic activity of Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate
All present enzymatic activity of Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate:
2.5.1.1;
2.5.1.10;
Protein crystallography data
The structure of Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate, PDB code: 4lfv
was solved by
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)
|
51.03 /
2.00
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.020,
111.020,
67.040,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.6 /
21.8
|
Other elements in 4lfv:
The structure of Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate
(pdb code 4lfv). 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 YS0470 and Two Molecules of Inorganic Phosphate, PDB code: 4lfv:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 4lfv
Go back to
Magnesium Binding Sites List in 4lfv
Magnesium binding site 1 out
of 3 in the Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate
 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 YS0470 and Two Molecules of Inorganic Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg404
b:22.8
occ:1.00
|
O
|
F:HOH542
|
1.9
|
24.2
|
1.0
|
O
|
F:HOH505
|
2.0
|
21.5
|
1.0
|
O
|
F:HOH525
|
2.1
|
23.0
|
1.0
|
OD2
|
F:ASP107
|
2.1
|
24.4
|
1.0
|
OD2
|
F:ASP103
|
2.1
|
23.4
|
1.0
|
O3
|
F:YS4401
|
2.1
|
25.5
|
1.0
|
CG
|
F:ASP107
|
3.0
|
23.6
|
1.0
|
CG
|
F:ASP103
|
3.1
|
23.1
|
1.0
|
OD1
|
F:ASP107
|
3.2
|
27.1
|
1.0
|
MG
|
F:MG405
|
3.2
|
24.6
|
1.0
|
OD1
|
F:ASP103
|
3.4
|
22.8
|
1.0
|
P1
|
F:YS4401
|
3.4
|
24.9
|
1.0
|
O2
|
F:YS4401
|
3.5
|
25.1
|
1.0
|
NZ
|
F:LYS266
|
4.0
|
34.7
|
1.0
|
NE2
|
F:GLN171
|
4.1
|
31.0
|
1.0
|
OD2
|
F:ASP174
|
4.1
|
39.3
|
1.0
|
OE1
|
F:GLN171
|
4.1
|
29.5
|
1.0
|
O
|
F:HOH506
|
4.2
|
24.0
|
1.0
|
O
|
F:HOH526
|
4.3
|
28.4
|
1.0
|
OD1
|
F:ASP174
|
4.3
|
34.9
|
1.0
|
O4
|
F:YS4401
|
4.4
|
27.6
|
1.0
|
CB
|
F:ASP107
|
4.4
|
22.4
|
1.0
|
N1
|
F:YS4401
|
4.4
|
25.7
|
1.0
|
CD
|
F:GLN171
|
4.5
|
29.1
|
1.0
|
CB
|
F:ASP103
|
4.5
|
21.4
|
1.0
|
CG
|
F:ASP174
|
4.5
|
32.9
|
1.0
|
C11
|
F:YS4401
|
4.5
|
25.5
|
1.0
|
C13
|
F:YS4401
|
4.6
|
26.7
|
1.0
|
C12
|
F:YS4401
|
4.6
|
24.7
|
1.0
|
O
|
F:ASP103
|
4.8
|
22.2
|
1.0
|
O
|
F:HOH519
|
4.8
|
26.6
|
1.0
|
O6
|
F:YS4401
|
4.8
|
23.4
|
1.0
|
NZ
|
F:LYS200
|
4.9
|
24.1
|
1.0
|
O
|
F:HOH512
|
4.9
|
21.3
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 4lfv
Go back to
Magnesium Binding Sites List in 4lfv
Magnesium binding site 2 out
of 3 in the Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate
 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 YS0470 and Two Molecules of Inorganic Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg405
b:24.6
occ:1.00
|
O
|
F:HOH512
|
2.1
|
21.3
|
1.0
|
OD1
|
F:ASP103
|
2.1
|
22.8
|
1.0
|
O6
|
F:YS4401
|
2.1
|
23.4
|
1.0
|
O
|
F:HOH506
|
2.1
|
24.0
|
1.0
|
O3
|
F:YS4401
|
2.1
|
25.5
|
1.0
|
OD2
|
F:ASP107
|
2.3
|
24.4
|
1.0
|
CG
|
F:ASP103
|
3.0
|
23.1
|
1.0
|
MG
|
F:MG404
|
3.2
|
22.8
|
1.0
|
CG
|
F:ASP107
|
3.3
|
23.6
|
1.0
|
P2
|
F:YS4401
|
3.4
|
23.8
|
1.0
|
OD2
|
F:ASP103
|
3.4
|
23.4
|
1.0
|
P1
|
F:YS4401
|
3.4
|
24.9
|
1.0
|
CB
|
F:ASP107
|
3.7
|
22.4
|
1.0
|
C13
|
F:YS4401
|
3.7
|
26.7
|
1.0
|
N1
|
F:YS4401
|
3.8
|
25.7
|
1.0
|
O
|
F:HOH524
|
3.8
|
23.1
|
1.0
|
O5
|
F:YS4401
|
4.1
|
24.3
|
1.0
|
O4
|
F:YS4401
|
4.1
|
27.6
|
1.0
|
NH2
|
F:ARG112
|
4.3
|
23.0
|
1.0
|
O
|
F:ASP103
|
4.3
|
22.2
|
1.0
|
O
|
F:HOH505
|
4.3
|
21.5
|
1.0
|
O
|
F:HOH510
|
4.3
|
23.3
|
1.0
|
CB
|
F:ASP103
|
4.4
|
21.4
|
1.0
|
O
|
F:HOH519
|
4.4
|
26.6
|
1.0
|
OD1
|
F:ASP104
|
4.4
|
21.1
|
1.0
|
OD1
|
F:ASP107
|
4.4
|
27.1
|
1.0
|
OG
|
F:SER109
|
4.4
|
23.9
|
1.0
|
O7
|
F:YS4401
|
4.4
|
24.7
|
1.0
|
C
|
F:ASP103
|
4.6
|
20.9
|
1.0
|
O
|
F:HOH542
|
4.6
|
24.2
|
1.0
|
O2
|
F:YS4401
|
4.6
|
25.1
|
1.0
|
O
|
F:HOH550
|
4.8
|
26.4
|
1.0
|
C12
|
F:YS4401
|
4.8
|
24.7
|
1.0
|
MG
|
F:MG406
|
4.9
|
26.0
|
1.0
|
O
|
F:HOH525
|
5.0
|
23.0
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 4lfv
Go back to
Magnesium Binding Sites List in 4lfv
Magnesium binding site 3 out
of 3 in the Crystal Structure of Human Fpps in Complex with YS0470 and Two Molecules of Inorganic Phosphate
 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 YS0470 and Two Molecules of Inorganic Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg406
b:26.0
occ:1.00
|
O5
|
F:YS4401
|
1.9
|
24.3
|
1.0
|
O4
|
F:YS4401
|
2.1
|
27.6
|
1.0
|
O
|
F:HOH501
|
2.1
|
21.4
|
1.0
|
O
|
F:HOH510
|
2.1
|
23.3
|
1.0
|
OD2
|
F:ASP243
|
2.2
|
26.7
|
1.0
|
O
|
F:HOH516
|
2.2
|
25.1
|
1.0
|
CG
|
F:ASP243
|
3.2
|
29.3
|
1.0
|
P1
|
F:YS4401
|
3.3
|
24.9
|
1.0
|
P2
|
F:YS4401
|
3.3
|
23.8
|
1.0
|
OD1
|
F:ASP243
|
3.5
|
28.9
|
1.0
|
C13
|
F:YS4401
|
3.5
|
26.7
|
1.0
|
O
|
F:HOH526
|
3.9
|
28.4
|
1.0
|
O
|
F:HOH586
|
4.1
|
34.6
|
1.0
|
O6
|
F:YS4401
|
4.1
|
23.4
|
1.0
|
O
|
F:HOH506
|
4.1
|
24.0
|
1.0
|
NZ
|
F:LYS257
|
4.1
|
32.3
|
1.0
|
OD2
|
F:ASP247
|
4.1
|
27.8
|
1.0
|
NE2
|
F:GLN240
|
4.2
|
23.1
|
1.0
|
O3
|
F:YS4401
|
4.2
|
25.5
|
1.0
|
O
|
F:ASP243
|
4.2
|
27.0
|
1.0
|
OD2
|
F:ASP261
|
4.2
|
26.6
|
1.0
|
OD1
|
F:ASP261
|
4.3
|
29.7
|
1.0
|
O2
|
F:YS4401
|
4.4
|
25.1
|
1.0
|
OD1
|
F:ASP244
|
4.4
|
28.6
|
1.0
|
CB
|
F:ASP243
|
4.5
|
27.9
|
1.0
|
O7
|
F:YS4401
|
4.5
|
24.7
|
1.0
|
C
|
F:ASP243
|
4.5
|
24.4
|
1.0
|
CG
|
F:ASP247
|
4.7
|
27.0
|
1.0
|
CG
|
F:ASP261
|
4.7
|
28.8
|
1.0
|
O
|
F:HOH524
|
4.7
|
23.1
|
1.0
|
CB
|
F:ASP247
|
4.7
|
26.8
|
1.0
|
N
|
F:ASP244
|
4.9
|
26.8
|
1.0
|
MG
|
F:MG405
|
4.9
|
24.6
|
1.0
|
|
Reference:
J.Park,
Y.S.Lin,
Y.S.Tsantrizos,
A.M.Berghuis.
Structure of Human Farnesyl Pyrophosphate Synthase in Complex with An Aminopyridine Bisphosphonate and Two Molecules of Inorganic Phosphate. Acta Crystallogr F Struct V. 70 299 2014BIOL Commun.
ISSN: ISSN 1744-3091
PubMed: 24598914
DOI: 10.1107/S2053230X14002106
Page generated: Mon Aug 19 17:43:24 2024
|