Iron in PDB 4dt2: Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209
Enzymatic activity of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209
All present enzymatic activity of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209:
3.1.3.2;
Protein crystallography data
The structure of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209, PDB code: 4dt2
was solved by
D.Feder,
W.M.Hussein,
D.J.Clayton,
M.Kan,
G.Schenk,
R.P.Mcgeary,
L.W.Guddat,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.72 /
2.70
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.760,
126.760,
298.954,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.5 /
22.8
|
Other elements in 4dt2:
The structure of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209
(pdb code 4dt2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209, PDB code: 4dt2:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4dt2
Go back to
Iron Binding Sites List in 4dt2
Iron binding site 1 out
of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:45.9
occ:0.85
|
OH
|
A:TYR167
|
2.1
|
37.4
|
1.0
|
OD2
|
A:ASP164
|
2.2
|
38.3
|
1.0
|
OD2
|
A:ASP135
|
2.2
|
34.7
|
1.0
|
NE2
|
A:HIS325
|
2.4
|
38.5
|
1.0
|
CAD
|
A:0LV504
|
2.6
|
35.4
|
1.0
|
CAE
|
A:0LV504
|
2.7
|
44.2
|
1.0
|
CG
|
A:ASP135
|
3.2
|
35.9
|
1.0
|
CZ
|
A:TYR167
|
3.2
|
38.3
|
1.0
|
ZN
|
A:ZN501
|
3.2
|
44.3
|
1.0
|
CG
|
A:ASP164
|
3.2
|
37.4
|
1.0
|
CE1
|
A:HIS325
|
3.3
|
35.6
|
1.0
|
CD2
|
A:HIS325
|
3.4
|
36.1
|
1.0
|
CB
|
A:ASP135
|
3.6
|
31.1
|
1.0
|
CB
|
A:ASP164
|
3.7
|
34.1
|
1.0
|
CE2
|
A:TYR167
|
3.7
|
39.5
|
1.0
|
O
|
A:HIS323
|
3.9
|
42.4
|
1.0
|
CAF
|
A:0LV504
|
4.0
|
49.5
|
1.0
|
CAJ
|
A:0LV504
|
4.0
|
53.6
|
1.0
|
CD2
|
A:HIS202
|
4.1
|
37.3
|
1.0
|
CA
|
A:HIS323
|
4.2
|
35.2
|
1.0
|
OD1
|
A:ASP135
|
4.3
|
37.9
|
1.0
|
OD1
|
A:ASP164
|
4.3
|
34.9
|
1.0
|
CE1
|
A:TYR167
|
4.3
|
33.9
|
1.0
|
NE2
|
A:HIS202
|
4.3
|
41.8
|
1.0
|
C
|
A:HIS323
|
4.4
|
38.7
|
1.0
|
ND1
|
A:HIS325
|
4.5
|
37.2
|
1.0
|
NE2
|
A:HIS286
|
4.5
|
35.3
|
1.0
|
CA
|
A:ASP135
|
4.5
|
32.1
|
1.0
|
CE1
|
A:HIS286
|
4.5
|
35.9
|
1.0
|
CG
|
A:HIS325
|
4.6
|
36.4
|
1.0
|
N
|
A:HIS323
|
4.7
|
33.4
|
1.0
|
OD1
|
A:ASN201
|
4.7
|
45.7
|
1.0
|
CAG
|
A:0LV504
|
4.8
|
55.8
|
1.0
|
ND1
|
A:HIS323
|
4.9
|
39.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 4dt2
Go back to
Iron Binding Sites List in 4dt2
Iron binding site 2 out
of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:48.9
occ:0.87
|
OD2
|
B:ASP135
|
2.0
|
40.3
|
1.0
|
OH
|
B:TYR167
|
2.1
|
42.2
|
1.0
|
NE2
|
B:HIS325
|
2.5
|
40.1
|
1.0
|
OD2
|
B:ASP164
|
2.5
|
41.9
|
1.0
|
CAD
|
B:0LV504
|
2.7
|
46.6
|
1.0
|
CAE
|
B:0LV504
|
3.0
|
53.1
|
1.0
|
CG
|
B:ASP135
|
3.2
|
42.6
|
1.0
|
CZ
|
B:TYR167
|
3.2
|
44.0
|
1.0
|
ZN
|
B:ZN501
|
3.2
|
51.0
|
1.0
|
CD2
|
B:HIS325
|
3.4
|
37.3
|
1.0
|
CG
|
B:ASP164
|
3.5
|
41.3
|
1.0
|
CE1
|
B:HIS325
|
3.5
|
39.3
|
1.0
|
CE1
|
B:TYR167
|
3.5
|
44.4
|
1.0
|
CB
|
B:ASP135
|
3.8
|
40.6
|
1.0
|
CB
|
B:ASP164
|
3.8
|
36.0
|
1.0
|
CAF
|
B:0LV504
|
3.9
|
55.4
|
1.0
|
O
|
B:HIS323
|
3.9
|
43.3
|
1.0
|
CD2
|
B:HIS202
|
4.0
|
48.6
|
1.0
|
NE2
|
B:HIS202
|
4.2
|
52.0
|
1.0
|
OD1
|
B:ASP135
|
4.2
|
41.9
|
1.0
|
CAJ
|
B:0LV504
|
4.3
|
62.1
|
1.0
|
CA
|
B:HIS323
|
4.4
|
41.5
|
1.0
|
CE2
|
B:TYR167
|
4.4
|
39.0
|
1.0
|
C
|
B:HIS323
|
4.5
|
38.7
|
1.0
|
NE2
|
B:HIS286
|
4.6
|
41.3
|
1.0
|
ND1
|
B:HIS325
|
4.6
|
43.0
|
1.0
|
CG
|
B:HIS325
|
4.6
|
42.3
|
1.0
|
OD1
|
B:ASP164
|
4.6
|
41.5
|
1.0
|
CE1
|
B:HIS286
|
4.7
|
40.2
|
1.0
|
CA
|
B:ASP135
|
4.7
|
39.5
|
1.0
|
N
|
B:HIS323
|
4.8
|
39.1
|
1.0
|
ND1
|
B:HIS323
|
4.8
|
45.9
|
1.0
|
OD1
|
B:ASN201
|
4.9
|
41.1
|
1.0
|
CD1
|
B:TYR167
|
4.9
|
42.9
|
1.0
|
CB
|
B:ASN364
|
4.9
|
37.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 4dt2
Go back to
Iron Binding Sites List in 4dt2
Iron binding site 3 out
of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe506
b:56.0
occ:0.98
|
OH
|
C:TYR167
|
2.2
|
44.5
|
1.0
|
OD2
|
C:ASP135
|
2.4
|
44.3
|
1.0
|
OD2
|
C:ASP164
|
2.4
|
42.5
|
1.0
|
CAD
|
C:0LV512
|
2.7
|
48.8
|
1.0
|
CE1
|
C:HIS325
|
2.9
|
53.0
|
1.0
|
NE2
|
C:HIS325
|
3.0
|
50.9
|
1.0
|
ZN
|
C:ZN502
|
3.1
|
42.4
|
1.0
|
CZ
|
C:TYR167
|
3.2
|
43.8
|
1.0
|
CAE
|
C:0LV512
|
3.3
|
61.1
|
1.0
|
CG
|
C:ASP135
|
3.4
|
44.7
|
1.0
|
CG
|
C:ASP164
|
3.5
|
44.2
|
1.0
|
CE2
|
C:TYR167
|
3.6
|
45.4
|
1.0
|
O
|
C:HIS323
|
3.7
|
41.0
|
1.0
|
CB
|
C:ASP135
|
3.8
|
43.8
|
1.0
|
CAF
|
C:0LV512
|
3.9
|
57.5
|
1.0
|
CB
|
C:ASP164
|
3.9
|
40.3
|
1.0
|
ND1
|
C:HIS325
|
3.9
|
52.8
|
1.0
|
CD2
|
C:HIS202
|
4.0
|
50.1
|
1.0
|
CD2
|
C:HIS325
|
4.1
|
52.7
|
1.0
|
CA
|
C:HIS323
|
4.3
|
36.8
|
1.0
|
C
|
C:HIS323
|
4.3
|
37.1
|
1.0
|
NE2
|
C:HIS202
|
4.4
|
52.0
|
1.0
|
CE1
|
C:TYR167
|
4.4
|
39.6
|
1.0
|
OD1
|
C:ASP135
|
4.5
|
40.4
|
1.0
|
OD1
|
C:ASP164
|
4.6
|
44.0
|
1.0
|
CG
|
C:HIS325
|
4.6
|
51.4
|
1.0
|
CE1
|
C:HIS286
|
4.6
|
40.9
|
1.0
|
NE2
|
C:HIS286
|
4.6
|
40.0
|
1.0
|
CAJ
|
C:0LV512
|
4.7
|
64.2
|
1.0
|
OD1
|
C:ASN201
|
4.7
|
49.2
|
1.0
|
N
|
C:HIS323
|
4.8
|
38.9
|
1.0
|
CA
|
C:ASP135
|
4.8
|
37.0
|
1.0
|
ND1
|
C:HIS323
|
4.9
|
37.9
|
1.0
|
CD2
|
C:TYR167
|
4.9
|
46.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 4dt2
Go back to
Iron Binding Sites List in 4dt2
Iron binding site 4 out
of 4 in the Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Red Kidney Bean Purple Acid Phosphatase in Complex with Maybridge Fragment CC27209 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe509
b:48.2
occ:0.77
|
OD1
|
D:ASP135
|
2.0
|
37.1
|
1.0
|
OH
|
D:TYR167
|
2.0
|
32.9
|
1.0
|
CAD
|
D:0LV511
|
2.4
|
38.4
|
1.0
|
OD2
|
D:ASP164
|
2.4
|
36.8
|
1.0
|
NE2
|
D:HIS325
|
2.6
|
37.5
|
1.0
|
CAE
|
D:0LV511
|
2.7
|
53.8
|
1.0
|
CZ
|
D:TYR167
|
3.0
|
39.2
|
1.0
|
CG
|
D:ASP135
|
3.2
|
36.5
|
1.0
|
ZN
|
D:ZN508
|
3.2
|
41.5
|
0.9
|
CE2
|
D:TYR167
|
3.3
|
39.7
|
1.0
|
CG
|
D:ASP164
|
3.4
|
37.5
|
1.0
|
CE1
|
D:HIS325
|
3.5
|
34.8
|
1.0
|
CD2
|
D:HIS325
|
3.6
|
35.9
|
1.0
|
CAF
|
D:0LV511
|
3.7
|
50.9
|
1.0
|
CD2
|
D:HIS202
|
3.7
|
47.4
|
1.0
|
O
|
D:HIS323
|
3.7
|
38.3
|
1.0
|
CB
|
D:ASP164
|
3.9
|
33.9
|
1.0
|
NE2
|
D:HIS202
|
3.9
|
51.0
|
1.0
|
CB
|
D:ASP135
|
3.9
|
30.6
|
1.0
|
CAJ
|
D:0LV511
|
4.1
|
60.2
|
1.0
|
OD2
|
D:ASP135
|
4.1
|
31.6
|
1.0
|
CE1
|
D:TYR167
|
4.2
|
37.0
|
1.0
|
CA
|
D:HIS323
|
4.4
|
32.7
|
1.0
|
C
|
D:HIS323
|
4.5
|
35.0
|
1.0
|
OD1
|
D:ASP164
|
4.5
|
38.1
|
1.0
|
NE2
|
D:HIS286
|
4.5
|
35.8
|
1.0
|
CE1
|
D:HIS286
|
4.6
|
34.8
|
1.0
|
ND1
|
D:HIS325
|
4.6
|
40.5
|
1.0
|
CD2
|
D:TYR167
|
4.7
|
37.5
|
1.0
|
CG
|
D:HIS325
|
4.7
|
41.4
|
1.0
|
ND1
|
D:HIS323
|
4.7
|
34.5
|
1.0
|
CAK
|
D:0LV511
|
4.8
|
59.9
|
1.0
|
OD1
|
D:ASN201
|
4.8
|
44.4
|
1.0
|
CA
|
D:ASP135
|
4.8
|
34.1
|
1.0
|
CG
|
D:HIS202
|
4.8
|
46.4
|
1.0
|
CAL
|
D:0LV511
|
4.9
|
63.4
|
1.0
|
N
|
D:HIS323
|
4.9
|
30.4
|
1.0
|
CAG
|
D:0LV511
|
5.0
|
57.7
|
1.0
|
|
Reference:
D.Feder,
W.M.Hussein,
D.J.Clayton,
M.W.Kan,
G.Schenk,
R.P.Mcgeary,
L.W.Guddat.
Identification of Purple Acid Phosphatase Inhibitors By Fragment-Based Screening: Promising New Leads For Osteoporosis Therapeutics. Chem.Biol.Drug Des. V. 80 665 2012.
ISSN: ISSN 1747-0277
PubMed: 22943065
DOI: 10.1111/CBDD.12001
Page generated: Mon Aug 5 01:22:42 2024
|