Iron in PDB 1qxd: Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds
Protein crystallography data
The structure of Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds, PDB code: 1qxd
was solved by
M.K.Safo,
O.Abdulmalik,
R.Danso-Danquah,
S.Nokuri,
G.S.Joshi,
F.N.Musayev,
T.Asakura,
D.J.Abraham,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
69.14 /
2.25
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.398,
91.398,
142.003,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.7 /
27.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds
(pdb code 1qxd). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds, PDB code: 1qxd:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1qxd
Go back to
Iron Binding Sites List in 1qxd
Iron binding site 1 out
of 4 in the Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe143
b:31.0
occ:1.00
|
FE
|
A:HEM143
|
0.0
|
31.0
|
1.0
|
NA
|
A:HEM143
|
2.0
|
33.9
|
1.0
|
NB
|
A:HEM143
|
2.0
|
31.2
|
1.0
|
ND
|
A:HEM143
|
2.0
|
32.5
|
1.0
|
NE2
|
A:HIS87
|
2.0
|
35.0
|
1.0
|
NC
|
A:HEM143
|
2.0
|
29.2
|
1.0
|
O
|
A:HOH9002
|
2.8
|
23.2
|
1.0
|
CE1
|
A:HIS87
|
2.9
|
34.2
|
1.0
|
C4A
|
A:HEM143
|
3.0
|
32.2
|
1.0
|
C1A
|
A:HEM143
|
3.0
|
32.7
|
1.0
|
C1B
|
A:HEM143
|
3.0
|
31.9
|
1.0
|
C4B
|
A:HEM143
|
3.1
|
25.4
|
1.0
|
C4D
|
A:HEM143
|
3.1
|
30.0
|
1.0
|
C1C
|
A:HEM143
|
3.1
|
23.2
|
1.0
|
CD2
|
A:HIS87
|
3.1
|
29.6
|
1.0
|
C1D
|
A:HEM143
|
3.1
|
32.5
|
1.0
|
C4C
|
A:HEM143
|
3.1
|
28.7
|
1.0
|
CHB
|
A:HEM143
|
3.4
|
28.9
|
1.0
|
CHA
|
A:HEM143
|
3.5
|
30.2
|
1.0
|
CHC
|
A:HEM143
|
3.5
|
19.4
|
1.0
|
CHD
|
A:HEM143
|
3.5
|
24.8
|
1.0
|
ND1
|
A:HIS87
|
4.1
|
35.4
|
1.0
|
CG
|
A:HIS87
|
4.2
|
30.6
|
1.0
|
C2A
|
A:HEM143
|
4.2
|
32.7
|
1.0
|
C3A
|
A:HEM143
|
4.2
|
32.5
|
1.0
|
C2B
|
A:HEM143
|
4.3
|
29.7
|
1.0
|
C3D
|
A:HEM143
|
4.3
|
33.3
|
1.0
|
C2D
|
A:HEM143
|
4.3
|
31.8
|
1.0
|
C3B
|
A:HEM143
|
4.3
|
28.9
|
1.0
|
C2C
|
A:HEM143
|
4.3
|
24.9
|
1.0
|
C3C
|
A:HEM143
|
4.3
|
24.9
|
1.0
|
NE2
|
A:HIS58
|
4.7
|
33.7
|
1.0
|
CG2
|
A:VAL62
|
4.8
|
24.6
|
1.0
|
CE1
|
A:HIS58
|
5.0
|
30.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 1qxd
Go back to
Iron Binding Sites List in 1qxd
Iron binding site 2 out
of 4 in the Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe148
b:27.7
occ:1.00
|
FE
|
B:HEM148
|
0.0
|
27.7
|
1.0
|
NB
|
B:HEM148
|
2.0
|
30.2
|
1.0
|
NE2
|
B:HIS92
|
2.0
|
27.8
|
1.0
|
NC
|
B:HEM148
|
2.0
|
32.9
|
1.0
|
NA
|
B:HEM148
|
2.0
|
33.8
|
1.0
|
ND
|
B:HEM148
|
2.0
|
35.2
|
1.0
|
O
|
B:HOH5147
|
2.7
|
17.1
|
1.0
|
CE1
|
B:HIS92
|
2.9
|
26.9
|
1.0
|
C1B
|
B:HEM148
|
3.0
|
34.1
|
1.0
|
C4B
|
B:HEM148
|
3.0
|
30.1
|
1.0
|
C4A
|
B:HEM148
|
3.0
|
32.1
|
1.0
|
C4C
|
B:HEM148
|
3.0
|
31.6
|
1.0
|
C1C
|
B:HEM148
|
3.0
|
31.2
|
1.0
|
C4D
|
B:HEM148
|
3.1
|
38.4
|
1.0
|
C1A
|
B:HEM148
|
3.1
|
37.5
|
1.0
|
CD2
|
B:HIS92
|
3.1
|
28.4
|
1.0
|
C1D
|
B:HEM148
|
3.1
|
36.0
|
1.0
|
CHB
|
B:HEM148
|
3.4
|
34.9
|
1.0
|
CHC
|
B:HEM148
|
3.4
|
30.2
|
1.0
|
CHA
|
B:HEM148
|
3.4
|
38.2
|
1.0
|
CHD
|
B:HEM148
|
3.5
|
35.0
|
1.0
|
ND1
|
B:HIS92
|
4.0
|
28.1
|
1.0
|
CG
|
B:HIS92
|
4.2
|
27.8
|
1.0
|
C3C
|
B:HEM148
|
4.2
|
33.4
|
1.0
|
C3B
|
B:HEM148
|
4.3
|
28.1
|
1.0
|
C2C
|
B:HEM148
|
4.3
|
29.9
|
1.0
|
C2B
|
B:HEM148
|
4.3
|
31.6
|
1.0
|
C3A
|
B:HEM148
|
4.3
|
37.9
|
1.0
|
C3D
|
B:HEM148
|
4.3
|
38.0
|
1.0
|
C2A
|
B:HEM148
|
4.3
|
37.0
|
1.0
|
C2D
|
B:HEM148
|
4.3
|
36.6
|
1.0
|
NE2
|
B:HIS63
|
4.6
|
43.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 1qxd
Go back to
Iron Binding Sites List in 1qxd
Iron binding site 3 out
of 4 in the Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe143
b:22.0
occ:1.00
|
FE
|
C:HEM143
|
0.0
|
22.0
|
1.0
|
ND
|
C:HEM143
|
2.0
|
21.9
|
1.0
|
NB
|
C:HEM143
|
2.0
|
24.4
|
1.0
|
NC
|
C:HEM143
|
2.0
|
22.1
|
1.0
|
NA
|
C:HEM143
|
2.0
|
28.4
|
1.0
|
NE2
|
C:HIS87
|
2.0
|
20.3
|
1.0
|
O
|
C:HOH9142
|
2.8
|
19.7
|
1.0
|
CE1
|
C:HIS87
|
3.0
|
20.6
|
1.0
|
C4B
|
C:HEM143
|
3.0
|
24.3
|
1.0
|
C1D
|
C:HEM143
|
3.0
|
26.2
|
1.0
|
C4D
|
C:HEM143
|
3.0
|
24.7
|
1.0
|
C1C
|
C:HEM143
|
3.0
|
21.0
|
1.0
|
C1B
|
C:HEM143
|
3.0
|
26.0
|
1.0
|
C4A
|
C:HEM143
|
3.1
|
30.9
|
1.0
|
C4C
|
C:HEM143
|
3.1
|
17.6
|
1.0
|
CD2
|
C:HIS87
|
3.1
|
18.8
|
1.0
|
C1A
|
C:HEM143
|
3.1
|
27.4
|
1.0
|
CHC
|
C:HEM143
|
3.3
|
21.5
|
1.0
|
CHB
|
C:HEM143
|
3.4
|
30.2
|
1.0
|
CHD
|
C:HEM143
|
3.4
|
20.3
|
1.0
|
CHA
|
C:HEM143
|
3.4
|
26.7
|
1.0
|
ND1
|
C:HIS87
|
4.1
|
19.0
|
1.0
|
CG
|
C:HIS87
|
4.2
|
22.6
|
1.0
|
C3D
|
C:HEM143
|
4.2
|
28.1
|
1.0
|
C3B
|
C:HEM143
|
4.2
|
22.4
|
1.0
|
C2D
|
C:HEM143
|
4.2
|
26.2
|
1.0
|
C2B
|
C:HEM143
|
4.2
|
23.2
|
1.0
|
C3A
|
C:HEM143
|
4.3
|
28.3
|
1.0
|
NE2
|
C:HIS58
|
4.3
|
29.9
|
1.0
|
C2C
|
C:HEM143
|
4.3
|
29.1
|
1.0
|
C3C
|
C:HEM143
|
4.3
|
24.4
|
1.0
|
C2A
|
C:HEM143
|
4.3
|
30.3
|
1.0
|
CE1
|
C:HIS58
|
4.9
|
31.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 1qxd
Go back to
Iron Binding Sites List in 1qxd
Iron binding site 4 out
of 4 in the Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structural Basis For the Potent Antisickling Effect of A Novel Class of 5-Membered Heterocyclic Aldehydic Compounds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe148
b:24.1
occ:1.00
|
FE
|
D:HEM148
|
0.0
|
24.1
|
1.0
|
ND
|
D:HEM148
|
2.0
|
20.8
|
1.0
|
NA
|
D:HEM148
|
2.0
|
23.8
|
1.0
|
NB
|
D:HEM148
|
2.0
|
24.4
|
1.0
|
NC
|
D:HEM148
|
2.0
|
25.5
|
1.0
|
NE2
|
D:HIS92
|
2.1
|
25.3
|
1.0
|
O
|
D:HOH9147
|
2.8
|
23.6
|
1.0
|
C1A
|
D:HEM148
|
3.0
|
24.1
|
1.0
|
CD2
|
D:HIS92
|
3.0
|
25.2
|
1.0
|
C4D
|
D:HEM148
|
3.0
|
25.8
|
1.0
|
C1D
|
D:HEM148
|
3.0
|
26.4
|
1.0
|
C4B
|
D:HEM148
|
3.0
|
24.6
|
1.0
|
C4A
|
D:HEM148
|
3.1
|
23.9
|
1.0
|
C1C
|
D:HEM148
|
3.1
|
26.7
|
1.0
|
C1B
|
D:HEM148
|
3.1
|
25.0
|
1.0
|
C4C
|
D:HEM148
|
3.1
|
23.9
|
1.0
|
CE1
|
D:HIS92
|
3.1
|
29.0
|
1.0
|
CHA
|
D:HEM148
|
3.4
|
24.7
|
1.0
|
CHC
|
D:HEM148
|
3.4
|
24.9
|
1.0
|
CHD
|
D:HEM148
|
3.4
|
19.7
|
1.0
|
CHB
|
D:HEM148
|
3.5
|
26.9
|
1.0
|
CG
|
D:HIS92
|
4.2
|
28.4
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
21.3
|
1.0
|
C2A
|
D:HEM148
|
4.2
|
25.8
|
1.0
|
C3D
|
D:HEM148
|
4.2
|
24.6
|
1.0
|
C2D
|
D:HEM148
|
4.2
|
19.6
|
1.0
|
C3B
|
D:HEM148
|
4.2
|
25.4
|
1.0
|
C3A
|
D:HEM148
|
4.3
|
20.4
|
1.0
|
NE2
|
D:HIS63
|
4.3
|
33.7
|
1.0
|
C2B
|
D:HEM148
|
4.3
|
23.5
|
1.0
|
C2C
|
D:HEM148
|
4.3
|
22.6
|
1.0
|
C3C
|
D:HEM148
|
4.3
|
21.6
|
1.0
|
CG2
|
D:VAL67
|
5.0
|
21.4
|
1.0
|
|
Reference:
M.K.Safo,
O.Abdulmalik,
R.Danso-Danquah,
J.C.Burnett,
S.Nokuri,
G.S.Joshi,
F.N.Musayev,
T.Asakura,
D.J.Abraham.
Structural Basis For the Potent Antisickling Effect of A Novel Class of Five-Membered Heterocyclic Aldehydic Compounds J.Med.Chem. V. 47 4665 2004.
ISSN: ISSN 0022-2623
PubMed: 15341482
DOI: 10.1021/JM0498001
Page generated: Sat Aug 3 13:56:08 2024
|