Iron in PDB 4rol: Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives
Protein crystallography data
The structure of Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives, PDB code: 4rol
was solved by
A.M.Omar,
M.A.Mahran,
M.N.Ghatge,
N.Chowdhury,
F.H.A.Bamane,
M.E.El-Araby,
O.Abdulmalik,
M.K.Safo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.97 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.645,
76.570,
53.198,
90.00,
98.02,
90.00
|
R / Rfree (%)
|
18.2 /
20.5
|
Other elements in 4rol:
The structure of Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives
(pdb code 4rol). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives, PDB code: 4rol:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4rol
Go back to
Iron Binding Sites List in 4rol
Iron binding site 1 out
of 4 in the Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:8.9
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
8.9
|
1.0
|
ND
|
A:HEM201
|
2.0
|
9.4
|
1.0
|
NC
|
A:HEM201
|
2.0
|
9.4
|
1.0
|
NA
|
A:HEM201
|
2.0
|
9.9
|
1.0
|
NB
|
A:HEM201
|
2.0
|
9.6
|
1.0
|
NE2
|
A:HIS87
|
2.1
|
9.0
|
1.0
|
CE1
|
A:HIS87
|
3.0
|
9.1
|
1.0
|
C1D
|
A:HEM201
|
3.0
|
9.4
|
1.0
|
C4D
|
A:HEM201
|
3.0
|
9.4
|
1.0
|
C4C
|
A:HEM201
|
3.1
|
9.0
|
1.0
|
C1C
|
A:HEM201
|
3.1
|
9.1
|
1.0
|
C1A
|
A:HEM201
|
3.1
|
10.1
|
1.0
|
C4B
|
A:HEM201
|
3.1
|
9.3
|
1.0
|
C4A
|
A:HEM201
|
3.1
|
10.0
|
1.0
|
C1B
|
A:HEM201
|
3.1
|
9.8
|
1.0
|
CD2
|
A:HIS87
|
3.2
|
8.7
|
1.0
|
CHD
|
A:HEM201
|
3.4
|
9.1
|
1.0
|
CHA
|
A:HEM201
|
3.5
|
9.4
|
1.0
|
CHC
|
A:HEM201
|
3.5
|
9.3
|
1.0
|
CHB
|
A:HEM201
|
3.5
|
9.9
|
1.0
|
O
|
A:HOH312
|
3.7
|
13.0
|
1.0
|
ND1
|
A:HIS87
|
4.2
|
9.1
|
1.0
|
CE1
|
A:HIS58
|
4.2
|
10.8
|
1.0
|
C3D
|
A:HEM201
|
4.3
|
9.6
|
1.0
|
CG
|
A:HIS87
|
4.3
|
9.4
|
1.0
|
C2D
|
A:HEM201
|
4.3
|
9.4
|
1.0
|
C2C
|
A:HEM201
|
4.3
|
8.9
|
1.0
|
C3C
|
A:HEM201
|
4.3
|
9.0
|
1.0
|
C2A
|
A:HEM201
|
4.3
|
10.7
|
1.0
|
C2B
|
A:HEM201
|
4.3
|
9.7
|
1.0
|
C3A
|
A:HEM201
|
4.4
|
10.4
|
1.0
|
C3B
|
A:HEM201
|
4.4
|
9.7
|
1.0
|
CD1
|
A:LEU91
|
4.4
|
9.3
|
1.0
|
NE2
|
A:HIS58
|
4.5
|
11.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 4rol
Go back to
Iron Binding Sites List in 4rol
Iron binding site 2 out
of 4 in the Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:8.7
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
8.7
|
1.0
|
NB
|
B:HEM201
|
2.0
|
8.3
|
1.0
|
NA
|
B:HEM201
|
2.0
|
8.9
|
1.0
|
ND
|
B:HEM201
|
2.0
|
8.5
|
1.0
|
NC
|
B:HEM201
|
2.0
|
8.1
|
1.0
|
NE2
|
B:HIS92
|
2.1
|
8.2
|
1.0
|
CE1
|
B:HIS92
|
3.0
|
8.4
|
1.0
|
C4A
|
B:HEM201
|
3.0
|
8.7
|
1.0
|
C1B
|
B:HEM201
|
3.0
|
8.3
|
1.0
|
C1A
|
B:HEM201
|
3.1
|
8.8
|
1.0
|
C4B
|
B:HEM201
|
3.1
|
8.6
|
1.0
|
C1D
|
B:HEM201
|
3.1
|
8.3
|
1.0
|
C4D
|
B:HEM201
|
3.1
|
8.6
|
1.0
|
C1C
|
B:HEM201
|
3.1
|
7.8
|
1.0
|
C4C
|
B:HEM201
|
3.1
|
8.1
|
1.0
|
CD2
|
B:HIS92
|
3.2
|
8.8
|
1.0
|
CHB
|
B:HEM201
|
3.4
|
8.8
|
1.0
|
CHC
|
B:HEM201
|
3.5
|
8.1
|
1.0
|
CHA
|
B:HEM201
|
3.5
|
8.6
|
1.0
|
CHD
|
B:HEM201
|
3.5
|
8.1
|
1.0
|
CG2
|
B:VAL67
|
4.0
|
16.3
|
1.0
|
ND1
|
B:HIS92
|
4.1
|
8.7
|
1.0
|
NE2
|
B:HIS63
|
4.2
|
13.0
|
1.0
|
CG
|
B:HIS92
|
4.3
|
8.8
|
1.0
|
C2B
|
B:HEM201
|
4.3
|
8.6
|
1.0
|
C2A
|
B:HEM201
|
4.3
|
9.2
|
1.0
|
C3A
|
B:HEM201
|
4.3
|
9.0
|
1.0
|
C3B
|
B:HEM201
|
4.3
|
8.6
|
1.0
|
C2D
|
B:HEM201
|
4.3
|
8.5
|
1.0
|
C3D
|
B:HEM201
|
4.3
|
8.6
|
1.0
|
C3C
|
B:HEM201
|
4.4
|
8.2
|
1.0
|
C2C
|
B:HEM201
|
4.4
|
7.9
|
1.0
|
CE1
|
B:HIS63
|
4.4
|
13.7
|
1.0
|
CE1
|
B:PHE103
|
5.0
|
9.5
|
1.0
|
CD1
|
B:LEU96
|
5.0
|
9.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 4rol
Go back to
Iron Binding Sites List in 4rol
Iron binding site 3 out
of 4 in the Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:8.6
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
8.6
|
1.0
|
ND
|
C:HEM201
|
2.0
|
9.1
|
1.0
|
NC
|
C:HEM201
|
2.0
|
9.0
|
1.0
|
NA
|
C:HEM201
|
2.0
|
10.1
|
1.0
|
NB
|
C:HEM201
|
2.0
|
9.6
|
1.0
|
NE2
|
C:HIS87
|
2.1
|
9.2
|
1.0
|
CE1
|
C:HIS87
|
3.0
|
9.0
|
1.0
|
C1D
|
C:HEM201
|
3.0
|
9.0
|
1.0
|
C4C
|
C:HEM201
|
3.1
|
8.7
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
9.0
|
1.0
|
C4D
|
C:HEM201
|
3.1
|
9.6
|
1.0
|
C4B
|
C:HEM201
|
3.1
|
8.8
|
1.0
|
C1A
|
C:HEM201
|
3.1
|
10.7
|
1.0
|
C4A
|
C:HEM201
|
3.1
|
10.3
|
1.0
|
C1B
|
C:HEM201
|
3.1
|
9.7
|
1.0
|
CD2
|
C:HIS87
|
3.2
|
9.0
|
1.0
|
O
|
C:HOH486
|
3.4
|
17.1
|
1.0
|
CHD
|
C:HEM201
|
3.4
|
8.9
|
1.0
|
CHC
|
C:HEM201
|
3.5
|
9.0
|
1.0
|
CHA
|
C:HEM201
|
3.5
|
9.8
|
1.0
|
CHB
|
C:HEM201
|
3.5
|
9.7
|
1.0
|
ND1
|
C:HIS87
|
4.1
|
9.1
|
1.0
|
CG
|
C:HIS87
|
4.3
|
9.4
|
1.0
|
NE2
|
C:HIS58
|
4.3
|
15.5
|
1.0
|
C2D
|
C:HEM201
|
4.3
|
9.5
|
1.0
|
C2C
|
C:HEM201
|
4.3
|
9.2
|
1.0
|
C3D
|
C:HEM201
|
4.3
|
10.0
|
1.0
|
C3C
|
C:HEM201
|
4.3
|
9.0
|
1.0
|
C3A
|
C:HEM201
|
4.3
|
11.1
|
1.0
|
C2A
|
C:HEM201
|
4.3
|
11.6
|
1.0
|
C2B
|
C:HEM201
|
4.3
|
9.7
|
1.0
|
C3B
|
C:HEM201
|
4.4
|
9.2
|
1.0
|
CD1
|
C:LEU91
|
4.4
|
12.4
|
1.0
|
CE1
|
C:HIS58
|
4.4
|
14.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 4rol
Go back to
Iron Binding Sites List in 4rol
Iron binding site 4 out
of 4 in the Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Deoxyhemoglobin in Complex with Imidazolylacryloyl Derivatives within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:9.1
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
9.1
|
1.0
|
NA
|
D:HEM201
|
2.0
|
10.6
|
1.0
|
NB
|
D:HEM201
|
2.0
|
10.2
|
1.0
|
ND
|
D:HEM201
|
2.0
|
9.6
|
1.0
|
NC
|
D:HEM201
|
2.0
|
9.2
|
1.0
|
NE2
|
D:HIS92
|
2.1
|
10.0
|
1.0
|
CE1
|
D:HIS92
|
3.0
|
10.4
|
1.0
|
C1A
|
D:HEM201
|
3.0
|
10.8
|
1.0
|
C4A
|
D:HEM201
|
3.1
|
10.6
|
1.0
|
C1B
|
D:HEM201
|
3.1
|
10.3
|
1.0
|
C1D
|
D:HEM201
|
3.1
|
9.6
|
1.0
|
C1C
|
D:HEM201
|
3.1
|
9.1
|
1.0
|
C4B
|
D:HEM201
|
3.1
|
9.9
|
1.0
|
C4C
|
D:HEM201
|
3.1
|
9.2
|
1.0
|
C4D
|
D:HEM201
|
3.1
|
10.0
|
1.0
|
CD2
|
D:HIS92
|
3.2
|
10.1
|
1.0
|
CHB
|
D:HEM201
|
3.5
|
11.0
|
1.0
|
CHA
|
D:HEM201
|
3.5
|
10.2
|
1.0
|
CHC
|
D:HEM201
|
3.5
|
9.7
|
1.0
|
CHD
|
D:HEM201
|
3.5
|
9.4
|
1.0
|
ND1
|
D:HIS92
|
4.1
|
10.3
|
1.0
|
CG
|
D:HIS92
|
4.2
|
10.8
|
1.0
|
CG2
|
D:VAL67
|
4.3
|
13.4
|
1.0
|
C2A
|
D:HEM201
|
4.3
|
11.3
|
1.0
|
C3A
|
D:HEM201
|
4.3
|
11.4
|
1.0
|
C2B
|
D:HEM201
|
4.3
|
10.4
|
1.0
|
C2D
|
D:HEM201
|
4.3
|
10.4
|
1.0
|
CE1
|
D:HIS63
|
4.3
|
11.6
|
1.0
|
C3B
|
D:HEM201
|
4.3
|
10.2
|
1.0
|
C2C
|
D:HEM201
|
4.3
|
9.1
|
1.0
|
C3C
|
D:HEM201
|
4.3
|
8.8
|
1.0
|
C3D
|
D:HEM201
|
4.3
|
10.6
|
1.0
|
NE2
|
D:HIS63
|
4.5
|
12.3
|
1.0
|
CD1
|
D:LEU96
|
4.8
|
11.7
|
1.0
|
CE1
|
D:PHE103
|
4.9
|
10.1
|
1.0
|
|
Reference:
A.M.Omar,
M.A.Mahran,
M.N.Ghatge,
N.Chowdhury,
F.H.A.Bamane,
M.E.El-Araby,
O.Abdulmalik,
M.K.Safo.
Identification of A Novel Class of Covalent Modifiers of Hemoglobin As Potential Antisickling Agents Org.Biomol.Chem. 2015.
ISSN: ESSN 1477-0539
Page generated: Mon Aug 5 09:22:36 2024
|