Iron in PDB 6di4: Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation
Protein crystallography data
The structure of Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation, PDB code: 6di4
was solved by
P.P.Pagare,
F.N.Musayev,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.34 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.696,
83.404,
104.934,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
24.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation
(pdb code 6di4). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation, PDB code: 6di4:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6di4
Go back to
Iron Binding Sites List in 6di4
Iron binding site 1 out
of 4 in the Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:28.3
occ:1.00
|
FE
|
A:HEM202
|
0.0
|
28.3
|
1.0
|
C
|
A:CMO201
|
1.9
|
25.8
|
1.0
|
ND
|
A:HEM202
|
2.0
|
28.0
|
1.0
|
NB
|
A:HEM202
|
2.0
|
26.0
|
1.0
|
NE2
|
A:HIS87
|
2.0
|
28.1
|
1.0
|
NA
|
A:HEM202
|
2.0
|
26.5
|
1.0
|
NC
|
A:HEM202
|
2.0
|
26.3
|
1.0
|
CE1
|
A:HIS87
|
3.0
|
26.9
|
1.0
|
C4D
|
A:HEM202
|
3.0
|
27.4
|
1.0
|
C4B
|
A:HEM202
|
3.1
|
27.1
|
1.0
|
C1A
|
A:HEM202
|
3.1
|
26.5
|
1.0
|
C1B
|
A:HEM202
|
3.1
|
27.2
|
1.0
|
C1C
|
A:HEM202
|
3.1
|
23.4
|
1.0
|
C1D
|
A:HEM202
|
3.1
|
25.9
|
1.0
|
O
|
A:CMO201
|
3.1
|
33.2
|
1.0
|
C4A
|
A:HEM202
|
3.1
|
25.6
|
1.0
|
C4C
|
A:HEM202
|
3.1
|
26.1
|
1.0
|
CD2
|
A:HIS87
|
3.1
|
25.0
|
1.0
|
CHA
|
A:HEM202
|
3.4
|
26.4
|
1.0
|
CHC
|
A:HEM202
|
3.4
|
25.3
|
1.0
|
CHB
|
A:HEM202
|
3.5
|
23.0
|
1.0
|
CHD
|
A:HEM202
|
3.5
|
23.5
|
1.0
|
ND1
|
A:HIS87
|
4.2
|
28.2
|
1.0
|
CG
|
A:HIS87
|
4.2
|
27.1
|
1.0
|
C3D
|
A:HEM202
|
4.3
|
29.8
|
1.0
|
C2B
|
A:HEM202
|
4.3
|
26.2
|
1.0
|
C3B
|
A:HEM202
|
4.3
|
28.1
|
1.0
|
C2D
|
A:HEM202
|
4.3
|
27.0
|
1.0
|
C2A
|
A:HEM202
|
4.3
|
27.4
|
1.0
|
C2C
|
A:HEM202
|
4.3
|
25.0
|
1.0
|
C3A
|
A:HEM202
|
4.3
|
26.4
|
1.0
|
C3C
|
A:HEM202
|
4.4
|
25.3
|
1.0
|
CE1
|
A:HIS58
|
4.4
|
28.5
|
1.0
|
CG2
|
A:VAL62
|
5.0
|
26.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 6di4
Go back to
Iron Binding Sites List in 6di4
Iron binding site 2 out
of 4 in the Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:30.6
occ:1.00
|
FE
|
B:HEM202
|
0.0
|
30.6
|
1.0
|
C
|
B:CMO201
|
1.9
|
28.7
|
1.0
|
NC
|
B:HEM202
|
2.0
|
29.4
|
1.0
|
NA
|
B:HEM202
|
2.0
|
30.1
|
1.0
|
NE2
|
B:HIS92
|
2.0
|
25.6
|
1.0
|
ND
|
B:HEM202
|
2.0
|
33.3
|
1.0
|
NB
|
B:HEM202
|
2.0
|
29.1
|
1.0
|
CE1
|
B:HIS92
|
3.0
|
28.6
|
1.0
|
C4C
|
B:HEM202
|
3.1
|
31.7
|
1.0
|
C4A
|
B:HEM202
|
3.1
|
29.4
|
1.0
|
C1C
|
B:HEM202
|
3.1
|
28.2
|
1.0
|
C1A
|
B:HEM202
|
3.1
|
29.9
|
1.0
|
C1D
|
B:HEM202
|
3.1
|
32.6
|
1.0
|
C4D
|
B:HEM202
|
3.1
|
30.2
|
1.0
|
O
|
B:CMO201
|
3.1
|
29.7
|
1.0
|
C1B
|
B:HEM202
|
3.1
|
28.2
|
1.0
|
CD2
|
B:HIS92
|
3.1
|
27.1
|
1.0
|
C4B
|
B:HEM202
|
3.1
|
27.3
|
1.0
|
CHD
|
B:HEM202
|
3.4
|
32.4
|
1.0
|
CHA
|
B:HEM202
|
3.4
|
29.1
|
1.0
|
CHB
|
B:HEM202
|
3.5
|
28.6
|
1.0
|
CHC
|
B:HEM202
|
3.5
|
27.6
|
1.0
|
ND1
|
B:HIS92
|
4.1
|
28.8
|
1.0
|
CG
|
B:HIS92
|
4.2
|
26.2
|
1.0
|
C2A
|
B:HEM202
|
4.3
|
28.8
|
1.0
|
C3A
|
B:HEM202
|
4.3
|
28.8
|
1.0
|
C3C
|
B:HEM202
|
4.3
|
30.3
|
1.0
|
C2C
|
B:HEM202
|
4.3
|
28.0
|
1.0
|
C3D
|
B:HEM202
|
4.3
|
34.2
|
1.0
|
CE1
|
B:HIS63
|
4.3
|
27.2
|
1.0
|
C2D
|
B:HEM202
|
4.3
|
33.5
|
1.0
|
C2B
|
B:HEM202
|
4.3
|
28.3
|
1.0
|
C3B
|
B:HEM202
|
4.4
|
29.5
|
1.0
|
CG2
|
B:VAL67
|
5.0
|
24.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 6di4
Go back to
Iron Binding Sites List in 6di4
Iron binding site 3 out
of 4 in the Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe202
b:26.2
occ:1.00
|
FE
|
C:HEM202
|
0.0
|
26.2
|
1.0
|
C
|
C:CMO201
|
1.9
|
25.9
|
1.0
|
ND
|
C:HEM202
|
2.0
|
25.8
|
1.0
|
NC
|
C:HEM202
|
2.0
|
24.0
|
1.0
|
NA
|
C:HEM202
|
2.0
|
26.9
|
1.0
|
NB
|
C:HEM202
|
2.0
|
26.9
|
1.0
|
NE2
|
C:HIS87
|
2.0
|
25.3
|
1.0
|
C4D
|
C:HEM202
|
3.0
|
27.0
|
1.0
|
CE1
|
C:HIS87
|
3.0
|
29.7
|
1.0
|
C1D
|
C:HEM202
|
3.0
|
26.9
|
1.0
|
C1C
|
C:HEM202
|
3.1
|
21.2
|
1.0
|
C1A
|
C:HEM202
|
3.1
|
26.7
|
1.0
|
C4C
|
C:HEM202
|
3.1
|
24.4
|
1.0
|
C4B
|
C:HEM202
|
3.1
|
25.6
|
1.0
|
C1B
|
C:HEM202
|
3.1
|
26.2
|
1.0
|
O
|
C:CMO201
|
3.1
|
32.1
|
1.0
|
CD2
|
C:HIS87
|
3.1
|
27.2
|
1.0
|
C4A
|
C:HEM202
|
3.1
|
26.2
|
1.0
|
CHA
|
C:HEM202
|
3.4
|
26.3
|
1.0
|
CHD
|
C:HEM202
|
3.4
|
25.8
|
1.0
|
CHC
|
C:HEM202
|
3.4
|
22.4
|
1.0
|
CHB
|
C:HEM202
|
3.5
|
24.1
|
1.0
|
ND1
|
C:HIS87
|
4.2
|
27.7
|
1.0
|
CG
|
C:HIS87
|
4.2
|
28.4
|
1.0
|
C3D
|
C:HEM202
|
4.3
|
23.6
|
1.0
|
C2D
|
C:HEM202
|
4.3
|
23.8
|
1.0
|
C2C
|
C:HEM202
|
4.3
|
25.1
|
1.0
|
C2A
|
C:HEM202
|
4.3
|
27.4
|
1.0
|
C3C
|
C:HEM202
|
4.3
|
24.6
|
1.0
|
C3A
|
C:HEM202
|
4.3
|
25.2
|
1.0
|
C2B
|
C:HEM202
|
4.3
|
26.1
|
1.0
|
C3B
|
C:HEM202
|
4.3
|
26.3
|
1.0
|
NE2
|
C:HIS58
|
4.5
|
28.9
|
1.0
|
CG2
|
C:VAL62
|
5.0
|
23.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 6di4
Go back to
Iron Binding Sites List in 6di4
Iron binding site 4 out
of 4 in the Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe202
b:27.7
occ:1.00
|
FE
|
D:HEM202
|
0.0
|
27.7
|
1.0
|
C
|
D:CMO201
|
1.9
|
28.9
|
1.0
|
NC
|
D:HEM202
|
2.0
|
27.2
|
1.0
|
NA
|
D:HEM202
|
2.0
|
24.4
|
1.0
|
ND
|
D:HEM202
|
2.0
|
26.3
|
1.0
|
NB
|
D:HEM202
|
2.0
|
27.2
|
1.0
|
NE2
|
D:HIS92
|
2.0
|
25.8
|
1.0
|
C1C
|
D:HEM202
|
3.0
|
27.5
|
1.0
|
CE1
|
D:HIS92
|
3.0
|
28.7
|
1.0
|
C4A
|
D:HEM202
|
3.1
|
25.6
|
1.0
|
C4B
|
D:HEM202
|
3.1
|
25.6
|
1.0
|
C1D
|
D:HEM202
|
3.1
|
28.2
|
1.0
|
C4C
|
D:HEM202
|
3.1
|
27.2
|
1.0
|
O
|
D:CMO201
|
3.1
|
32.4
|
1.0
|
C1B
|
D:HEM202
|
3.1
|
28.0
|
1.0
|
C4D
|
D:HEM202
|
3.1
|
26.8
|
1.0
|
CD2
|
D:HIS92
|
3.1
|
26.5
|
1.0
|
C1A
|
D:HEM202
|
3.1
|
26.8
|
1.0
|
CHC
|
D:HEM202
|
3.4
|
24.1
|
1.0
|
CHB
|
D:HEM202
|
3.4
|
27.0
|
1.0
|
CHD
|
D:HEM202
|
3.4
|
26.6
|
1.0
|
CHA
|
D:HEM202
|
3.5
|
26.1
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
27.0
|
1.0
|
CG
|
D:HIS92
|
4.2
|
25.1
|
1.0
|
C2C
|
D:HEM202
|
4.3
|
25.8
|
1.0
|
C3C
|
D:HEM202
|
4.3
|
26.8
|
1.0
|
C3A
|
D:HEM202
|
4.3
|
23.3
|
1.0
|
C3D
|
D:HEM202
|
4.3
|
27.5
|
1.0
|
C2B
|
D:HEM202
|
4.3
|
30.6
|
1.0
|
C2A
|
D:HEM202
|
4.3
|
26.0
|
1.0
|
C2D
|
D:HEM202
|
4.3
|
29.6
|
1.0
|
C3B
|
D:HEM202
|
4.3
|
30.8
|
1.0
|
CE1
|
D:HIS63
|
4.4
|
19.4
|
1.0
|
CG2
|
D:VAL67
|
4.7
|
26.3
|
1.0
|
|
Reference:
T.M.Deshpande,
P.P.Pagare,
M.S.Ghatge,
Q.Chen,
F.N.Musayev,
J.Venitz,
Y.Zhang,
O.Abdulmalik,
M.K.Safo.
Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation. Acta Crystallogr D Struct V. 74 956 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289405
DOI: 10.1107/S2059798318009919
Page generated: Tue Aug 6 16:59:57 2024
|