Iron in PDB 6bwp: Crystal Structure of Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3
Protein crystallography data
The structure of Crystal Structure of Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3, PDB code: 6bwp
was solved by
F.N.Musayev,
R.M.Safo,
M.K.Safo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
12.80 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.675,
82.225,
53.519,
90.00,
99.60,
90.00
|
R / Rfree (%)
|
15.8 /
19.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3
(pdb code 6bwp). 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 Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3, PDB code: 6bwp:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6bwp
Go back to
Iron Binding Sites List in 6bwp
Iron binding site 1 out
of 4 in the Crystal Structure of Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3
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 Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:10.7
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
10.7
|
1.0
|
NA
|
A:HEM201
|
2.1
|
7.6
|
1.0
|
NC
|
A:HEM201
|
2.1
|
9.2
|
1.0
|
NB
|
A:HEM201
|
2.1
|
9.0
|
1.0
|
ND
|
A:HEM201
|
2.1
|
8.9
|
1.0
|
NE2
|
A:HIS87
|
2.3
|
10.7
|
1.0
|
C4A
|
A:HEM201
|
3.1
|
12.1
|
1.0
|
C1B
|
A:HEM201
|
3.1
|
9.7
|
1.0
|
C1C
|
A:HEM201
|
3.1
|
9.2
|
1.0
|
C4C
|
A:HEM201
|
3.1
|
8.0
|
1.0
|
C1A
|
A:HEM201
|
3.1
|
10.1
|
1.0
|
C4D
|
A:HEM201
|
3.1
|
10.2
|
1.0
|
C4B
|
A:HEM201
|
3.1
|
8.8
|
1.0
|
C1D
|
A:HEM201
|
3.1
|
8.0
|
1.0
|
CE1
|
A:HIS87
|
3.2
|
10.2
|
1.0
|
CD2
|
A:HIS87
|
3.4
|
7.8
|
1.0
|
CHB
|
A:HEM201
|
3.4
|
9.3
|
1.0
|
CHC
|
A:HEM201
|
3.5
|
8.3
|
1.0
|
CHA
|
A:HEM201
|
3.5
|
9.5
|
1.0
|
CHD
|
A:HEM201
|
3.5
|
8.3
|
1.0
|
NE2
|
A:HIS58
|
4.2
|
13.1
|
1.0
|
C3A
|
A:HEM201
|
4.3
|
11.5
|
1.0
|
C2B
|
A:HEM201
|
4.3
|
9.5
|
1.0
|
C2A
|
A:HEM201
|
4.3
|
11.1
|
1.0
|
C3C
|
A:HEM201
|
4.3
|
7.7
|
1.0
|
C2C
|
A:HEM201
|
4.3
|
10.3
|
1.0
|
C3D
|
A:HEM201
|
4.4
|
9.4
|
1.0
|
C3B
|
A:HEM201
|
4.4
|
8.7
|
1.0
|
ND1
|
A:HIS87
|
4.4
|
8.2
|
1.0
|
C2D
|
A:HEM201
|
4.4
|
9.6
|
1.0
|
CD1
|
A:LEU91
|
4.4
|
8.4
|
1.0
|
CG
|
A:HIS87
|
4.5
|
7.9
|
1.0
|
CE1
|
A:HIS58
|
4.5
|
8.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 6bwp
Go back to
Iron Binding Sites List in 6bwp
Iron binding site 2 out
of 4 in the Crystal Structure of Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3
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 Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:9.3
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
9.3
|
1.0
|
NC
|
B:HEM201
|
2.1
|
7.6
|
1.0
|
NB
|
B:HEM201
|
2.1
|
6.8
|
1.0
|
NA
|
B:HEM201
|
2.1
|
9.9
|
1.0
|
ND
|
B:HEM201
|
2.1
|
8.7
|
1.0
|
NE2
|
B:HIS92
|
2.3
|
8.5
|
1.0
|
C1C
|
B:HEM201
|
3.1
|
6.0
|
1.0
|
C1B
|
B:HEM201
|
3.1
|
8.8
|
1.0
|
C4C
|
B:HEM201
|
3.1
|
6.8
|
1.0
|
C4B
|
B:HEM201
|
3.1
|
8.7
|
1.0
|
C4A
|
B:HEM201
|
3.1
|
9.1
|
1.0
|
C1A
|
B:HEM201
|
3.1
|
9.5
|
1.0
|
C4D
|
B:HEM201
|
3.1
|
9.8
|
1.0
|
C1D
|
B:HEM201
|
3.1
|
10.5
|
1.0
|
CE1
|
B:HIS92
|
3.2
|
8.7
|
1.0
|
CD2
|
B:HIS92
|
3.3
|
8.1
|
1.0
|
CHB
|
B:HEM201
|
3.5
|
10.7
|
1.0
|
CHC
|
B:HEM201
|
3.5
|
9.4
|
1.0
|
CHA
|
B:HEM201
|
3.5
|
11.2
|
1.0
|
CHD
|
B:HEM201
|
3.5
|
10.5
|
1.0
|
CG2
|
B:VAL67
|
3.9
|
11.3
|
1.0
|
NE2
|
B:HIS63
|
4.2
|
14.5
|
1.0
|
CE1
|
B:HIS63
|
4.3
|
12.1
|
1.0
|
C2B
|
B:HEM201
|
4.3
|
8.5
|
1.0
|
C3B
|
B:HEM201
|
4.3
|
9.2
|
1.0
|
C2C
|
B:HEM201
|
4.3
|
7.8
|
1.0
|
C3C
|
B:HEM201
|
4.3
|
8.9
|
1.0
|
C3A
|
B:HEM201
|
4.3
|
10.8
|
1.0
|
C2A
|
B:HEM201
|
4.3
|
9.3
|
1.0
|
ND1
|
B:HIS92
|
4.3
|
9.2
|
1.0
|
C3D
|
B:HEM201
|
4.4
|
10.5
|
1.0
|
C2D
|
B:HEM201
|
4.4
|
10.8
|
1.0
|
CG
|
B:HIS92
|
4.4
|
10.0
|
1.0
|
CD1
|
B:LEU96
|
4.9
|
9.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 6bwp
Go back to
Iron Binding Sites List in 6bwp
Iron binding site 3 out
of 4 in the Crystal Structure of Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3
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 Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:8.9
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
8.9
|
1.0
|
NC
|
C:HEM201
|
2.1
|
8.5
|
1.0
|
NB
|
C:HEM201
|
2.1
|
8.3
|
1.0
|
NA
|
C:HEM201
|
2.1
|
8.8
|
1.0
|
ND
|
C:HEM201
|
2.1
|
8.9
|
1.0
|
NE2
|
C:HIS87
|
2.3
|
8.8
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
8.1
|
1.0
|
C4B
|
C:HEM201
|
3.1
|
7.2
|
1.0
|
C4C
|
C:HEM201
|
3.1
|
8.0
|
1.0
|
C1B
|
C:HEM201
|
3.1
|
8.0
|
1.0
|
C4A
|
C:HEM201
|
3.1
|
10.1
|
1.0
|
C1A
|
C:HEM201
|
3.1
|
10.0
|
1.0
|
C1D
|
C:HEM201
|
3.1
|
7.5
|
1.0
|
C4D
|
C:HEM201
|
3.2
|
9.0
|
1.0
|
CE1
|
C:HIS87
|
3.2
|
7.0
|
1.0
|
CD2
|
C:HIS87
|
3.3
|
7.6
|
1.0
|
CHC
|
C:HEM201
|
3.4
|
8.0
|
1.0
|
CHB
|
C:HEM201
|
3.5
|
8.5
|
1.0
|
CHD
|
C:HEM201
|
3.5
|
7.4
|
1.0
|
CHA
|
C:HEM201
|
3.5
|
10.5
|
1.0
|
NE2
|
C:HIS58
|
4.0
|
11.7
|
1.0
|
C2C
|
C:HEM201
|
4.3
|
7.1
|
1.0
|
C3B
|
C:HEM201
|
4.3
|
9.3
|
1.0
|
C3C
|
C:HEM201
|
4.3
|
7.5
|
1.0
|
C2B
|
C:HEM201
|
4.3
|
6.9
|
1.0
|
ND1
|
C:HIS87
|
4.3
|
8.8
|
1.0
|
C3A
|
C:HEM201
|
4.3
|
10.8
|
1.0
|
C2A
|
C:HEM201
|
4.3
|
9.1
|
1.0
|
C3D
|
C:HEM201
|
4.4
|
9.3
|
1.0
|
C2D
|
C:HEM201
|
4.4
|
10.7
|
1.0
|
CG
|
C:HIS87
|
4.4
|
9.8
|
1.0
|
CE1
|
C:HIS58
|
4.5
|
8.3
|
1.0
|
CD1
|
C:LEU91
|
4.5
|
10.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 6bwp
Go back to
Iron Binding Sites List in 6bwp
Iron binding site 4 out
of 4 in the Crystal Structure of Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3
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 Deoxy Hemoglobin in Complex with Beta CYS93 Modifying Agent, TD3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:9.8
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
9.8
|
1.0
|
NA
|
D:HEM201
|
2.1
|
9.3
|
1.0
|
NB
|
D:HEM201
|
2.1
|
8.2
|
1.0
|
NC
|
D:HEM201
|
2.1
|
10.3
|
1.0
|
ND
|
D:HEM201
|
2.1
|
7.4
|
1.0
|
NE2
|
D:HIS92
|
2.3
|
9.4
|
1.0
|
C1A
|
D:HEM201
|
3.1
|
12.0
|
1.0
|
C4A
|
D:HEM201
|
3.1
|
9.6
|
1.0
|
C1B
|
D:HEM201
|
3.1
|
10.6
|
1.0
|
C4C
|
D:HEM201
|
3.1
|
9.5
|
1.0
|
C1D
|
D:HEM201
|
3.1
|
9.6
|
1.0
|
C1C
|
D:HEM201
|
3.1
|
8.1
|
1.0
|
C4D
|
D:HEM201
|
3.1
|
12.0
|
1.0
|
C4B
|
D:HEM201
|
3.1
|
9.8
|
1.0
|
CE1
|
D:HIS92
|
3.2
|
8.0
|
1.0
|
CD2
|
D:HIS92
|
3.4
|
8.3
|
1.0
|
CHA
|
D:HEM201
|
3.5
|
11.5
|
1.0
|
CHB
|
D:HEM201
|
3.5
|
9.5
|
1.0
|
CHD
|
D:HEM201
|
3.5
|
9.3
|
1.0
|
CHC
|
D:HEM201
|
3.5
|
9.5
|
1.0
|
CG2
|
D:VAL67
|
4.0
|
10.0
|
1.0
|
CE1
|
D:HIS63
|
4.2
|
8.9
|
1.0
|
C3A
|
D:HEM201
|
4.3
|
13.1
|
1.0
|
C2A
|
D:HEM201
|
4.3
|
11.8
|
1.0
|
C2B
|
D:HEM201
|
4.3
|
9.5
|
1.0
|
C3B
|
D:HEM201
|
4.3
|
10.2
|
1.0
|
C2C
|
D:HEM201
|
4.3
|
9.6
|
1.0
|
C3C
|
D:HEM201
|
4.3
|
9.2
|
1.0
|
ND1
|
D:HIS92
|
4.3
|
8.4
|
1.0
|
C2D
|
D:HEM201
|
4.3
|
11.3
|
1.0
|
C3D
|
D:HEM201
|
4.3
|
10.7
|
1.0
|
CG
|
D:HIS92
|
4.5
|
8.9
|
1.0
|
NE2
|
D:HIS63
|
4.5
|
14.2
|
1.0
|
CD1
|
D:LEU96
|
4.9
|
9.8
|
1.0
|
|
Reference:
A.Nakagawa,
M.Ferrari,
G.Schleifer,
M.K.Cooper,
C.Liu,
B.Yu,
L.Berra,
E.S.Klings,
R.S.Safo,
Q.Chen,
F.N.Musayev,
M.K.Safo,
O.Abdulmalik,
D.B.Bloch,
W.M.Zapol.
A Triazole Disulfide Compound Increases the Affinity of Hemoglobin For Oxygen and Reduces the Sickling of Human Sickle Cells. Mol. Pharm. V. 15 1954 2018.
ISSN: ESSN 1543-8392
PubMed: 29634905
DOI: 10.1021/ACS.MOLPHARMACEUT.8B00108
Page generated: Tue Aug 6 14:38:58 2024
|