Iron in PDB 3nmm: Human Hemoglobin A Mutant Alpha H58W Deoxy-Form
Protein crystallography data
The structure of Human Hemoglobin A Mutant Alpha H58W Deoxy-Form, PDB code: 3nmm
was solved by
I.Birukou,
J.Soman,
J.S.Olson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
28.82 /
1.60
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.550,
81.830,
53.450,
90.00,
99.76,
90.00
|
|
R / Rfree (%)
|
17.3 /
19.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Human Hemoglobin A Mutant Alpha H58W Deoxy-Form
(pdb code 3nmm). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Human Hemoglobin A Mutant Alpha H58W Deoxy-Form, PDB code: 3nmm:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3nmm
Go back to
Iron Binding Sites List in 3nmm
Iron binding site 1 out
of 4 in the Human Hemoglobin A Mutant Alpha H58W Deoxy-Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Human Hemoglobin A Mutant Alpha H58W Deoxy-Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe142
b:14.8
occ:1.00
|
FE
|
A:HEM142
|
0.0
|
14.8
|
1.0
|
|
HE2
|
A:HIS87
|
1.4
|
15.5
|
1.0
|
|
NA
|
A:HEM142
|
2.1
|
17.6
|
1.0
|
|
NB
|
A:HEM142
|
2.1
|
13.1
|
1.0
|
|
ND
|
A:HEM142
|
2.1
|
12.3
|
1.0
|
|
NC
|
A:HEM142
|
2.1
|
16.6
|
1.0
|
|
NE2
|
A:HIS87
|
2.2
|
12.9
|
1.0
|
|
CE1
|
A:HIS87
|
3.0
|
15.9
|
1.0
|
|
C4A
|
A:HEM142
|
3.1
|
14.1
|
1.0
|
|
C4B
|
A:HEM142
|
3.1
|
13.1
|
1.0
|
|
C1A
|
A:HEM142
|
3.1
|
16.1
|
1.0
|
|
HE1
|
A:HIS87
|
3.1
|
19.1
|
1.0
|
|
C4D
|
A:HEM142
|
3.1
|
14.2
|
1.0
|
|
C1D
|
A:HEM142
|
3.1
|
12.7
|
1.0
|
|
C1B
|
A:HEM142
|
3.1
|
13.8
|
1.0
|
|
C1C
|
A:HEM142
|
3.1
|
13.9
|
1.0
|
|
C4C
|
A:HEM142
|
3.2
|
13.0
|
1.0
|
|
CD2
|
A:HIS87
|
3.3
|
12.7
|
1.0
|
|
CHC
|
A:HEM142
|
3.4
|
13.4
|
1.0
|
|
CHB
|
A:HEM142
|
3.5
|
14.6
|
1.0
|
|
CHA
|
A:HEM142
|
3.5
|
15.6
|
1.0
|
|
HE1
|
A:TRP58
|
3.5
|
17.5
|
1.0
|
|
CHD
|
A:HEM142
|
3.5
|
13.3
|
1.0
|
|
HZ2
|
A:TRP58
|
3.5
|
17.6
|
1.0
|
|
HD2
|
A:HIS87
|
3.6
|
15.2
|
1.0
|
|
HD13
|
A:LEU91
|
3.9
|
18.2
|
1.0
|
|
NE1
|
A:TRP58
|
4.2
|
14.6
|
1.0
|
|
ND1
|
A:HIS87
|
4.2
|
13.9
|
1.0
|
|
CZ2
|
A:TRP58
|
4.3
|
14.7
|
1.0
|
|
C2A
|
A:HEM142
|
4.3
|
16.4
|
1.0
|
|
C3B
|
A:HEM142
|
4.3
|
12.9
|
1.0
|
|
C3A
|
A:HEM142
|
4.3
|
14.8
|
1.0
|
|
C2B
|
A:HEM142
|
4.3
|
12.5
|
1.0
|
|
C2D
|
A:HEM142
|
4.3
|
13.9
|
1.0
|
|
HD12
|
A:LEU91
|
4.3
|
18.2
|
1.0
|
|
C3D
|
A:HEM142
|
4.3
|
13.7
|
1.0
|
|
C2C
|
A:HEM142
|
4.4
|
13.8
|
1.0
|
|
HHC
|
A:HEM142
|
4.4
|
16.0
|
1.0
|
|
CG
|
A:HIS87
|
4.4
|
12.5
|
1.0
|
|
C3C
|
A:HEM142
|
4.4
|
10.9
|
1.0
|
|
HHB
|
A:HEM142
|
4.4
|
17.5
|
1.0
|
|
CD1
|
A:LEU91
|
4.4
|
15.2
|
1.0
|
|
HHA
|
A:HEM142
|
4.5
|
18.7
|
1.0
|
|
HHD
|
A:HEM142
|
4.5
|
16.0
|
1.0
|
|
HG22
|
A:VAL62
|
4.5
|
18.1
|
1.0
|
|
HD11
|
A:LEU91
|
4.5
|
18.2
|
1.0
|
|
CE2
|
A:TRP58
|
4.6
|
12.8
|
1.0
|
|
HG21
|
A:VAL93
|
4.8
|
22.0
|
1.0
|
|
HD13
|
A:LEU136
|
4.9
|
28.5
|
1.0
|
|
HD1
|
A:HIS87
|
5.0
|
16.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 3nmm
Go back to
Iron Binding Sites List in 3nmm
Iron binding site 2 out
of 4 in the Human Hemoglobin A Mutant Alpha H58W Deoxy-Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Human Hemoglobin A Mutant Alpha H58W Deoxy-Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe147
b:15.1
occ:1.00
|
FE
|
B:HEM147
|
0.0
|
15.1
|
1.0
|
|
HE2
|
B:HIS92
|
1.3
|
19.5
|
1.0
|
|
NC
|
B:HEM147
|
2.0
|
11.7
|
1.0
|
|
ND
|
B:HEM147
|
2.1
|
14.4
|
1.0
|
|
NA
|
B:HEM147
|
2.1
|
12.0
|
1.0
|
|
NB
|
B:HEM147
|
2.1
|
13.6
|
1.0
|
|
NE2
|
B:HIS92
|
2.2
|
16.2
|
1.0
|
|
C1D
|
B:HEM147
|
3.0
|
15.1
|
1.0
|
|
C1C
|
B:HEM147
|
3.0
|
11.8
|
1.0
|
|
C4C
|
B:HEM147
|
3.1
|
12.3
|
1.0
|
|
C4D
|
B:HEM147
|
3.1
|
13.1
|
1.0
|
|
C1A
|
B:HEM147
|
3.1
|
14.5
|
1.0
|
|
C4B
|
B:HEM147
|
3.1
|
13.8
|
1.0
|
|
C4A
|
B:HEM147
|
3.1
|
12.9
|
1.0
|
|
CE1
|
B:HIS92
|
3.1
|
14.4
|
1.0
|
|
C1B
|
B:HEM147
|
3.1
|
12.3
|
1.0
|
|
HG22
|
B:VAL67
|
3.2
|
17.8
|
1.0
|
|
CD2
|
B:HIS92
|
3.2
|
14.8
|
1.0
|
|
HE1
|
B:HIS92
|
3.3
|
17.3
|
1.0
|
|
HD2
|
B:HIS92
|
3.4
|
17.8
|
1.0
|
|
CHD
|
B:HEM147
|
3.4
|
15.0
|
1.0
|
|
CHC
|
B:HEM147
|
3.4
|
13.7
|
1.0
|
|
CHA
|
B:HEM147
|
3.5
|
17.1
|
1.0
|
|
CHB
|
B:HEM147
|
3.5
|
12.4
|
1.0
|
|
HE2
|
B:HIS63
|
3.6
|
23.5
|
1.0
|
|
HG21
|
B:VAL67
|
3.9
|
17.8
|
1.0
|
|
CG2
|
B:VAL67
|
3.9
|
14.9
|
1.0
|
|
HE1
|
B:HIS63
|
4.0
|
25.4
|
1.0
|
|
HE1
|
B:PHE103
|
4.2
|
16.2
|
1.0
|
|
NE2
|
B:HIS63
|
4.2
|
19.6
|
1.0
|
|
C2C
|
B:HEM147
|
4.3
|
13.2
|
1.0
|
|
C3C
|
B:HEM147
|
4.3
|
12.6
|
1.0
|
|
C2D
|
B:HEM147
|
4.3
|
15.4
|
1.0
|
|
ND1
|
B:HIS92
|
4.3
|
14.8
|
1.0
|
|
C3D
|
B:HEM147
|
4.3
|
14.5
|
1.0
|
|
HHD
|
B:HEM147
|
4.3
|
18.0
|
1.0
|
|
C2A
|
B:HEM147
|
4.3
|
15.3
|
1.0
|
|
C3B
|
B:HEM147
|
4.3
|
14.3
|
1.0
|
|
C3A
|
B:HEM147
|
4.3
|
15.0
|
1.0
|
|
CG
|
B:HIS92
|
4.3
|
14.1
|
1.0
|
|
C2B
|
B:HEM147
|
4.4
|
14.0
|
1.0
|
|
HG23
|
B:VAL67
|
4.4
|
17.8
|
1.0
|
|
HHA
|
B:HEM147
|
4.4
|
20.5
|
1.0
|
|
HHC
|
B:HEM147
|
4.4
|
16.4
|
1.0
|
|
CE1
|
B:HIS63
|
4.4
|
21.2
|
1.0
|
|
HD13
|
B:LEU96
|
4.4
|
19.6
|
1.0
|
|
HHB
|
B:HEM147
|
4.5
|
14.8
|
1.0
|
|
HD12
|
B:LEU96
|
4.7
|
19.6
|
1.0
|
|
HG13
|
B:VAL67
|
4.7
|
20.7
|
1.0
|
|
HG21
|
B:VAL98
|
4.8
|
19.7
|
1.0
|
|
CD1
|
B:LEU96
|
4.9
|
16.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 3nmm
Go back to
Iron Binding Sites List in 3nmm
Iron binding site 3 out
of 4 in the Human Hemoglobin A Mutant Alpha H58W Deoxy-Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Human Hemoglobin A Mutant Alpha H58W Deoxy-Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe142
b:14.2
occ:1.00
|
FE
|
C:HEM142
|
0.0
|
14.2
|
1.0
|
|
HE2
|
C:HIS87
|
1.4
|
15.0
|
1.0
|
|
NB
|
C:HEM142
|
2.1
|
12.0
|
1.0
|
|
NA
|
C:HEM142
|
2.1
|
16.2
|
1.0
|
|
NC
|
C:HEM142
|
2.1
|
11.4
|
1.0
|
|
ND
|
C:HEM142
|
2.1
|
14.3
|
1.0
|
|
NE2
|
C:HIS87
|
2.2
|
12.5
|
1.0
|
|
CE1
|
C:HIS87
|
3.0
|
12.9
|
1.0
|
|
C1B
|
C:HEM142
|
3.1
|
13.6
|
1.0
|
|
HE1
|
C:HIS87
|
3.1
|
15.5
|
1.0
|
|
C4B
|
C:HEM142
|
3.1
|
13.2
|
1.0
|
|
C4D
|
C:HEM142
|
3.1
|
13.0
|
1.0
|
|
C4A
|
C:HEM142
|
3.1
|
15.1
|
1.0
|
|
C1C
|
C:HEM142
|
3.1
|
10.7
|
1.0
|
|
C1A
|
C:HEM142
|
3.1
|
11.8
|
1.0
|
|
C4C
|
C:HEM142
|
3.2
|
9.5
|
1.0
|
|
C1D
|
C:HEM142
|
3.2
|
15.6
|
1.0
|
|
CD2
|
C:HIS87
|
3.3
|
12.2
|
1.0
|
|
HE1
|
C:TRP58
|
3.4
|
19.9
|
1.0
|
|
HZ2
|
C:TRP58
|
3.4
|
20.5
|
1.0
|
|
CHB
|
C:HEM142
|
3.4
|
14.7
|
1.0
|
|
CHA
|
C:HEM142
|
3.5
|
13.1
|
1.0
|
|
CHC
|
C:HEM142
|
3.5
|
14.9
|
1.0
|
|
CHD
|
C:HEM142
|
3.5
|
11.2
|
1.0
|
|
HD2
|
C:HIS87
|
3.6
|
14.7
|
1.0
|
|
HD13
|
C:LEU91
|
3.9
|
16.1
|
1.0
|
|
NE1
|
C:TRP58
|
4.0
|
16.5
|
1.0
|
|
CZ2
|
C:TRP58
|
4.1
|
17.1
|
1.0
|
|
ND1
|
C:HIS87
|
4.2
|
14.5
|
1.0
|
|
HD12
|
C:LEU91
|
4.2
|
16.1
|
1.0
|
|
C2B
|
C:HEM142
|
4.3
|
14.8
|
1.0
|
|
C3B
|
C:HEM142
|
4.3
|
14.0
|
1.0
|
|
HG22
|
C:VAL62
|
4.3
|
23.4
|
1.0
|
|
C2C
|
C:HEM142
|
4.3
|
11.7
|
1.0
|
|
C3D
|
C:HEM142
|
4.3
|
12.9
|
1.0
|
|
C3A
|
C:HEM142
|
4.3
|
15.8
|
1.0
|
|
C2A
|
C:HEM142
|
4.4
|
11.8
|
1.0
|
|
C2D
|
C:HEM142
|
4.4
|
15.3
|
1.0
|
|
C3C
|
C:HEM142
|
4.4
|
13.2
|
1.0
|
|
CG
|
C:HIS87
|
4.4
|
12.6
|
1.0
|
|
CD1
|
C:LEU91
|
4.4
|
13.4
|
1.0
|
|
CE2
|
C:TRP58
|
4.4
|
14.1
|
1.0
|
|
HHC
|
C:HEM142
|
4.4
|
17.9
|
1.0
|
|
HHA
|
C:HEM142
|
4.4
|
15.7
|
1.0
|
|
HHB
|
C:HEM142
|
4.4
|
17.6
|
1.0
|
|
HD11
|
C:LEU91
|
4.5
|
16.1
|
1.0
|
|
HHD
|
C:HEM142
|
4.5
|
13.4
|
1.0
|
|
HG21
|
C:VAL93
|
4.8
|
16.9
|
1.0
|
|
HG21
|
C:VAL62
|
4.9
|
23.4
|
1.0
|
|
HD1
|
C:HIS87
|
4.9
|
17.4
|
1.0
|
|
CG2
|
C:VAL62
|
5.0
|
19.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 3nmm
Go back to
Iron Binding Sites List in 3nmm
Iron binding site 4 out
of 4 in the Human Hemoglobin A Mutant Alpha H58W Deoxy-Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Human Hemoglobin A Mutant Alpha H58W Deoxy-Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe147
b:16.1
occ:1.00
|
FE
|
D:HEM147
|
0.0
|
16.1
|
1.0
|
|
HE2
|
D:HIS92
|
1.3
|
18.4
|
1.0
|
|
NC
|
D:HEM147
|
2.0
|
14.1
|
1.0
|
|
ND
|
D:HEM147
|
2.0
|
13.9
|
1.0
|
|
NA
|
D:HEM147
|
2.1
|
13.6
|
1.0
|
|
NB
|
D:HEM147
|
2.1
|
14.5
|
1.0
|
|
NE2
|
D:HIS92
|
2.2
|
15.3
|
1.0
|
|
C1D
|
D:HEM147
|
3.0
|
15.2
|
1.0
|
|
C4C
|
D:HEM147
|
3.0
|
15.5
|
1.0
|
|
C1C
|
D:HEM147
|
3.1
|
13.5
|
1.0
|
|
C4A
|
D:HEM147
|
3.1
|
14.6
|
1.0
|
|
C1B
|
D:HEM147
|
3.1
|
14.6
|
1.0
|
|
CE1
|
D:HIS92
|
3.1
|
14.3
|
1.0
|
|
C4B
|
D:HEM147
|
3.1
|
14.9
|
1.0
|
|
C1A
|
D:HEM147
|
3.1
|
17.3
|
1.0
|
|
C4D
|
D:HEM147
|
3.1
|
15.9
|
1.0
|
|
HE1
|
D:HIS92
|
3.2
|
17.2
|
1.0
|
|
HG22
|
D:VAL67
|
3.2
|
20.4
|
1.0
|
|
CD2
|
D:HIS92
|
3.3
|
13.7
|
1.0
|
|
CHD
|
D:HEM147
|
3.3
|
14.3
|
1.0
|
|
CHB
|
D:HEM147
|
3.4
|
13.7
|
1.0
|
|
HE2
|
D:HIS63
|
3.4
|
20.5
|
1.0
|
|
CHC
|
D:HEM147
|
3.5
|
14.4
|
1.0
|
|
CHA
|
D:HEM147
|
3.5
|
16.8
|
1.0
|
|
HD2
|
D:HIS92
|
3.5
|
16.4
|
1.0
|
|
HG21
|
D:VAL67
|
4.0
|
20.4
|
1.0
|
|
CG2
|
D:VAL67
|
4.0
|
17.0
|
1.0
|
|
NE2
|
D:HIS63
|
4.2
|
17.1
|
1.0
|
|
C3C
|
D:HEM147
|
4.3
|
16.9
|
1.0
|
|
ND1
|
D:HIS92
|
4.3
|
14.8
|
1.0
|
|
C2C
|
D:HEM147
|
4.3
|
16.9
|
1.0
|
|
C2D
|
D:HEM147
|
4.3
|
19.6
|
1.0
|
|
C2B
|
D:HEM147
|
4.3
|
13.9
|
1.0
|
|
C3B
|
D:HEM147
|
4.3
|
14.1
|
1.0
|
|
C3D
|
D:HEM147
|
4.3
|
16.2
|
1.0
|
|
C2A
|
D:HEM147
|
4.3
|
14.0
|
1.0
|
|
C3A
|
D:HEM147
|
4.3
|
16.8
|
1.0
|
|
HHD
|
D:HEM147
|
4.3
|
17.2
|
1.0
|
|
HE1
|
D:PHE103
|
4.4
|
20.9
|
1.0
|
|
CG
|
D:HIS92
|
4.4
|
13.7
|
1.0
|
|
HHB
|
D:HEM147
|
4.4
|
16.5
|
1.0
|
|
HHC
|
D:HEM147
|
4.4
|
17.3
|
1.0
|
|
HHA
|
D:HEM147
|
4.4
|
20.1
|
1.0
|
|
HD13
|
D:LEU96
|
4.4
|
18.2
|
1.0
|
|
HG23
|
D:VAL67
|
4.5
|
20.4
|
1.0
|
|
HG13
|
D:VAL67
|
4.6
|
19.4
|
1.0
|
|
HE1
|
D:HIS63
|
4.6
|
24.0
|
1.0
|
|
HD12
|
D:LEU96
|
4.6
|
18.2
|
1.0
|
|
CE1
|
D:HIS63
|
4.8
|
20.0
|
1.0
|
|
CD1
|
D:LEU96
|
4.9
|
15.2
|
1.0
|
|
HG21
|
D:VAL98
|
5.0
|
18.1
|
1.0
|
|
HD11
|
D:LEU96
|
5.0
|
18.2
|
1.0
|
|
Reference:
I.Birukou,
J.Soman,
J.S.Olson.
Blocking the Gate to Ligand Entry in Human Hemoglobin. J.Biol.Chem. V. 286 10515 2011.
ISSN: ISSN 0021-9258
PubMed: 21193395
DOI: 10.1074/JBC.M110.176271
Page generated: Sun Aug 4 16:36:05 2024
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