Iron in PDB 1f5o: 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
Protein crystallography data
The structure of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1), PDB code: 1f5o
was solved by
H.A.Heaslet,
W.E.Royer Jr.,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.500,
96.200,
146.100,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.2 /
23.4
|
Iron Binding Sites:
The binding sites of Iron atom in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
(pdb code 1f5o). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1), PDB code: 1f5o:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1f5o
Go back to
Iron Binding Sites List in 1f5o
Iron binding site 1 out
of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:52.5
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
52.5
|
1.0
|
NA
|
A:HEM150
|
2.0
|
52.5
|
1.0
|
ND
|
A:HEM150
|
2.0
|
52.5
|
1.0
|
NC
|
A:HEM150
|
2.0
|
52.5
|
1.0
|
NB
|
A:HEM150
|
2.0
|
52.5
|
1.0
|
NE2
|
A:HIS105
|
2.0
|
33.8
|
1.0
|
CE1
|
A:HIS105
|
2.9
|
33.8
|
1.0
|
C1A
|
A:HEM150
|
3.0
|
52.5
|
1.0
|
C1D
|
A:HEM150
|
3.0
|
52.5
|
1.0
|
C4A
|
A:HEM150
|
3.0
|
52.5
|
1.0
|
C4C
|
A:HEM150
|
3.1
|
52.5
|
1.0
|
C4D
|
A:HEM150
|
3.1
|
52.5
|
1.0
|
C1C
|
A:HEM150
|
3.1
|
52.5
|
1.0
|
C4B
|
A:HEM150
|
3.1
|
52.5
|
1.0
|
C1B
|
A:HEM150
|
3.1
|
52.5
|
1.0
|
CD2
|
A:HIS105
|
3.2
|
33.8
|
1.0
|
CHD
|
A:HEM150
|
3.4
|
52.5
|
1.0
|
CHA
|
A:HEM150
|
3.4
|
52.5
|
1.0
|
CHB
|
A:HEM150
|
3.5
|
52.5
|
1.0
|
CHC
|
A:HEM150
|
3.5
|
52.5
|
1.0
|
ND1
|
A:HIS105
|
4.1
|
33.8
|
1.0
|
NE2
|
A:HIS73
|
4.2
|
49.5
|
1.0
|
CG
|
A:HIS105
|
4.3
|
33.8
|
1.0
|
C2D
|
A:HEM150
|
4.3
|
52.5
|
1.0
|
C2A
|
A:HEM150
|
4.3
|
52.5
|
1.0
|
C3D
|
A:HEM150
|
4.3
|
52.5
|
1.0
|
C3A
|
A:HEM150
|
4.3
|
52.5
|
1.0
|
C2C
|
A:HEM150
|
4.3
|
52.5
|
1.0
|
C3C
|
A:HEM150
|
4.3
|
52.5
|
1.0
|
C3B
|
A:HEM150
|
4.3
|
52.5
|
1.0
|
C2B
|
A:HEM150
|
4.4
|
52.5
|
1.0
|
CG1
|
A:ILE77
|
4.4
|
37.4
|
1.0
|
CD1
|
A:ILE77
|
4.4
|
37.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 1f5o
Go back to
Iron Binding Sites List in 1f5o
Iron binding site 2 out
of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:38.0
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
38.0
|
1.0
|
ND
|
B:HEM150
|
2.0
|
38.0
|
1.0
|
NA
|
B:HEM150
|
2.0
|
38.0
|
1.0
|
NC
|
B:HEM150
|
2.0
|
38.0
|
1.0
|
NB
|
B:HEM150
|
2.0
|
38.0
|
1.0
|
NE2
|
B:HIS105
|
2.1
|
39.2
|
1.0
|
CE1
|
B:HIS105
|
2.9
|
39.2
|
1.0
|
C1A
|
B:HEM150
|
3.0
|
38.0
|
1.0
|
C1D
|
B:HEM150
|
3.0
|
38.0
|
1.0
|
C4D
|
B:HEM150
|
3.0
|
38.0
|
1.0
|
C4C
|
B:HEM150
|
3.0
|
38.0
|
1.0
|
C4A
|
B:HEM150
|
3.1
|
38.0
|
1.0
|
C1C
|
B:HEM150
|
3.1
|
38.0
|
1.0
|
C4B
|
B:HEM150
|
3.1
|
38.0
|
1.0
|
C1B
|
B:HEM150
|
3.1
|
38.0
|
1.0
|
CD2
|
B:HIS105
|
3.2
|
39.2
|
1.0
|
CHD
|
B:HEM150
|
3.4
|
38.0
|
1.0
|
CHA
|
B:HEM150
|
3.4
|
38.0
|
1.0
|
CHC
|
B:HEM150
|
3.5
|
38.0
|
1.0
|
CHB
|
B:HEM150
|
3.5
|
38.0
|
1.0
|
ND1
|
B:HIS105
|
4.1
|
39.2
|
1.0
|
NE2
|
B:HIS73
|
4.2
|
39.3
|
1.0
|
C2A
|
B:HEM150
|
4.2
|
38.0
|
1.0
|
C2D
|
B:HEM150
|
4.3
|
38.0
|
1.0
|
C3D
|
B:HEM150
|
4.3
|
38.0
|
1.0
|
CG
|
B:HIS105
|
4.3
|
39.2
|
1.0
|
C3A
|
B:HEM150
|
4.3
|
38.0
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
38.0
|
1.0
|
C3C
|
B:HEM150
|
4.3
|
38.0
|
1.0
|
C3B
|
B:HEM150
|
4.4
|
38.0
|
1.0
|
C2B
|
B:HEM150
|
4.4
|
38.0
|
1.0
|
CG1
|
B:ILE77
|
4.4
|
26.0
|
1.0
|
CD1
|
B:ILE77
|
4.4
|
26.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 1f5o
Go back to
Iron Binding Sites List in 1f5o
Iron binding site 3 out
of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:42.8
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
42.8
|
1.0
|
ND
|
C:HEM150
|
2.0
|
42.8
|
1.0
|
NC
|
C:HEM150
|
2.0
|
42.8
|
1.0
|
NA
|
C:HEM150
|
2.0
|
42.8
|
1.0
|
NB
|
C:HEM150
|
2.0
|
42.8
|
1.0
|
NE2
|
C:HIS105
|
2.1
|
57.2
|
1.0
|
CE1
|
C:HIS105
|
3.0
|
57.2
|
1.0
|
C1D
|
C:HEM150
|
3.0
|
42.8
|
1.0
|
C4D
|
C:HEM150
|
3.0
|
42.8
|
1.0
|
C4C
|
C:HEM150
|
3.0
|
42.8
|
1.0
|
C1A
|
C:HEM150
|
3.0
|
42.8
|
1.0
|
C1C
|
C:HEM150
|
3.1
|
42.8
|
1.0
|
C4A
|
C:HEM150
|
3.1
|
42.8
|
1.0
|
C4B
|
C:HEM150
|
3.1
|
42.8
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
42.8
|
1.0
|
CD2
|
C:HIS105
|
3.2
|
57.2
|
1.0
|
CHD
|
C:HEM150
|
3.4
|
42.8
|
1.0
|
CHA
|
C:HEM150
|
3.4
|
42.8
|
1.0
|
CHC
|
C:HEM150
|
3.5
|
42.8
|
1.0
|
CHB
|
C:HEM150
|
3.5
|
42.8
|
1.0
|
ND1
|
C:HIS105
|
4.2
|
57.2
|
1.0
|
NE2
|
C:HIS73
|
4.2
|
54.7
|
1.0
|
C2D
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
C3D
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
C2A
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
CG
|
C:HIS105
|
4.3
|
57.2
|
1.0
|
C2C
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
C3C
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
C3A
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
C3B
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
42.8
|
1.0
|
CG1
|
C:ILE77
|
4.4
|
33.7
|
1.0
|
CD1
|
C:ILE77
|
4.4
|
33.7
|
1.0
|
|
Iron binding site 4 out
of 6 in 1f5o
Go back to
Iron Binding Sites List in 1f5o
Iron binding site 4 out
of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:38.2
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
38.2
|
1.0
|
ND
|
D:HEM150
|
2.0
|
38.2
|
1.0
|
NA
|
D:HEM150
|
2.0
|
38.2
|
1.0
|
NC
|
D:HEM150
|
2.0
|
38.2
|
1.0
|
NE2
|
D:HIS105
|
2.0
|
53.6
|
1.0
|
NB
|
D:HEM150
|
2.1
|
38.2
|
1.0
|
CE1
|
D:HIS105
|
2.9
|
53.6
|
1.0
|
C1D
|
D:HEM150
|
3.0
|
38.2
|
1.0
|
C4D
|
D:HEM150
|
3.0
|
38.2
|
1.0
|
C1A
|
D:HEM150
|
3.0
|
38.2
|
1.0
|
C4A
|
D:HEM150
|
3.0
|
38.2
|
1.0
|
C4C
|
D:HEM150
|
3.1
|
38.2
|
1.0
|
C1C
|
D:HEM150
|
3.1
|
38.2
|
1.0
|
C1B
|
D:HEM150
|
3.1
|
38.2
|
1.0
|
C4B
|
D:HEM150
|
3.1
|
38.2
|
1.0
|
CD2
|
D:HIS105
|
3.2
|
53.6
|
1.0
|
CHA
|
D:HEM150
|
3.4
|
38.2
|
1.0
|
CHD
|
D:HEM150
|
3.4
|
38.2
|
1.0
|
CHB
|
D:HEM150
|
3.5
|
38.2
|
1.0
|
CHC
|
D:HEM150
|
3.5
|
38.2
|
1.0
|
ND1
|
D:HIS105
|
4.1
|
53.6
|
1.0
|
NE2
|
D:HIS73
|
4.2
|
55.0
|
1.0
|
C3D
|
D:HEM150
|
4.2
|
38.2
|
1.0
|
C2A
|
D:HEM150
|
4.2
|
38.2
|
1.0
|
C2D
|
D:HEM150
|
4.2
|
38.2
|
1.0
|
CG
|
D:HIS105
|
4.3
|
53.6
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
38.2
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
38.2
|
1.0
|
C3C
|
D:HEM150
|
4.3
|
38.2
|
1.0
|
C3B
|
D:HEM150
|
4.4
|
38.2
|
1.0
|
C2B
|
D:HEM150
|
4.4
|
38.2
|
1.0
|
CG1
|
D:ILE77
|
4.4
|
30.2
|
1.0
|
CD1
|
D:ILE77
|
4.4
|
30.2
|
1.0
|
|
Iron binding site 5 out
of 6 in 1f5o
Go back to
Iron Binding Sites List in 1f5o
Iron binding site 5 out
of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe150
b:41.0
occ:1.00
|
FE
|
E:HEM150
|
0.0
|
41.0
|
1.0
|
NC
|
E:HEM150
|
2.0
|
41.0
|
1.0
|
ND
|
E:HEM150
|
2.0
|
41.0
|
1.0
|
NA
|
E:HEM150
|
2.0
|
41.0
|
1.0
|
NB
|
E:HEM150
|
2.0
|
41.0
|
1.0
|
NE2
|
E:HIS105
|
2.1
|
33.8
|
1.0
|
CE1
|
E:HIS105
|
3.0
|
33.8
|
1.0
|
C1D
|
E:HEM150
|
3.0
|
41.0
|
1.0
|
C4C
|
E:HEM150
|
3.0
|
41.0
|
1.0
|
C4D
|
E:HEM150
|
3.1
|
41.0
|
1.0
|
C1C
|
E:HEM150
|
3.1
|
41.0
|
1.0
|
C1A
|
E:HEM150
|
3.1
|
41.0
|
1.0
|
C4B
|
E:HEM150
|
3.1
|
41.0
|
1.0
|
C4A
|
E:HEM150
|
3.1
|
41.0
|
1.0
|
C1B
|
E:HEM150
|
3.1
|
41.0
|
1.0
|
CD2
|
E:HIS105
|
3.2
|
33.8
|
1.0
|
CHD
|
E:HEM150
|
3.4
|
41.0
|
1.0
|
CHC
|
E:HEM150
|
3.4
|
41.0
|
1.0
|
CHA
|
E:HEM150
|
3.4
|
41.0
|
1.0
|
CHB
|
E:HEM150
|
3.5
|
41.0
|
1.0
|
ND1
|
E:HIS105
|
4.1
|
33.8
|
1.0
|
NE2
|
E:HIS73
|
4.2
|
58.3
|
1.0
|
C2D
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
C3D
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
CG
|
E:HIS105
|
4.3
|
33.8
|
1.0
|
C2C
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
C2A
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
C3C
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
C3A
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
C3B
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
C2B
|
E:HEM150
|
4.3
|
41.0
|
1.0
|
CD1
|
E:ILE77
|
4.4
|
36.2
|
1.0
|
CG1
|
E:ILE77
|
4.4
|
36.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 1f5o
Go back to
Iron Binding Sites List in 1f5o
Iron binding site 6 out
of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe150
b:42.2
occ:1.00
|
FE
|
F:HEM150
|
0.0
|
42.2
|
1.0
|
NA
|
F:HEM150
|
1.9
|
42.2
|
1.0
|
ND
|
F:HEM150
|
2.0
|
42.2
|
1.0
|
NB
|
F:HEM150
|
2.0
|
42.2
|
1.0
|
NC
|
F:HEM150
|
2.0
|
42.2
|
1.0
|
NE2
|
F:HIS105
|
2.1
|
41.0
|
1.0
|
CE1
|
F:HIS105
|
2.9
|
41.0
|
1.0
|
C1A
|
F:HEM150
|
3.0
|
42.2
|
1.0
|
C4A
|
F:HEM150
|
3.0
|
42.2
|
1.0
|
C4D
|
F:HEM150
|
3.0
|
42.2
|
1.0
|
C1D
|
F:HEM150
|
3.1
|
42.2
|
1.0
|
C1B
|
F:HEM150
|
3.1
|
42.2
|
1.0
|
C4B
|
F:HEM150
|
3.1
|
42.2
|
1.0
|
C4C
|
F:HEM150
|
3.1
|
42.2
|
1.0
|
C1C
|
F:HEM150
|
3.1
|
42.2
|
1.0
|
CD2
|
F:HIS105
|
3.2
|
41.0
|
1.0
|
CHA
|
F:HEM150
|
3.4
|
42.2
|
1.0
|
CHB
|
F:HEM150
|
3.4
|
42.2
|
1.0
|
CHD
|
F:HEM150
|
3.5
|
42.2
|
1.0
|
CHC
|
F:HEM150
|
3.5
|
42.2
|
1.0
|
ND1
|
F:HIS105
|
4.2
|
41.0
|
1.0
|
NE2
|
F:HIS73
|
4.2
|
54.6
|
1.0
|
C2A
|
F:HEM150
|
4.2
|
42.2
|
1.0
|
C3A
|
F:HEM150
|
4.3
|
42.2
|
1.0
|
C3D
|
F:HEM150
|
4.3
|
42.2
|
1.0
|
C2D
|
F:HEM150
|
4.3
|
42.2
|
1.0
|
CG
|
F:HIS105
|
4.3
|
41.0
|
1.0
|
C3B
|
F:HEM150
|
4.3
|
42.2
|
1.0
|
C2B
|
F:HEM150
|
4.3
|
42.2
|
1.0
|
C2C
|
F:HEM150
|
4.3
|
42.2
|
1.0
|
C3C
|
F:HEM150
|
4.4
|
42.2
|
1.0
|
CG1
|
F:ILE77
|
4.4
|
39.1
|
1.0
|
CD1
|
F:ILE77
|
4.4
|
39.1
|
1.0
|
|
Reference:
H.A.Heaslet,
W.E.Royer Jr..
Crystalline Ligand Transitions in Lamprey Hemoglobin. Structural Evidence For the Regulation of Oxygen Affinity. J.Biol.Chem. V. 276 26230 2001.
ISSN: ISSN 0021-9258
PubMed: 11340069
DOI: 10.1074/JBC.M101391200
Page generated: Sat Aug 3 04:44:05 2024
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