Iron in PDB 1jzk: Crystal Structure of Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy)
Protein crystallography data
The structure of Crystal Structure of Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy), PDB code: 1jzk
was solved by
J.E.Knapp,
Q.H.Gibson,
L.Cushing,
W.E.Royer Jr.,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.69 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.720,
44.180,
87.230,
90.00,
115.49,
90.00
|
R / Rfree (%)
|
17.9 /
21.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy)
(pdb code 1jzk). 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 Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy), PDB code: 1jzk:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1jzk
Go back to
Iron Binding Sites List in 1jzk
Iron binding site 1 out
of 4 in the Crystal Structure of Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy)
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 Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe147
b:24.1
occ:1.00
|
FE
|
A:HEM147
|
0.0
|
24.1
|
1.0
|
NC
|
A:HEM147
|
2.0
|
24.1
|
1.0
|
ND
|
A:HEM147
|
2.0
|
24.1
|
1.0
|
NB
|
A:HEM147
|
2.0
|
24.1
|
1.0
|
NE2
|
A:HIS101
|
2.0
|
21.3
|
1.0
|
NA
|
A:HEM147
|
2.1
|
24.1
|
1.0
|
C4C
|
A:HEM147
|
3.0
|
24.1
|
1.0
|
CD2
|
A:HIS101
|
3.1
|
21.3
|
1.0
|
C1C
|
A:HEM147
|
3.1
|
24.1
|
1.0
|
C1D
|
A:HEM147
|
3.1
|
24.1
|
1.0
|
CE1
|
A:HIS101
|
3.1
|
21.3
|
1.0
|
C4B
|
A:HEM147
|
3.1
|
24.1
|
1.0
|
C4D
|
A:HEM147
|
3.1
|
24.1
|
1.0
|
C4A
|
A:HEM147
|
3.1
|
24.1
|
1.0
|
C1B
|
A:HEM147
|
3.1
|
24.1
|
1.0
|
C1A
|
A:HEM147
|
3.1
|
24.1
|
1.0
|
O
|
A:HOH149
|
3.2
|
35.0
|
1.0
|
CHD
|
A:HEM147
|
3.4
|
24.1
|
1.0
|
CHC
|
A:HEM147
|
3.4
|
24.1
|
1.0
|
CHB
|
A:HEM147
|
3.5
|
24.1
|
1.0
|
CHA
|
A:HEM147
|
3.5
|
24.1
|
1.0
|
ND1
|
A:HIS101
|
4.2
|
21.3
|
1.0
|
CG
|
A:HIS101
|
4.2
|
21.3
|
1.0
|
C2C
|
A:HEM147
|
4.3
|
24.1
|
1.0
|
C3C
|
A:HEM147
|
4.3
|
24.1
|
1.0
|
C2D
|
A:HEM147
|
4.3
|
24.1
|
1.0
|
C3D
|
A:HEM147
|
4.3
|
24.1
|
1.0
|
C3A
|
A:HEM147
|
4.3
|
24.1
|
1.0
|
C3B
|
A:HEM147
|
4.3
|
24.1
|
1.0
|
C2B
|
A:HEM147
|
4.4
|
24.1
|
1.0
|
C2A
|
A:HEM147
|
4.4
|
24.1
|
1.0
|
CE1
|
A:HIS69
|
4.7
|
11.3
|
1.0
|
CZ
|
A:PHE97
|
4.8
|
19.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 1jzk
Go back to
Iron Binding Sites List in 1jzk
Iron binding site 2 out
of 4 in the Crystal Structure of Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy)
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 Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe147
b:20.8
occ:1.00
|
FE
|
B:HEM147
|
0.0
|
20.8
|
1.0
|
ND
|
B:HEM147
|
2.0
|
20.8
|
1.0
|
NA
|
B:HEM147
|
2.0
|
20.8
|
1.0
|
NC
|
B:HEM147
|
2.0
|
20.8
|
1.0
|
NE2
|
B:HIS101
|
2.1
|
15.7
|
1.0
|
NB
|
B:HEM147
|
2.1
|
20.8
|
1.0
|
C4D
|
B:HEM147
|
3.0
|
20.8
|
1.0
|
C1A
|
B:HEM147
|
3.1
|
20.8
|
1.0
|
C4A
|
B:HEM147
|
3.1
|
20.8
|
1.0
|
CE1
|
B:HIS101
|
3.1
|
15.7
|
1.0
|
C1D
|
B:HEM147
|
3.1
|
20.8
|
1.0
|
C4C
|
B:HEM147
|
3.1
|
20.8
|
1.0
|
C1C
|
B:HEM147
|
3.1
|
20.8
|
1.0
|
CD2
|
B:HIS101
|
3.1
|
15.7
|
1.0
|
C1B
|
B:HEM147
|
3.1
|
20.8
|
1.0
|
C4B
|
B:HEM147
|
3.1
|
20.8
|
1.0
|
O
|
B:HOH149
|
3.2
|
22.2
|
1.0
|
CHA
|
B:HEM147
|
3.4
|
20.8
|
1.0
|
CHD
|
B:HEM147
|
3.5
|
20.8
|
1.0
|
CHB
|
B:HEM147
|
3.5
|
20.8
|
1.0
|
CHC
|
B:HEM147
|
3.5
|
20.8
|
1.0
|
ND1
|
B:HIS101
|
4.2
|
15.7
|
1.0
|
C3D
|
B:HEM147
|
4.2
|
20.8
|
1.0
|
CG
|
B:HIS101
|
4.3
|
15.7
|
1.0
|
C3A
|
B:HEM147
|
4.3
|
20.8
|
1.0
|
C2D
|
B:HEM147
|
4.3
|
20.8
|
1.0
|
C2A
|
B:HEM147
|
4.3
|
20.8
|
1.0
|
C3C
|
B:HEM147
|
4.3
|
20.8
|
1.0
|
C2C
|
B:HEM147
|
4.3
|
20.8
|
1.0
|
C2B
|
B:HEM147
|
4.4
|
20.8
|
1.0
|
C3B
|
B:HEM147
|
4.4
|
20.8
|
1.0
|
CE1
|
B:HIS69
|
4.6
|
16.2
|
1.0
|
CZ
|
B:PHE97
|
4.9
|
15.1
|
1.0
|
NE2
|
B:HIS69
|
5.0
|
16.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 1jzk
Go back to
Iron Binding Sites List in 1jzk
Iron binding site 3 out
of 4 in the Crystal Structure of Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy)
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 Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe147
b:26.7
occ:1.00
|
FE
|
C:HEM147
|
0.0
|
26.7
|
1.0
|
NA
|
C:HEM147
|
2.0
|
26.7
|
1.0
|
ND
|
C:HEM147
|
2.0
|
26.7
|
1.0
|
NC
|
C:HEM147
|
2.0
|
26.7
|
1.0
|
NE2
|
C:HIS101
|
2.1
|
18.6
|
1.0
|
NB
|
C:HEM147
|
2.1
|
26.7
|
1.0
|
C4A
|
C:HEM147
|
3.0
|
26.7
|
1.0
|
C1A
|
C:HEM147
|
3.1
|
26.7
|
1.0
|
C4D
|
C:HEM147
|
3.1
|
26.7
|
1.0
|
CE1
|
C:HIS101
|
3.1
|
18.6
|
1.0
|
C1D
|
C:HEM147
|
3.1
|
26.7
|
1.0
|
C1C
|
C:HEM147
|
3.1
|
26.7
|
1.0
|
C4C
|
C:HEM147
|
3.1
|
26.7
|
1.0
|
CD2
|
C:HIS101
|
3.1
|
18.6
|
1.0
|
C1B
|
C:HEM147
|
3.1
|
26.7
|
1.0
|
C4B
|
C:HEM147
|
3.1
|
26.7
|
1.0
|
CHA
|
C:HEM147
|
3.4
|
26.7
|
1.0
|
CHB
|
C:HEM147
|
3.4
|
26.7
|
1.0
|
CHD
|
C:HEM147
|
3.5
|
26.7
|
1.0
|
O
|
C:HOH160
|
3.5
|
31.2
|
1.0
|
CHC
|
C:HEM147
|
3.5
|
26.7
|
1.0
|
ND1
|
C:HIS101
|
4.2
|
18.6
|
1.0
|
CG
|
C:HIS101
|
4.2
|
18.6
|
1.0
|
C3A
|
C:HEM147
|
4.3
|
26.7
|
1.0
|
C3D
|
C:HEM147
|
4.3
|
26.7
|
1.0
|
C2A
|
C:HEM147
|
4.3
|
26.7
|
1.0
|
C2D
|
C:HEM147
|
4.3
|
26.7
|
1.0
|
C2C
|
C:HEM147
|
4.3
|
26.7
|
1.0
|
C3C
|
C:HEM147
|
4.3
|
26.7
|
1.0
|
C2B
|
C:HEM147
|
4.4
|
26.7
|
1.0
|
C3B
|
C:HEM147
|
4.4
|
26.7
|
1.0
|
CE1
|
C:HIS69
|
4.5
|
17.8
|
1.0
|
CZ
|
C:PHE97
|
4.8
|
29.4
|
1.0
|
NE2
|
C:HIS69
|
5.0
|
17.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 1jzk
Go back to
Iron Binding Sites List in 1jzk
Iron binding site 4 out
of 4 in the Crystal Structure of Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy)
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 Scapharca Inaequivalvis Hbi, I114F Mutant (Deoxy) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe147
b:25.2
occ:1.00
|
FE
|
D:HEM147
|
0.0
|
25.2
|
1.0
|
NC
|
D:HEM147
|
2.0
|
25.2
|
1.0
|
ND
|
D:HEM147
|
2.0
|
25.2
|
1.0
|
NB
|
D:HEM147
|
2.0
|
25.2
|
1.0
|
NA
|
D:HEM147
|
2.1
|
25.2
|
1.0
|
NE2
|
D:HIS101
|
2.1
|
25.1
|
1.0
|
CE1
|
D:HIS101
|
3.0
|
25.1
|
1.0
|
C1C
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
C4C
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
C1D
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
C4B
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
C4D
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
C1B
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
C4A
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
C1A
|
D:HEM147
|
3.1
|
25.2
|
1.0
|
CD2
|
D:HIS101
|
3.1
|
25.1
|
1.0
|
O
|
D:HOH149
|
3.2
|
26.8
|
1.0
|
CHD
|
D:HEM147
|
3.4
|
25.2
|
1.0
|
CHC
|
D:HEM147
|
3.4
|
25.2
|
1.0
|
CHB
|
D:HEM147
|
3.5
|
25.2
|
1.0
|
CHA
|
D:HEM147
|
3.5
|
25.2
|
1.0
|
ND1
|
D:HIS101
|
4.2
|
25.1
|
1.0
|
CG
|
D:HIS101
|
4.2
|
25.1
|
1.0
|
C3D
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
C2C
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
C3C
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
C2D
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
C3A
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
C3B
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
C2B
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
C2A
|
D:HEM147
|
4.3
|
25.2
|
1.0
|
CE1
|
D:HIS69
|
4.5
|
15.2
|
1.0
|
CZ
|
D:PHE97
|
4.8
|
24.6
|
1.0
|
NH1
|
D:ARG104
|
5.0
|
34.2
|
1.0
|
NE2
|
D:HIS69
|
5.0
|
15.2
|
1.0
|
|
Reference:
J.E.Knapp,
Q.H.Gibson,
L.Cushing,
W.E.Royer Jr..
Restricting the Ligand-Linked Heme Movement in Scapharca Dimeric Hemoglobin Reveals Tight Coupling Between Distal and Proximal Contributions to Cooperativity. Biochemistry V. 40 14795 2001.
ISSN: ISSN 0006-2960
PubMed: 11732898
DOI: 10.1021/BI011071T
Page generated: Sat Aug 3 08:48:36 2024
|