Iron in PDB 1j40: Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed)
Protein crystallography data
The structure of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed), PDB code: 1j40
was solved by
S.Adachi,
S.-Y.Park,
J.R.H.Tame,
Y.Shiro,
N.Shibayama,
Rikenstructural Genomics/Proteomics Initiative (Rsgi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.45
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.708,
94.860,
99.730,
90.00,
101.97,
90.00
|
R / Rfree (%)
|
16.5 /
19.7
|
Other elements in 1j40:
The structure of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed)
(pdb code 1j40). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed), PDB code: 1j40:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1j40
Go back to
Iron Binding Sites List in 1j40
Iron binding site 1 out
of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed)
![](/pictures/FE/pdb/j4/1j40-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/j4/1j40-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe147
b:8.4
occ:1.00
|
FE
|
B:HEM147
|
0.0
|
8.4
|
1.0
|
C
|
B:CMO148
|
1.7
|
16.6
|
1.0
|
NC
|
B:HEM147
|
2.0
|
7.8
|
1.0
|
NB
|
B:HEM147
|
2.0
|
8.8
|
1.0
|
NA
|
B:HEM147
|
2.0
|
7.3
|
1.0
|
ND
|
B:HEM147
|
2.1
|
8.3
|
1.0
|
NE2
|
B:HIS92
|
2.1
|
8.4
|
1.0
|
O
|
B:CMO148
|
2.9
|
21.5
|
1.0
|
C4B
|
B:HEM147
|
3.0
|
7.7
|
1.0
|
C1C
|
B:HEM147
|
3.0
|
8.2
|
1.0
|
CE1
|
B:HIS92
|
3.1
|
9.8
|
1.0
|
C1A
|
B:HEM147
|
3.1
|
7.1
|
1.0
|
C1D
|
B:HEM147
|
3.1
|
7.8
|
1.0
|
C4C
|
B:HEM147
|
3.1
|
6.8
|
1.0
|
C1B
|
B:HEM147
|
3.1
|
8.3
|
1.0
|
C4A
|
B:HEM147
|
3.1
|
8.4
|
1.0
|
C4D
|
B:HEM147
|
3.1
|
6.8
|
1.0
|
CD2
|
B:HIS92
|
3.2
|
7.7
|
1.0
|
CHC
|
B:HEM147
|
3.4
|
9.6
|
1.0
|
CHA
|
B:HEM147
|
3.5
|
7.0
|
1.0
|
CHD
|
B:HEM147
|
3.5
|
8.4
|
1.0
|
CHB
|
B:HEM147
|
3.5
|
7.3
|
1.0
|
ND1
|
B:HIS92
|
4.2
|
8.1
|
1.0
|
C3B
|
B:HEM147
|
4.3
|
8.8
|
1.0
|
C2C
|
B:HEM147
|
4.3
|
7.6
|
1.0
|
C3C
|
B:HEM147
|
4.3
|
9.0
|
1.0
|
C2B
|
B:HEM147
|
4.3
|
8.6
|
1.0
|
C2A
|
B:HEM147
|
4.3
|
8.3
|
1.0
|
NE2
|
B:HIS63
|
4.3
|
13.1
|
1.0
|
C3A
|
B:HEM147
|
4.3
|
9.2
|
1.0
|
CG
|
B:HIS92
|
4.3
|
6.5
|
1.0
|
C2D
|
B:HEM147
|
4.3
|
8.2
|
1.0
|
C3D
|
B:HEM147
|
4.3
|
8.8
|
1.0
|
CG2
|
B:VAL67
|
4.3
|
16.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 1j40
Go back to
Iron Binding Sites List in 1j40
Iron binding site 2 out
of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed)
![](/pictures/FE/pdb/j4/1j40-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/j4/1j40-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe147
b:11.1
occ:1.00
|
FE
|
D:HEM147
|
0.0
|
11.1
|
1.0
|
C
|
D:CMO148
|
1.6
|
11.4
|
1.0
|
NC
|
D:HEM147
|
2.0
|
10.0
|
1.0
|
ND
|
D:HEM147
|
2.0
|
11.1
|
1.0
|
NA
|
D:HEM147
|
2.0
|
11.2
|
1.0
|
NB
|
D:HEM147
|
2.1
|
11.0
|
1.0
|
NE2
|
D:HIS92
|
2.1
|
12.1
|
1.0
|
O
|
D:CMO148
|
2.8
|
12.4
|
1.0
|
C1C
|
D:HEM147
|
3.0
|
10.9
|
1.0
|
C4C
|
D:HEM147
|
3.0
|
10.6
|
1.0
|
C1D
|
D:HEM147
|
3.0
|
11.9
|
1.0
|
CE1
|
D:HIS92
|
3.1
|
10.0
|
1.0
|
C4D
|
D:HEM147
|
3.1
|
11.5
|
1.0
|
C1A
|
D:HEM147
|
3.1
|
12.6
|
1.0
|
C4A
|
D:HEM147
|
3.1
|
12.3
|
1.0
|
C4B
|
D:HEM147
|
3.1
|
10.1
|
1.0
|
C1B
|
D:HEM147
|
3.1
|
9.6
|
1.0
|
CD2
|
D:HIS92
|
3.2
|
10.1
|
1.0
|
CHD
|
D:HEM147
|
3.4
|
11.0
|
1.0
|
CHA
|
D:HEM147
|
3.4
|
12.2
|
1.0
|
CHC
|
D:HEM147
|
3.4
|
10.4
|
1.0
|
CHB
|
D:HEM147
|
3.5
|
11.3
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
9.9
|
1.0
|
C2C
|
D:HEM147
|
4.2
|
11.3
|
1.0
|
C3C
|
D:HEM147
|
4.2
|
12.2
|
1.0
|
C3A
|
D:HEM147
|
4.3
|
13.7
|
1.0
|
C2A
|
D:HEM147
|
4.3
|
14.2
|
1.0
|
CG
|
D:HIS92
|
4.3
|
10.9
|
1.0
|
C2D
|
D:HEM147
|
4.3
|
12.3
|
1.0
|
C3D
|
D:HEM147
|
4.3
|
12.9
|
1.0
|
C2B
|
D:HEM147
|
4.3
|
9.7
|
1.0
|
C3B
|
D:HEM147
|
4.3
|
10.7
|
1.0
|
NE2
|
D:HIS63
|
4.4
|
13.9
|
1.0
|
CG2
|
D:VAL67
|
4.6
|
13.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 1j40
Go back to
Iron Binding Sites List in 1j40
Iron binding site 3 out
of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed)
![](/pictures/FE/pdb/j4/1j40-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/j4/1j40-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe147
b:11.3
occ:1.00
|
FE
|
F:HEM147
|
0.0
|
11.3
|
1.0
|
C
|
F:CMO148
|
1.7
|
13.7
|
1.0
|
NC
|
F:HEM147
|
2.0
|
10.6
|
1.0
|
NB
|
F:HEM147
|
2.0
|
9.4
|
1.0
|
ND
|
F:HEM147
|
2.1
|
9.7
|
1.0
|
NA
|
F:HEM147
|
2.1
|
12.2
|
1.0
|
NE2
|
F:HIS92
|
2.1
|
9.8
|
1.0
|
O
|
F:CMO148
|
2.9
|
16.5
|
1.0
|
C1C
|
F:HEM147
|
3.0
|
10.2
|
1.0
|
C4C
|
F:HEM147
|
3.0
|
8.3
|
1.0
|
C4B
|
F:HEM147
|
3.0
|
10.3
|
1.0
|
CE1
|
F:HIS92
|
3.0
|
10.9
|
1.0
|
C1D
|
F:HEM147
|
3.1
|
9.8
|
1.0
|
C1A
|
F:HEM147
|
3.1
|
12.1
|
1.0
|
C4D
|
F:HEM147
|
3.1
|
11.2
|
1.0
|
C1B
|
F:HEM147
|
3.1
|
12.3
|
1.0
|
C4A
|
F:HEM147
|
3.1
|
12.9
|
1.0
|
CD2
|
F:HIS92
|
3.2
|
9.7
|
1.0
|
CHC
|
F:HEM147
|
3.4
|
11.7
|
1.0
|
CHD
|
F:HEM147
|
3.4
|
8.6
|
1.0
|
CHA
|
F:HEM147
|
3.4
|
11.8
|
1.0
|
CHB
|
F:HEM147
|
3.5
|
11.4
|
1.0
|
ND1
|
F:HIS92
|
4.2
|
9.7
|
1.0
|
C3C
|
F:HEM147
|
4.2
|
10.7
|
1.0
|
C2C
|
F:HEM147
|
4.2
|
10.9
|
1.0
|
C3B
|
F:HEM147
|
4.3
|
12.4
|
1.0
|
C2B
|
F:HEM147
|
4.3
|
11.9
|
1.0
|
C2D
|
F:HEM147
|
4.3
|
11.2
|
1.0
|
CG
|
F:HIS92
|
4.3
|
10.7
|
1.0
|
C3D
|
F:HEM147
|
4.3
|
12.2
|
1.0
|
C2A
|
F:HEM147
|
4.3
|
13.5
|
1.0
|
C3A
|
F:HEM147
|
4.3
|
13.8
|
1.0
|
NE2
|
F:HIS63
|
4.4
|
13.1
|
1.0
|
CG2
|
F:VAL67
|
4.5
|
17.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 1j40
Go back to
Iron Binding Sites List in 1j40
Iron binding site 4 out
of 4 in the Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed)
![](/pictures/FE/pdb/j4/1j40-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/j4/1j40-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Direct Observation of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe147
b:10.7
occ:1.00
|
FE
|
H:HEM147
|
0.0
|
10.7
|
1.0
|
C
|
H:CMO148
|
1.7
|
12.0
|
1.0
|
NB
|
H:HEM147
|
2.0
|
10.0
|
1.0
|
NA
|
H:HEM147
|
2.0
|
11.4
|
1.0
|
NC
|
H:HEM147
|
2.0
|
9.4
|
1.0
|
ND
|
H:HEM147
|
2.1
|
10.3
|
1.0
|
NE2
|
H:HIS92
|
2.1
|
10.0
|
1.0
|
O
|
H:CMO148
|
2.9
|
14.6
|
1.0
|
CE1
|
H:HIS92
|
3.0
|
10.5
|
1.0
|
C1B
|
H:HEM147
|
3.0
|
11.1
|
1.0
|
C1D
|
H:HEM147
|
3.1
|
12.7
|
1.0
|
C4A
|
H:HEM147
|
3.1
|
11.9
|
1.0
|
C4C
|
H:HEM147
|
3.1
|
10.3
|
1.0
|
C1C
|
H:HEM147
|
3.1
|
10.6
|
1.0
|
C1A
|
H:HEM147
|
3.1
|
11.8
|
1.0
|
C4B
|
H:HEM147
|
3.1
|
12.0
|
1.0
|
C4D
|
H:HEM147
|
3.1
|
10.1
|
1.0
|
CD2
|
H:HIS92
|
3.2
|
10.5
|
1.0
|
CHD
|
H:HEM147
|
3.4
|
10.8
|
1.0
|
CHB
|
H:HEM147
|
3.4
|
11.3
|
1.0
|
CHA
|
H:HEM147
|
3.4
|
11.3
|
1.0
|
CHC
|
H:HEM147
|
3.5
|
11.4
|
1.0
|
ND1
|
H:HIS92
|
4.2
|
9.4
|
1.0
|
C2C
|
H:HEM147
|
4.3
|
11.4
|
1.0
|
CG
|
H:HIS92
|
4.3
|
10.7
|
1.0
|
C2B
|
H:HEM147
|
4.3
|
10.8
|
1.0
|
C3C
|
H:HEM147
|
4.3
|
10.1
|
1.0
|
C3A
|
H:HEM147
|
4.3
|
12.7
|
1.0
|
C3B
|
H:HEM147
|
4.3
|
10.9
|
1.0
|
C2A
|
H:HEM147
|
4.3
|
13.8
|
1.0
|
C2D
|
H:HEM147
|
4.3
|
12.2
|
1.0
|
C3D
|
H:HEM147
|
4.3
|
11.5
|
1.0
|
NE2
|
H:HIS63
|
4.4
|
12.2
|
1.0
|
CG2
|
H:VAL67
|
4.6
|
13.3
|
1.0
|
|
Reference:
S.Adachi,
S.-Y.Park,
J.R.H.Tame,
Y.Shiro,
N.Shibayama.
Direct Observation of Photolysis-Induced Tertiary Structural Changes in Hemoglobin Proc.Natl.Acad.Sci.Usa V. 100 7039 2003.
ISSN: ISSN 0027-8424
PubMed: 12773618
DOI: 10.1073/PNAS.1230629100
Page generated: Sat Aug 3 08:23:05 2024
|