Iron in PDB 4n7p: Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
Protein crystallography data
The structure of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution., PDB code: 4n7p
was solved by
K.Sugiyama,
N.Shibayama,
S.Y.Park,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.81
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
228.331,
55.531,
139.681,
90.00,
103.08,
90.00
|
R / Rfree (%)
|
25.9 /
28.7
|
Other elements in 4n7p:
The structure of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
(pdb code 4n7p). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution., PDB code: 4n7p:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4n7p
Go back to
Iron Binding Sites List in 4n7p
Iron binding site 1 out
of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:53.5
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
53.5
|
1.0
|
NC
|
B:HEM201
|
2.0
|
48.2
|
1.0
|
NA
|
B:HEM201
|
2.0
|
52.4
|
1.0
|
NB
|
B:HEM201
|
2.1
|
52.6
|
1.0
|
ND
|
B:HEM201
|
2.1
|
51.8
|
1.0
|
NE2
|
B:HIS92
|
2.2
|
40.5
|
1.0
|
CD2
|
B:HIS92
|
2.9
|
46.3
|
1.0
|
C4C
|
B:HEM201
|
3.0
|
47.5
|
1.0
|
C1B
|
B:HEM201
|
3.1
|
52.9
|
1.0
|
C4A
|
B:HEM201
|
3.1
|
54.3
|
1.0
|
C1C
|
B:HEM201
|
3.1
|
49.6
|
1.0
|
C1A
|
B:HEM201
|
3.1
|
54.5
|
1.0
|
C1D
|
B:HEM201
|
3.1
|
53.1
|
1.0
|
C4B
|
B:HEM201
|
3.1
|
53.8
|
1.0
|
C4D
|
B:HEM201
|
3.1
|
53.8
|
1.0
|
CE1
|
B:HIS92
|
3.3
|
47.0
|
1.0
|
CHB
|
B:HEM201
|
3.4
|
53.6
|
1.0
|
CHD
|
B:HEM201
|
3.4
|
49.1
|
1.0
|
CHA
|
B:HEM201
|
3.4
|
54.1
|
1.0
|
CHC
|
B:HEM201
|
3.5
|
51.5
|
1.0
|
CG
|
B:HIS92
|
4.2
|
50.0
|
1.0
|
NE2
|
B:HIS63
|
4.2
|
78.2
|
1.0
|
C3C
|
B:HEM201
|
4.3
|
45.9
|
1.0
|
C2C
|
B:HEM201
|
4.3
|
45.6
|
1.0
|
C3A
|
B:HEM201
|
4.3
|
53.2
|
1.0
|
C2A
|
B:HEM201
|
4.3
|
54.4
|
1.0
|
ND1
|
B:HIS92
|
4.3
|
49.5
|
1.0
|
C2B
|
B:HEM201
|
4.3
|
55.6
|
1.0
|
C3B
|
B:HEM201
|
4.3
|
56.5
|
1.0
|
C2D
|
B:HEM201
|
4.4
|
53.2
|
1.0
|
C3D
|
B:HEM201
|
4.4
|
54.9
|
1.0
|
CG2
|
B:VAL67
|
4.8
|
65.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 4n7p
Go back to
Iron Binding Sites List in 4n7p
Iron binding site 2 out
of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:77.5
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
77.5
|
1.0
|
NC
|
C:HEM201
|
2.0
|
77.6
|
1.0
|
NA
|
C:HEM201
|
2.0
|
81.7
|
1.0
|
NB
|
C:HEM201
|
2.0
|
77.6
|
1.0
|
ND
|
C:HEM201
|
2.1
|
77.7
|
1.0
|
NE2
|
C:HIS87
|
2.5
|
82.3
|
1.0
|
C1B
|
C:HEM201
|
3.0
|
80.0
|
1.0
|
C4C
|
C:HEM201
|
3.0
|
75.1
|
1.0
|
C4A
|
C:HEM201
|
3.1
|
82.3
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
76.5
|
1.0
|
C1A
|
C:HEM201
|
3.1
|
83.7
|
1.0
|
C1D
|
C:HEM201
|
3.1
|
78.3
|
1.0
|
C4B
|
C:HEM201
|
3.1
|
76.6
|
1.0
|
C4D
|
C:HEM201
|
3.1
|
80.5
|
1.0
|
CD2
|
C:HIS87
|
3.4
|
84.7
|
1.0
|
CHB
|
C:HEM201
|
3.4
|
80.5
|
1.0
|
CHD
|
C:HEM201
|
3.4
|
77.5
|
1.0
|
CHA
|
C:HEM201
|
3.5
|
82.2
|
1.0
|
CHC
|
C:HEM201
|
3.5
|
76.6
|
1.0
|
CE1
|
C:HIS87
|
3.6
|
83.3
|
1.0
|
NE2
|
C:HIS58
|
4.2
|
0.9
|
1.0
|
C3C
|
C:HEM201
|
4.3
|
74.0
|
1.0
|
C2B
|
C:HEM201
|
4.3
|
79.8
|
1.0
|
C2C
|
C:HEM201
|
4.3
|
75.1
|
1.0
|
C3A
|
C:HEM201
|
4.3
|
83.8
|
1.0
|
C3B
|
C:HEM201
|
4.3
|
78.1
|
1.0
|
C2A
|
C:HEM201
|
4.3
|
85.1
|
1.0
|
C2D
|
C:HEM201
|
4.4
|
79.6
|
1.0
|
C3D
|
C:HEM201
|
4.4
|
82.7
|
1.0
|
CE1
|
C:HIS58
|
4.4
|
0.4
|
1.0
|
CG
|
C:HIS87
|
4.6
|
85.4
|
1.0
|
ND1
|
C:HIS87
|
4.6
|
84.5
|
1.0
|
|
Iron binding site 3 out
of 6 in 4n7p
Go back to
Iron Binding Sites List in 4n7p
Iron binding site 3 out
of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:48.6
occ:1.00
|
FE
|
F:HEM201
|
0.0
|
48.6
|
1.0
|
NC
|
F:HEM201
|
2.0
|
47.4
|
1.0
|
NB
|
F:HEM201
|
2.0
|
47.2
|
1.0
|
NA
|
F:HEM201
|
2.1
|
49.9
|
1.0
|
ND
|
F:HEM201
|
2.1
|
49.8
|
1.0
|
NE2
|
F:HIS92
|
2.1
|
59.5
|
1.0
|
C1B
|
F:HEM201
|
3.0
|
47.2
|
1.0
|
C4C
|
F:HEM201
|
3.1
|
46.8
|
1.0
|
C4A
|
F:HEM201
|
3.1
|
49.4
|
1.0
|
C1C
|
F:HEM201
|
3.1
|
47.4
|
1.0
|
C4B
|
F:HEM201
|
3.1
|
48.9
|
1.0
|
C1A
|
F:HEM201
|
3.1
|
53.1
|
1.0
|
CD2
|
F:HIS92
|
3.1
|
60.4
|
1.0
|
C1D
|
F:HEM201
|
3.1
|
50.1
|
1.0
|
CE1
|
F:HIS92
|
3.1
|
61.4
|
1.0
|
C4D
|
F:HEM201
|
3.1
|
53.5
|
1.0
|
CHB
|
F:HEM201
|
3.4
|
48.6
|
1.0
|
CHD
|
F:HEM201
|
3.4
|
47.6
|
1.0
|
CHC
|
F:HEM201
|
3.5
|
49.1
|
1.0
|
CHA
|
F:HEM201
|
3.5
|
52.3
|
1.0
|
ND1
|
F:HIS92
|
4.2
|
61.1
|
1.0
|
CG
|
F:HIS92
|
4.3
|
61.6
|
1.0
|
C3C
|
F:HEM201
|
4.3
|
47.3
|
1.0
|
C2B
|
F:HEM201
|
4.3
|
47.5
|
1.0
|
C2C
|
F:HEM201
|
4.3
|
46.8
|
1.0
|
C3A
|
F:HEM201
|
4.3
|
51.4
|
1.0
|
C2A
|
F:HEM201
|
4.3
|
53.5
|
1.0
|
C3B
|
F:HEM201
|
4.3
|
48.5
|
1.0
|
C2D
|
F:HEM201
|
4.4
|
51.2
|
1.0
|
C3D
|
F:HEM201
|
4.4
|
56.0
|
1.0
|
NE2
|
F:HIS63
|
4.4
|
64.3
|
1.0
|
CG2
|
F:VAL67
|
4.5
|
47.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 4n7p
Go back to
Iron Binding Sites List in 4n7p
Iron binding site 4 out
of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:78.1
occ:1.00
|
FE
|
G:HEM201
|
0.0
|
78.1
|
1.0
|
NC
|
G:HEM201
|
2.0
|
81.5
|
1.0
|
NA
|
G:HEM201
|
2.0
|
82.7
|
1.0
|
NB
|
G:HEM201
|
2.1
|
81.3
|
1.0
|
ND
|
G:HEM201
|
2.1
|
80.9
|
1.0
|
NE2
|
G:HIS87
|
2.3
|
69.0
|
1.0
|
CE1
|
G:HIS87
|
2.9
|
70.8
|
1.0
|
C4C
|
G:HEM201
|
3.0
|
80.9
|
1.0
|
C4A
|
G:HEM201
|
3.1
|
83.2
|
1.0
|
C1B
|
G:HEM201
|
3.1
|
82.0
|
1.0
|
C1D
|
G:HEM201
|
3.1
|
80.8
|
1.0
|
C1A
|
G:HEM201
|
3.1
|
83.6
|
1.0
|
C1C
|
G:HEM201
|
3.1
|
81.4
|
1.0
|
C4D
|
G:HEM201
|
3.1
|
80.7
|
1.0
|
C4B
|
G:HEM201
|
3.1
|
80.7
|
1.0
|
CHD
|
G:HEM201
|
3.4
|
81.0
|
1.0
|
CHB
|
G:HEM201
|
3.4
|
83.4
|
1.0
|
CHA
|
G:HEM201
|
3.5
|
82.0
|
1.0
|
CD2
|
G:HIS87
|
3.5
|
71.4
|
1.0
|
CHC
|
G:HEM201
|
3.5
|
82.8
|
1.0
|
NE2
|
G:HIS58
|
4.2
|
68.9
|
1.0
|
ND1
|
G:HIS87
|
4.2
|
72.7
|
1.0
|
C3C
|
G:HEM201
|
4.3
|
80.9
|
1.0
|
C3A
|
G:HEM201
|
4.3
|
84.4
|
1.0
|
C2C
|
G:HEM201
|
4.3
|
80.3
|
1.0
|
C2A
|
G:HEM201
|
4.3
|
85.2
|
1.0
|
C2D
|
G:HEM201
|
4.3
|
80.6
|
1.0
|
C2B
|
G:HEM201
|
4.3
|
82.2
|
1.0
|
C3D
|
G:HEM201
|
4.4
|
80.4
|
1.0
|
C3B
|
G:HEM201
|
4.4
|
81.8
|
1.0
|
CG2
|
G:VAL62
|
4.5
|
71.5
|
1.0
|
CG
|
G:HIS87
|
4.5
|
72.8
|
1.0
|
CE1
|
G:HIS58
|
4.8
|
66.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 4n7p
Go back to
Iron Binding Sites List in 4n7p
Iron binding site 5 out
of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe201
b:0.4
occ:1.00
|
FE
|
J:HEM201
|
0.0
|
0.4
|
1.0
|
NC
|
J:HEM201
|
2.0
|
0.2
|
1.0
|
NA
|
J:HEM201
|
2.1
|
0.6
|
1.0
|
NB
|
J:HEM201
|
2.1
|
1.0
|
1.0
|
ND
|
J:HEM201
|
2.1
|
0.1
|
1.0
|
NE2
|
J:HIS92
|
2.2
|
94.4
|
1.0
|
CE1
|
J:HIS92
|
3.0
|
95.2
|
1.0
|
C4C
|
J:HEM201
|
3.1
|
0.4
|
1.0
|
C1B
|
J:HEM201
|
3.1
|
0.1
|
1.0
|
C4A
|
J:HEM201
|
3.1
|
0.6
|
1.0
|
C1A
|
J:HEM201
|
3.1
|
0.1
|
1.0
|
C1D
|
J:HEM201
|
3.1
|
0.4
|
1.0
|
C1C
|
J:HEM201
|
3.1
|
0.4
|
1.0
|
C4D
|
J:HEM201
|
3.1
|
0.1
|
1.0
|
CD2
|
J:HIS92
|
3.1
|
97.7
|
1.0
|
C4B
|
J:HEM201
|
3.1
|
0.2
|
1.0
|
CHB
|
J:HEM201
|
3.4
|
0.4
|
1.0
|
CHD
|
J:HEM201
|
3.4
|
0.5
|
1.0
|
CHA
|
J:HEM201
|
3.4
|
0.1
|
1.0
|
CHC
|
J:HEM201
|
3.5
|
0.5
|
1.0
|
ND1
|
J:HIS92
|
4.1
|
97.7
|
1.0
|
CG2
|
J:VAL67
|
4.2
|
77.2
|
1.0
|
CG
|
J:HIS92
|
4.2
|
99.1
|
1.0
|
NE2
|
J:HIS63
|
4.2
|
91.3
|
1.0
|
C3C
|
J:HEM201
|
4.3
|
0.9
|
1.0
|
C2C
|
J:HEM201
|
4.3
|
0.2
|
1.0
|
C3A
|
J:HEM201
|
4.3
|
0.9
|
1.0
|
C2A
|
J:HEM201
|
4.3
|
0.6
|
1.0
|
C2B
|
J:HEM201
|
4.3
|
0.2
|
1.0
|
C3B
|
J:HEM201
|
4.4
|
0.3
|
1.0
|
C2D
|
J:HEM201
|
4.4
|
0.4
|
1.0
|
C3D
|
J:HEM201
|
4.4
|
0.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 4n7p
Go back to
Iron Binding Sites List in 4n7p
Iron binding site 6 out
of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe201
b:0.0
occ:1.00
|
FE
|
K:HEM201
|
0.0
|
0.0
|
1.0
|
NC
|
K:HEM201
|
2.1
|
0.9
|
1.0
|
NA
|
K:HEM201
|
2.1
|
0.7
|
1.0
|
NB
|
K:HEM201
|
2.1
|
0.3
|
1.0
|
ND
|
K:HEM201
|
2.1
|
0.3
|
1.0
|
NE2
|
K:HIS87
|
2.4
|
96.2
|
1.0
|
C1B
|
K:HEM201
|
3.1
|
0.0
|
1.0
|
C4C
|
K:HEM201
|
3.1
|
0.1
|
1.0
|
C4A
|
K:HEM201
|
3.1
|
0.1
|
1.0
|
C1D
|
K:HEM201
|
3.1
|
0.8
|
1.0
|
C1A
|
K:HEM201
|
3.1
|
0.8
|
1.0
|
C1C
|
K:HEM201
|
3.1
|
0.7
|
1.0
|
C4D
|
K:HEM201
|
3.1
|
0.2
|
1.0
|
C4B
|
K:HEM201
|
3.1
|
0.7
|
1.0
|
CE1
|
K:HIS87
|
3.1
|
97.8
|
1.0
|
CHB
|
K:HEM201
|
3.4
|
0.4
|
1.0
|
CHD
|
K:HEM201
|
3.4
|
0.1
|
1.0
|
CHA
|
K:HEM201
|
3.5
|
0.4
|
1.0
|
CHC
|
K:HEM201
|
3.5
|
0.2
|
1.0
|
CD2
|
K:HIS87
|
3.6
|
98.1
|
1.0
|
CE1
|
K:HIS58
|
4.0
|
1.0
|
1.0
|
NE2
|
K:HIS58
|
4.1
|
0.9
|
1.0
|
C3A
|
K:HEM201
|
4.3
|
0.0
|
1.0
|
C2D
|
K:HEM201
|
4.3
|
0.1
|
1.0
|
C2A
|
K:HEM201
|
4.3
|
0.2
|
1.0
|
C2B
|
K:HEM201
|
4.3
|
0.6
|
1.0
|
C3C
|
K:HEM201
|
4.3
|
0.6
|
1.0
|
C2C
|
K:HEM201
|
4.4
|
0.3
|
1.0
|
C3B
|
K:HEM201
|
4.4
|
0.5
|
1.0
|
C3D
|
K:HEM201
|
4.4
|
0.3
|
1.0
|
ND1
|
K:HIS87
|
4.4
|
98.5
|
1.0
|
CG
|
K:HIS87
|
4.6
|
98.7
|
1.0
|
|
Reference:
N.Shibayama,
K.Sugiyama,
J.R.Tame,
S.Y.Park.
Capturing the Hemoglobin Allosteric Transition in A Single Crystal Form J.Am.Chem.Soc. V. 136 5097 2014.
ISSN: ISSN 0002-7863
PubMed: 24635037
DOI: 10.1021/JA500380E
Page generated: Mon Aug 5 07:16:30 2024
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