Iron in PDB 1si4: Crystal Structure of Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution
Protein crystallography data
The structure of Crystal Structure of Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution, PDB code: 1si4
was solved by
U.Sen,
J.Dasgupta,
D.Choudhury,
P.Datta,
A.Chakrabarti,
S.B.Chakrabarty,
A.Chakrabarty,
J.K.Dattagupta,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
14.96 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.450,
88.186,
104.595,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.8 /
25.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution
(pdb code 1si4). 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 Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution, PDB code: 1si4:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1si4
Go back to
Iron Binding Sites List in 1si4
Iron binding site 1 out
of 4 in the Crystal Structure of Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution
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 Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe142
b:0.0
occ:1.00
|
FE
|
A:HEM142
|
0.0
|
0.0
|
1.0
|
ND
|
A:HEM142
|
2.0
|
34.6
|
1.0
|
NC
|
A:HEM142
|
2.0
|
34.6
|
1.0
|
NB
|
A:HEM142
|
2.1
|
34.6
|
1.0
|
NA
|
A:HEM142
|
2.1
|
34.6
|
1.0
|
NE2
|
A:HIS87
|
2.1
|
27.6
|
1.0
|
C
|
A:CYN143
|
2.3
|
19.6
|
1.0
|
CD2
|
A:HIS87
|
3.0
|
28.7
|
1.0
|
C1D
|
A:HEM142
|
3.0
|
45.1
|
1.0
|
C4D
|
A:HEM142
|
3.0
|
45.5
|
1.0
|
C4C
|
A:HEM142
|
3.1
|
43.8
|
1.0
|
N
|
A:CYN143
|
3.1
|
26.4
|
1.0
|
C1C
|
A:HEM142
|
3.1
|
42.5
|
1.0
|
C4B
|
A:HEM142
|
3.1
|
45.1
|
1.0
|
C1B
|
A:HEM142
|
3.1
|
45.6
|
1.0
|
C4A
|
A:HEM142
|
3.1
|
44.6
|
1.0
|
C1A
|
A:HEM142
|
3.1
|
45.9
|
1.0
|
CE1
|
A:HIS87
|
3.2
|
27.8
|
1.0
|
CHD
|
A:HEM142
|
3.4
|
44.4
|
1.0
|
CHC
|
A:HEM142
|
3.5
|
43.3
|
1.0
|
CHA
|
A:HEM142
|
3.5
|
45.4
|
1.0
|
CHB
|
A:HEM142
|
3.5
|
44.9
|
1.0
|
CG
|
A:HIS87
|
4.2
|
28.1
|
1.0
|
ND1
|
A:HIS87
|
4.2
|
29.8
|
1.0
|
C2D
|
A:HEM142
|
4.2
|
44.0
|
1.0
|
C3D
|
A:HEM142
|
4.3
|
44.3
|
1.0
|
C3C
|
A:HEM142
|
4.3
|
41.9
|
1.0
|
C2C
|
A:HEM142
|
4.3
|
43.2
|
1.0
|
C2B
|
A:HEM142
|
4.3
|
45.4
|
1.0
|
NE2
|
A:HIS58
|
4.3
|
32.1
|
1.0
|
C3A
|
A:HEM142
|
4.3
|
45.4
|
1.0
|
C3B
|
A:HEM142
|
4.3
|
44.5
|
1.0
|
C2A
|
A:HEM142
|
4.3
|
46.1
|
1.0
|
CG2
|
A:VAL62
|
4.6
|
34.1
|
1.0
|
CE1
|
A:HIS58
|
4.8
|
34.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 1si4
Go back to
Iron Binding Sites List in 1si4
Iron binding site 2 out
of 4 in the Crystal Structure of Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution
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 Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe147
b:0.0
occ:1.00
|
FE
|
B:HEM147
|
0.0
|
0.0
|
1.0
|
ND
|
B:HEM147
|
2.0
|
34.6
|
1.0
|
NC
|
B:HEM147
|
2.0
|
34.6
|
1.0
|
C
|
B:CYN148
|
2.0
|
14.4
|
1.0
|
NA
|
B:HEM147
|
2.0
|
34.6
|
1.0
|
NB
|
B:HEM147
|
2.1
|
34.6
|
1.0
|
NE2
|
B:HIS92
|
2.3
|
21.5
|
1.0
|
N
|
B:CYN148
|
2.9
|
20.3
|
1.0
|
C1D
|
B:HEM147
|
3.0
|
27.5
|
1.0
|
C4C
|
B:HEM147
|
3.0
|
26.4
|
1.0
|
C4D
|
B:HEM147
|
3.0
|
26.0
|
1.0
|
C1C
|
B:HEM147
|
3.1
|
24.3
|
1.0
|
C1A
|
B:HEM147
|
3.1
|
26.9
|
1.0
|
C4A
|
B:HEM147
|
3.1
|
24.3
|
1.0
|
C4B
|
B:HEM147
|
3.1
|
25.2
|
1.0
|
C1B
|
B:HEM147
|
3.1
|
23.4
|
1.0
|
CD2
|
B:HIS92
|
3.2
|
19.9
|
1.0
|
CHD
|
B:HEM147
|
3.4
|
27.2
|
1.0
|
CE1
|
B:HIS92
|
3.4
|
19.6
|
1.0
|
CHA
|
B:HEM147
|
3.4
|
25.4
|
1.0
|
CHC
|
B:HEM147
|
3.4
|
25.2
|
1.0
|
CHB
|
B:HEM147
|
3.4
|
23.1
|
1.0
|
C2D
|
B:HEM147
|
4.2
|
26.5
|
1.0
|
C3D
|
B:HEM147
|
4.3
|
27.5
|
1.0
|
C3C
|
B:HEM147
|
4.3
|
27.1
|
1.0
|
C2C
|
B:HEM147
|
4.3
|
26.1
|
1.0
|
C3A
|
B:HEM147
|
4.3
|
25.7
|
1.0
|
C2A
|
B:HEM147
|
4.3
|
27.6
|
1.0
|
C2B
|
B:HEM147
|
4.3
|
24.6
|
1.0
|
C3B
|
B:HEM147
|
4.3
|
24.6
|
1.0
|
NE2
|
B:HIS63
|
4.3
|
24.9
|
1.0
|
CG
|
B:HIS92
|
4.4
|
20.2
|
1.0
|
ND1
|
B:HIS92
|
4.4
|
18.3
|
1.0
|
CG2
|
B:VAL67
|
4.7
|
14.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 1si4
Go back to
Iron Binding Sites List in 1si4
Iron binding site 3 out
of 4 in the Crystal Structure of Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution
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 Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe142
b:0.0
occ:1.00
|
FE
|
C:HEM142
|
0.0
|
0.0
|
1.0
|
ND
|
C:HEM142
|
2.0
|
34.6
|
1.0
|
NC
|
C:HEM142
|
2.0
|
34.6
|
1.0
|
NA
|
C:HEM142
|
2.0
|
34.6
|
1.0
|
NB
|
C:HEM142
|
2.0
|
34.6
|
1.0
|
C
|
C:CYN143
|
2.2
|
17.8
|
1.0
|
NE2
|
C:HIS87
|
2.2
|
33.4
|
1.0
|
C1D
|
C:HEM142
|
3.0
|
36.1
|
1.0
|
C4D
|
C:HEM142
|
3.0
|
38.6
|
1.0
|
C4C
|
C:HEM142
|
3.0
|
33.8
|
1.0
|
C4B
|
C:HEM142
|
3.0
|
33.9
|
1.0
|
C1C
|
C:HEM142
|
3.0
|
31.1
|
1.0
|
C1A
|
C:HEM142
|
3.1
|
39.4
|
1.0
|
C1B
|
C:HEM142
|
3.1
|
35.0
|
1.0
|
C4A
|
C:HEM142
|
3.1
|
39.7
|
1.0
|
CD2
|
C:HIS87
|
3.2
|
31.2
|
1.0
|
CE1
|
C:HIS87
|
3.2
|
32.8
|
1.0
|
N
|
C:CYN143
|
3.3
|
21.7
|
1.0
|
CHD
|
C:HEM142
|
3.4
|
35.0
|
1.0
|
CHA
|
C:HEM142
|
3.4
|
38.1
|
1.0
|
CHC
|
C:HEM142
|
3.4
|
31.4
|
1.0
|
CHB
|
C:HEM142
|
3.5
|
37.0
|
1.0
|
C3D
|
C:HEM142
|
4.2
|
38.7
|
1.0
|
C2D
|
C:HEM142
|
4.2
|
37.8
|
1.0
|
C2C
|
C:HEM142
|
4.3
|
32.6
|
1.0
|
C3C
|
C:HEM142
|
4.3
|
33.4
|
1.0
|
C3B
|
C:HEM142
|
4.3
|
33.8
|
1.0
|
C2A
|
C:HEM142
|
4.3
|
41.3
|
1.0
|
C2B
|
C:HEM142
|
4.3
|
34.1
|
1.0
|
C3A
|
C:HEM142
|
4.3
|
41.6
|
1.0
|
ND1
|
C:HIS87
|
4.3
|
32.9
|
1.0
|
CG
|
C:HIS87
|
4.4
|
30.6
|
1.0
|
NE2
|
C:HIS58
|
4.5
|
29.8
|
1.0
|
CE1
|
C:HIS58
|
4.9
|
29.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 1si4
Go back to
Iron Binding Sites List in 1si4
Iron binding site 4 out
of 4 in the Crystal Structure of Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution
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 Human Hemoglobin A2 (in R2 State) at 2.2 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe147
b:0.0
occ:1.00
|
FE
|
D:HEM147
|
0.0
|
0.0
|
1.0
|
ND
|
D:HEM147
|
2.0
|
34.6
|
1.0
|
NC
|
D:HEM147
|
2.0
|
34.6
|
1.0
|
NA
|
D:HEM147
|
2.1
|
34.6
|
1.0
|
NE2
|
D:HIS92
|
2.1
|
24.0
|
1.0
|
NB
|
D:HEM147
|
2.1
|
34.6
|
1.0
|
C
|
D:CYN148
|
2.2
|
13.8
|
1.0
|
CE1
|
D:HIS92
|
3.0
|
23.7
|
1.0
|
C4D
|
D:HEM147
|
3.0
|
49.5
|
1.0
|
C1D
|
D:HEM147
|
3.0
|
47.6
|
1.0
|
C1C
|
D:HEM147
|
3.1
|
46.8
|
1.0
|
C4C
|
D:HEM147
|
3.1
|
46.8
|
1.0
|
C4B
|
D:HEM147
|
3.1
|
46.5
|
1.0
|
C1A
|
D:HEM147
|
3.1
|
48.0
|
1.0
|
CD2
|
D:HIS92
|
3.1
|
23.1
|
1.0
|
C4A
|
D:HEM147
|
3.1
|
47.2
|
1.0
|
C1B
|
D:HEM147
|
3.1
|
46.9
|
1.0
|
N
|
D:CYN148
|
3.2
|
22.1
|
1.0
|
CHD
|
D:HEM147
|
3.4
|
46.8
|
1.0
|
CHA
|
D:HEM147
|
3.4
|
47.8
|
1.0
|
CHC
|
D:HEM147
|
3.4
|
46.9
|
1.0
|
CHB
|
D:HEM147
|
3.5
|
46.8
|
1.0
|
ND1
|
D:HIS92
|
4.1
|
24.0
|
1.0
|
CG
|
D:HIS92
|
4.2
|
24.9
|
1.0
|
C2D
|
D:HEM147
|
4.3
|
48.3
|
1.0
|
C3D
|
D:HEM147
|
4.3
|
49.1
|
1.0
|
C2C
|
D:HEM147
|
4.3
|
46.2
|
1.0
|
C3C
|
D:HEM147
|
4.3
|
47.0
|
1.0
|
C2A
|
D:HEM147
|
4.3
|
47.8
|
1.0
|
C3B
|
D:HEM147
|
4.3
|
45.9
|
1.0
|
C2B
|
D:HEM147
|
4.3
|
46.4
|
1.0
|
C3A
|
D:HEM147
|
4.3
|
47.9
|
1.0
|
NE2
|
D:HIS63
|
4.5
|
27.8
|
1.0
|
|
Reference:
U.Sen,
J.Dasgupta,
D.Choudhury,
P.Datta,
A.Chakrabarti,
S.B.Chakrabarty,
A.Chakrabarty,
J.K.Dattagupta.
Crystal Structures of HBA2 and Hbe and Modeling of Hemoglobin DELTA4: Interpretation of the Thermal Stability and the Antisickling Effect of HBA2 and Identification of the Ferrocyanide Binding Site in Hb. Biochemistry V. 43 12477 2004.
ISSN: ISSN 0006-2960
PubMed: 15449937
DOI: 10.1021/BI048903I
Page generated: Sat Aug 3 14:41:19 2024
|