Iron in PDB 1gbu: Deoxy (Beta-(C93A,C112G)) Human Hemoglobin
Protein crystallography data
The structure of Deoxy (Beta-(C93A,C112G)) Human Hemoglobin, PDB code: 1gbu
was solved by
G.B.Vasquez,
X.Ji,
C.Fronticelli,
G.L.Gilliland,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.020,
82.940,
53.830,
90.00,
99.16,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Iron Binding Sites:
The binding sites of Iron atom in the Deoxy (Beta-(C93A,C112G)) Human Hemoglobin
(pdb code 1gbu). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Deoxy (Beta-(C93A,C112G)) Human Hemoglobin, PDB code: 1gbu:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1gbu
Go back to
Iron Binding Sites List in 1gbu
Iron binding site 1 out
of 4 in the Deoxy (Beta-(C93A,C112G)) Human Hemoglobin
![](/pictures/FE/pdb/gb/1gbu-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/gb/1gbu-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 Deoxy (Beta-(C93A,C112G)) Human Hemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe142
b:15.6
occ:1.00
|
FE
|
A:HEM142
|
0.0
|
15.6
|
1.0
|
NE2
|
A:HIS87
|
1.8
|
8.3
|
1.0
|
ND
|
A:HEM142
|
2.0
|
14.0
|
1.0
|
NA
|
A:HEM142
|
2.1
|
15.2
|
1.0
|
NB
|
A:HEM142
|
2.1
|
14.8
|
1.0
|
NC
|
A:HEM142
|
2.1
|
14.4
|
1.0
|
CE1
|
A:HIS87
|
2.8
|
10.6
|
1.0
|
CD2
|
A:HIS87
|
2.9
|
10.3
|
1.0
|
C4B
|
A:HEM142
|
3.1
|
16.0
|
1.0
|
C4D
|
A:HEM142
|
3.1
|
13.6
|
1.0
|
C1A
|
A:HEM142
|
3.1
|
16.3
|
1.0
|
C1D
|
A:HEM142
|
3.1
|
13.2
|
1.0
|
C1B
|
A:HEM142
|
3.1
|
15.0
|
1.0
|
C1C
|
A:HEM142
|
3.1
|
15.0
|
1.0
|
C4A
|
A:HEM142
|
3.1
|
15.6
|
1.0
|
C4C
|
A:HEM142
|
3.1
|
13.4
|
1.0
|
CHA
|
A:HEM142
|
3.4
|
15.1
|
1.0
|
CHC
|
A:HEM142
|
3.4
|
15.5
|
1.0
|
CHB
|
A:HEM142
|
3.5
|
15.4
|
1.0
|
O
|
A:HOH149
|
3.5
|
24.0
|
1.0
|
CHD
|
A:HEM142
|
3.5
|
13.3
|
1.0
|
ND1
|
A:HIS87
|
3.9
|
12.4
|
1.0
|
CG
|
A:HIS87
|
4.0
|
8.9
|
1.0
|
C3D
|
A:HEM142
|
4.3
|
14.3
|
1.0
|
C3B
|
A:HEM142
|
4.3
|
15.0
|
1.0
|
C2A
|
A:HEM142
|
4.3
|
16.5
|
1.0
|
C2B
|
A:HEM142
|
4.3
|
15.6
|
1.0
|
C2D
|
A:HEM142
|
4.3
|
13.8
|
1.0
|
C2C
|
A:HEM142
|
4.3
|
13.6
|
1.0
|
C3A
|
A:HEM142
|
4.4
|
16.6
|
1.0
|
C3C
|
A:HEM142
|
4.4
|
12.7
|
1.0
|
CE1
|
A:HIS58
|
4.4
|
22.6
|
1.0
|
CD1
|
A:LEU91
|
4.5
|
15.9
|
1.0
|
NE2
|
A:HIS58
|
4.5
|
19.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 1gbu
Go back to
Iron Binding Sites List in 1gbu
Iron binding site 2 out
of 4 in the Deoxy (Beta-(C93A,C112G)) Human Hemoglobin
![](/pictures/FE/pdb/gb/1gbu-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/gb/1gbu-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 Deoxy (Beta-(C93A,C112G)) Human Hemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe148
b:17.8
occ:1.00
|
FE
|
B:HEM148
|
0.0
|
17.8
|
1.0
|
NC
|
B:HEM148
|
2.0
|
17.2
|
1.0
|
NB
|
B:HEM148
|
2.0
|
15.9
|
1.0
|
NA
|
B:HEM148
|
2.0
|
18.1
|
1.0
|
ND
|
B:HEM148
|
2.1
|
17.8
|
1.0
|
NE2
|
B:HIS92
|
2.2
|
11.7
|
1.0
|
C1C
|
B:HEM148
|
3.0
|
17.3
|
1.0
|
C4B
|
B:HEM148
|
3.0
|
17.1
|
1.0
|
C1B
|
B:HEM148
|
3.1
|
16.3
|
1.0
|
C4C
|
B:HEM148
|
3.1
|
16.9
|
1.0
|
C1D
|
B:HEM148
|
3.1
|
16.9
|
1.0
|
C4A
|
B:HEM148
|
3.1
|
17.8
|
1.0
|
C1A
|
B:HEM148
|
3.1
|
18.9
|
1.0
|
C4D
|
B:HEM148
|
3.1
|
18.1
|
1.0
|
CE1
|
B:HIS92
|
3.2
|
11.8
|
1.0
|
CD2
|
B:HIS92
|
3.2
|
12.3
|
1.0
|
CHC
|
B:HEM148
|
3.3
|
16.4
|
1.0
|
CHD
|
B:HEM148
|
3.5
|
16.9
|
1.0
|
CHA
|
B:HEM148
|
3.5
|
18.3
|
1.0
|
CHB
|
B:HEM148
|
3.5
|
17.2
|
1.0
|
NE2
|
B:HIS63
|
4.1
|
23.6
|
1.0
|
CG2
|
B:VAL67
|
4.1
|
20.9
|
1.0
|
C2C
|
B:HEM148
|
4.2
|
16.8
|
1.0
|
C3B
|
B:HEM148
|
4.3
|
17.1
|
1.0
|
C3C
|
B:HEM148
|
4.3
|
16.4
|
1.0
|
C3D
|
B:HEM148
|
4.3
|
17.5
|
1.0
|
C2B
|
B:HEM148
|
4.3
|
17.0
|
1.0
|
C2A
|
B:HEM148
|
4.3
|
19.9
|
1.0
|
ND1
|
B:HIS92
|
4.3
|
13.1
|
1.0
|
C2D
|
B:HEM148
|
4.3
|
17.2
|
1.0
|
C3A
|
B:HEM148
|
4.3
|
18.7
|
1.0
|
CG
|
B:HIS92
|
4.4
|
12.8
|
1.0
|
CE1
|
B:HIS63
|
4.4
|
23.4
|
1.0
|
CD1
|
B:LEU96
|
4.9
|
17.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 1gbu
Go back to
Iron Binding Sites List in 1gbu
Iron binding site 3 out
of 4 in the Deoxy (Beta-(C93A,C112G)) Human Hemoglobin
![](/pictures/FE/pdb/gb/1gbu-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/gb/1gbu-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 Deoxy (Beta-(C93A,C112G)) Human Hemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe142
b:15.8
occ:1.00
|
FE
|
C:HEM142
|
0.0
|
15.8
|
1.0
|
NC
|
C:HEM142
|
2.0
|
13.5
|
1.0
|
NA
|
C:HEM142
|
2.0
|
15.4
|
1.0
|
ND
|
C:HEM142
|
2.0
|
13.7
|
1.0
|
NB
|
C:HEM142
|
2.1
|
14.7
|
1.0
|
NE2
|
C:HIS87
|
2.1
|
8.9
|
1.0
|
C1C
|
C:HEM142
|
3.0
|
13.0
|
1.0
|
C1A
|
C:HEM142
|
3.1
|
15.7
|
1.0
|
C1D
|
C:HEM142
|
3.1
|
12.8
|
1.0
|
CE1
|
C:HIS87
|
3.1
|
10.9
|
1.0
|
C4D
|
C:HEM142
|
3.1
|
13.5
|
1.0
|
C4C
|
C:HEM142
|
3.1
|
12.1
|
1.0
|
C4B
|
C:HEM142
|
3.1
|
13.7
|
1.0
|
C1B
|
C:HEM142
|
3.1
|
13.3
|
1.0
|
CD2
|
C:HIS87
|
3.1
|
13.1
|
1.0
|
C4A
|
C:HEM142
|
3.1
|
15.4
|
1.0
|
CHC
|
C:HEM142
|
3.4
|
13.9
|
1.0
|
CHA
|
C:HEM142
|
3.4
|
14.9
|
1.0
|
O
|
C:HOH159
|
3.5
|
27.7
|
1.0
|
CHD
|
C:HEM142
|
3.5
|
12.9
|
1.0
|
CHB
|
C:HEM142
|
3.5
|
15.5
|
1.0
|
ND1
|
C:HIS87
|
4.2
|
12.3
|
1.0
|
CG
|
C:HIS87
|
4.3
|
11.8
|
1.0
|
C3D
|
C:HEM142
|
4.3
|
14.0
|
1.0
|
C2C
|
C:HEM142
|
4.3
|
12.8
|
1.0
|
C2A
|
C:HEM142
|
4.3
|
16.5
|
1.0
|
C2D
|
C:HEM142
|
4.3
|
13.3
|
1.0
|
C3B
|
C:HEM142
|
4.3
|
13.2
|
1.0
|
C3A
|
C:HEM142
|
4.3
|
16.1
|
1.0
|
C3C
|
C:HEM142
|
4.3
|
12.3
|
1.0
|
C2B
|
C:HEM142
|
4.4
|
13.8
|
1.0
|
NE2
|
C:HIS58
|
4.4
|
17.2
|
1.0
|
CD1
|
C:LEU91
|
4.5
|
18.8
|
1.0
|
CE1
|
C:HIS58
|
4.6
|
19.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 1gbu
Go back to
Iron Binding Sites List in 1gbu
Iron binding site 4 out
of 4 in the Deoxy (Beta-(C93A,C112G)) Human Hemoglobin
![](/pictures/FE/pdb/gb/1gbu-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/gb/1gbu-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 Deoxy (Beta-(C93A,C112G)) Human Hemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe148
b:15.1
occ:1.00
|
FE
|
D:HEM148
|
0.0
|
15.1
|
1.0
|
NC
|
D:HEM148
|
2.0
|
13.5
|
1.0
|
NA
|
D:HEM148
|
2.0
|
15.8
|
1.0
|
ND
|
D:HEM148
|
2.1
|
15.1
|
1.0
|
NB
|
D:HEM148
|
2.1
|
13.6
|
1.0
|
NE2
|
D:HIS92
|
2.2
|
7.8
|
1.0
|
C1C
|
D:HEM148
|
3.0
|
13.4
|
1.0
|
C4D
|
D:HEM148
|
3.1
|
15.4
|
1.0
|
C4C
|
D:HEM148
|
3.1
|
13.5
|
1.0
|
C1A
|
D:HEM148
|
3.1
|
17.4
|
1.0
|
C4B
|
D:HEM148
|
3.1
|
13.5
|
1.0
|
C1D
|
D:HEM148
|
3.1
|
14.2
|
1.0
|
C1B
|
D:HEM148
|
3.1
|
12.9
|
1.0
|
C4A
|
D:HEM148
|
3.1
|
15.9
|
1.0
|
CE1
|
D:HIS92
|
3.1
|
7.8
|
1.0
|
CD2
|
D:HIS92
|
3.3
|
6.9
|
1.0
|
CHA
|
D:HEM148
|
3.3
|
15.6
|
1.0
|
CHC
|
D:HEM148
|
3.4
|
13.5
|
1.0
|
CHB
|
D:HEM148
|
3.5
|
15.0
|
1.0
|
CHD
|
D:HEM148
|
3.5
|
13.8
|
1.0
|
CG2
|
D:VAL67
|
4.1
|
18.9
|
1.0
|
NE2
|
D:HIS63
|
4.2
|
18.7
|
1.0
|
C2C
|
D:HEM148
|
4.3
|
13.3
|
1.0
|
C2A
|
D:HEM148
|
4.3
|
18.4
|
1.0
|
C3D
|
D:HEM148
|
4.3
|
15.8
|
1.0
|
C3C
|
D:HEM148
|
4.3
|
13.2
|
1.0
|
C3B
|
D:HEM148
|
4.3
|
13.6
|
1.0
|
C3A
|
D:HEM148
|
4.3
|
17.9
|
1.0
|
C2D
|
D:HEM148
|
4.3
|
15.1
|
1.0
|
ND1
|
D:HIS92
|
4.3
|
10.1
|
1.0
|
C2B
|
D:HEM148
|
4.3
|
13.4
|
1.0
|
CG
|
D:HIS92
|
4.4
|
6.8
|
1.0
|
CE1
|
D:HIS63
|
4.7
|
20.1
|
1.0
|
CD1
|
D:LEU96
|
5.0
|
10.7
|
1.0
|
|
Reference:
G.B.Vasquez,
M.Karavitis,
X.Ji,
I.Pechik,
W.S.Brinigar,
G.L.Gilliland,
C.Fronticelli.
Cysteines BETA93 and BETA112 As Probes of Conformational and Functional Events at the Human Hemoglobin Subunit Interfaces. Biophys.J. V. 76 88 1999.
ISSN: ISSN 0006-3495
PubMed: 9876125
Page generated: Sat Aug 3 05:49:36 2024
|