Iron in PDB 1o1m: Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W)
Protein crystallography data
The structure of Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W), PDB code: 1o1m
was solved by
E.A.Brucker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.85
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.481,
83.642,
53.516,
90.00,
98.99,
90.00
|
R / Rfree (%)
|
19.8 /
25
|
Iron Binding Sites:
The binding sites of Iron atom in the Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W)
(pdb code 1o1m). 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 Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W), PDB code: 1o1m:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1o1m
Go back to
Iron Binding Sites List in 1o1m
Iron binding site 1 out
of 4 in the Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe286
b:16.4
occ:1.00
|
FE
|
A:HEM286
|
0.0
|
16.4
|
1.0
|
ND
|
A:HEM286
|
2.1
|
11.4
|
1.0
|
NC
|
A:HEM286
|
2.1
|
11.5
|
1.0
|
NA
|
A:HEM286
|
2.1
|
16.3
|
1.0
|
NB
|
A:HEM286
|
2.1
|
19.3
|
1.0
|
NE2
|
A:HIS87
|
2.2
|
17.0
|
1.0
|
CE1
|
A:HIS87
|
3.0
|
16.7
|
1.0
|
C4A
|
A:HEM286
|
3.1
|
18.1
|
1.0
|
C1B
|
A:HEM286
|
3.1
|
21.6
|
1.0
|
C4B
|
A:HEM286
|
3.1
|
23.4
|
1.0
|
C4D
|
A:HEM286
|
3.1
|
22.4
|
1.0
|
C1D
|
A:HEM286
|
3.1
|
13.8
|
1.0
|
C1A
|
A:HEM286
|
3.1
|
16.4
|
1.0
|
C1C
|
A:HEM286
|
3.1
|
20.3
|
1.0
|
C4C
|
A:HEM286
|
3.1
|
15.1
|
1.0
|
CD2
|
A:HIS87
|
3.3
|
18.4
|
1.0
|
CHB
|
A:HEM286
|
3.4
|
12.1
|
1.0
|
CHC
|
A:HEM286
|
3.4
|
18.6
|
1.0
|
CHA
|
A:HEM286
|
3.4
|
15.2
|
1.0
|
CHD
|
A:HEM286
|
3.4
|
17.4
|
1.0
|
NE2
|
A:GLN58
|
4.1
|
34.1
|
1.0
|
ND1
|
A:HIS87
|
4.2
|
17.3
|
1.0
|
C2D
|
A:HEM286
|
4.3
|
16.4
|
1.0
|
C2B
|
A:HEM286
|
4.3
|
15.8
|
1.0
|
C3A
|
A:HEM286
|
4.3
|
20.1
|
1.0
|
C2A
|
A:HEM286
|
4.3
|
21.6
|
1.0
|
C3D
|
A:HEM286
|
4.3
|
19.9
|
1.0
|
C3B
|
A:HEM286
|
4.3
|
19.9
|
1.0
|
C2C
|
A:HEM286
|
4.3
|
17.9
|
1.0
|
C3C
|
A:HEM286
|
4.4
|
14.1
|
1.0
|
CG
|
A:HIS87
|
4.4
|
17.9
|
1.0
|
CD1
|
A:LEU91
|
4.4
|
24.3
|
1.0
|
CG2
|
A:VAL62
|
4.9
|
17.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 1o1m
Go back to
Iron Binding Sites List in 1o1m
Iron binding site 2 out
of 4 in the Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe287
b:15.9
occ:1.00
|
FE
|
A:HEM287
|
0.0
|
15.9
|
1.0
|
ND
|
A:HEM287
|
2.0
|
12.2
|
1.0
|
NA
|
A:HEM287
|
2.0
|
17.2
|
1.0
|
NC
|
A:HEM287
|
2.1
|
12.1
|
1.0
|
NB
|
A:HEM287
|
2.1
|
15.8
|
1.0
|
NE2
|
A:HIS231
|
2.2
|
15.5
|
1.0
|
CE1
|
A:HIS231
|
2.9
|
14.4
|
1.0
|
C4B
|
A:HEM287
|
3.1
|
15.2
|
1.0
|
C1D
|
A:HEM287
|
3.1
|
13.3
|
1.0
|
C1A
|
A:HEM287
|
3.1
|
19.6
|
1.0
|
C1B
|
A:HEM287
|
3.1
|
17.7
|
1.0
|
C4A
|
A:HEM287
|
3.1
|
14.8
|
1.0
|
C4D
|
A:HEM287
|
3.1
|
11.7
|
1.0
|
C4C
|
A:HEM287
|
3.1
|
13.8
|
1.0
|
C1C
|
A:HEM287
|
3.1
|
11.3
|
1.0
|
CD2
|
A:HIS231
|
3.4
|
13.3
|
1.0
|
CHC
|
A:HEM287
|
3.4
|
13.2
|
1.0
|
CHA
|
A:HEM287
|
3.4
|
18.8
|
1.0
|
CHB
|
A:HEM287
|
3.4
|
16.8
|
1.0
|
CHD
|
A:HEM287
|
3.4
|
13.7
|
1.0
|
NE2
|
A:GLN202
|
4.0
|
20.8
|
1.0
|
ND1
|
A:HIS231
|
4.1
|
15.4
|
1.0
|
C2B
|
A:HEM287
|
4.3
|
15.6
|
1.0
|
C3D
|
A:HEM287
|
4.3
|
13.9
|
1.0
|
C2D
|
A:HEM287
|
4.3
|
18.5
|
1.0
|
C2A
|
A:HEM287
|
4.3
|
21.9
|
1.0
|
C3A
|
A:HEM287
|
4.3
|
20.9
|
1.0
|
C2C
|
A:HEM287
|
4.3
|
15.6
|
1.0
|
C3B
|
A:HEM287
|
4.3
|
16.9
|
1.0
|
C3C
|
A:HEM287
|
4.4
|
16.9
|
1.0
|
CG
|
A:HIS231
|
4.4
|
14.4
|
1.0
|
CD1
|
A:LEU235
|
4.4
|
12.0
|
1.0
|
CG2
|
A:VAL206
|
4.8
|
17.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 1o1m
Go back to
Iron Binding Sites List in 1o1m
Iron binding site 3 out
of 4 in the Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe147
b:17.1
occ:1.00
|
FE
|
B:HEM147
|
0.0
|
17.1
|
1.0
|
NC
|
B:HEM147
|
2.0
|
19.5
|
1.0
|
NB
|
B:HEM147
|
2.0
|
20.5
|
1.0
|
ND
|
B:HEM147
|
2.0
|
21.0
|
1.0
|
NA
|
B:HEM147
|
2.1
|
14.8
|
1.0
|
NE2
|
B:HIS92
|
2.2
|
20.8
|
1.0
|
CE1
|
B:HIS92
|
3.1
|
15.9
|
1.0
|
C4D
|
B:HEM147
|
3.1
|
14.2
|
1.0
|
C4C
|
B:HEM147
|
3.1
|
12.6
|
1.0
|
C1A
|
B:HEM147
|
3.1
|
16.1
|
1.0
|
C4B
|
B:HEM147
|
3.1
|
13.8
|
1.0
|
C1D
|
B:HEM147
|
3.1
|
17.9
|
1.0
|
C1C
|
B:HEM147
|
3.1
|
17.5
|
1.0
|
C1B
|
B:HEM147
|
3.1
|
14.7
|
1.0
|
C4A
|
B:HEM147
|
3.1
|
15.5
|
1.0
|
CD2
|
B:HIS92
|
3.3
|
22.7
|
1.0
|
CHA
|
B:HEM147
|
3.4
|
11.6
|
1.0
|
CHD
|
B:HEM147
|
3.4
|
13.2
|
1.0
|
CHC
|
B:HEM147
|
3.4
|
14.7
|
1.0
|
CHB
|
B:HEM147
|
3.4
|
15.1
|
1.0
|
O
|
B:HOH1001
|
4.0
|
42.4
|
1.0
|
NE2
|
B:HIS63
|
4.2
|
27.6
|
1.0
|
ND1
|
B:HIS92
|
4.2
|
16.4
|
1.0
|
C2A
|
B:HEM147
|
4.3
|
19.7
|
1.0
|
C3D
|
B:HEM147
|
4.3
|
19.9
|
1.0
|
C2B
|
B:HEM147
|
4.3
|
12.8
|
1.0
|
C2D
|
B:HEM147
|
4.3
|
18.9
|
1.0
|
C3B
|
B:HEM147
|
4.3
|
17.7
|
1.0
|
C2C
|
B:HEM147
|
4.3
|
15.3
|
1.0
|
C3A
|
B:HEM147
|
4.3
|
16.7
|
1.0
|
C3C
|
B:HEM147
|
4.3
|
14.5
|
1.0
|
CG
|
B:HIS92
|
4.4
|
14.5
|
1.0
|
CE1
|
B:HIS63
|
4.6
|
31.4
|
1.0
|
CD1
|
B:LEU96
|
4.9
|
17.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 1o1m
Go back to
Iron Binding Sites List in 1o1m
Iron binding site 4 out
of 4 in the Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Deoxy Hemoglobin (A-Glyglygly-C:V1M,L29F,H58Q B,D:V1M,V67W) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe147
b:16.2
occ:1.00
|
FE
|
D:HEM147
|
0.0
|
16.2
|
1.0
|
NC
|
D:HEM147
|
2.0
|
14.1
|
1.0
|
ND
|
D:HEM147
|
2.0
|
16.8
|
1.0
|
NB
|
D:HEM147
|
2.0
|
18.8
|
1.0
|
NA
|
D:HEM147
|
2.0
|
15.2
|
1.0
|
NE2
|
D:HIS92
|
2.2
|
16.9
|
1.0
|
CE1
|
D:HIS92
|
3.0
|
15.3
|
1.0
|
C4C
|
D:HEM147
|
3.1
|
10.6
|
1.0
|
C1C
|
D:HEM147
|
3.1
|
9.7
|
1.0
|
C1B
|
D:HEM147
|
3.1
|
17.4
|
1.0
|
C4B
|
D:HEM147
|
3.1
|
17.1
|
1.0
|
C1D
|
D:HEM147
|
3.1
|
19.8
|
1.0
|
C4A
|
D:HEM147
|
3.1
|
14.0
|
1.0
|
C4D
|
D:HEM147
|
3.1
|
14.3
|
1.0
|
C1A
|
D:HEM147
|
3.1
|
15.4
|
1.0
|
CD2
|
D:HIS92
|
3.3
|
15.3
|
1.0
|
CHC
|
D:HEM147
|
3.4
|
12.3
|
1.0
|
CHD
|
D:HEM147
|
3.4
|
12.9
|
1.0
|
CHB
|
D:HEM147
|
3.4
|
13.8
|
1.0
|
CHA
|
D:HEM147
|
3.4
|
13.6
|
1.0
|
O
|
D:HOH1002
|
3.7
|
28.6
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
19.9
|
1.0
|
C2B
|
D:HEM147
|
4.3
|
11.4
|
1.0
|
C3B
|
D:HEM147
|
4.3
|
19.4
|
1.0
|
C2C
|
D:HEM147
|
4.3
|
10.4
|
1.0
|
C2D
|
D:HEM147
|
4.3
|
20.3
|
1.0
|
C3D
|
D:HEM147
|
4.3
|
18.5
|
1.0
|
C3C
|
D:HEM147
|
4.3
|
10.2
|
1.0
|
C3A
|
D:HEM147
|
4.3
|
20.2
|
1.0
|
CG
|
D:HIS92
|
4.3
|
19.3
|
1.0
|
C2A
|
D:HEM147
|
4.3
|
14.2
|
1.0
|
NE2
|
D:HIS63
|
4.4
|
34.3
|
1.0
|
CE1
|
D:HIS63
|
4.7
|
29.0
|
1.0
|
CD1
|
D:LEU96
|
4.9
|
10.4
|
1.0
|
CB
|
D:TRP67
|
4.9
|
17.7
|
1.0
|
|
Reference:
E.A.Brucker,
N/A.
N/A N/A.
Page generated: Sat Aug 3 12:08:05 2024
|