Iron in PDB 3w4u: Human Zeta-2 Beta-2-S Hemoglobin
Protein crystallography data
The structure of Human Zeta-2 Beta-2-S Hemoglobin, PDB code: 3w4u
was solved by
M.K.Safo,
T.-P.Ko,
J.E.Russell,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.95 /
1.95
|
|
Space group
|
P 31 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.540,
115.540,
140.900,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
20.5 /
25.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Human Zeta-2 Beta-2-S Hemoglobin
(pdb code 3w4u). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Human Zeta-2 Beta-2-S Hemoglobin, PDB code: 3w4u:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3w4u
Go back to
Iron Binding Sites List in 3w4u
Iron binding site 1 out
of 6 in the Human Zeta-2 Beta-2-S Hemoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Human Zeta-2 Beta-2-S Hemoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:28.7
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
28.7
|
1.0
|
|
C
|
A:CMO202
|
1.7
|
30.1
|
1.0
|
|
ND
|
A:HEM201
|
2.0
|
31.1
|
1.0
|
|
NC
|
A:HEM201
|
2.0
|
26.9
|
1.0
|
|
NB
|
A:HEM201
|
2.0
|
28.0
|
1.0
|
|
NE2
|
A:HIS87
|
2.0
|
28.2
|
1.0
|
|
NA
|
A:HEM201
|
2.0
|
31.1
|
1.0
|
|
O
|
A:CMO202
|
2.9
|
35.6
|
1.0
|
|
CE1
|
A:HIS87
|
3.0
|
30.2
|
1.0
|
|
C1D
|
A:HEM201
|
3.0
|
30.0
|
1.0
|
|
C4D
|
A:HEM201
|
3.0
|
32.8
|
1.0
|
|
C4C
|
A:HEM201
|
3.0
|
26.5
|
1.0
|
|
C1C
|
A:HEM201
|
3.0
|
28.3
|
1.0
|
|
C1A
|
A:HEM201
|
3.0
|
32.7
|
1.0
|
|
CD2
|
A:HIS87
|
3.1
|
30.7
|
1.0
|
|
C4B
|
A:HEM201
|
3.1
|
27.5
|
1.0
|
|
C1B
|
A:HEM201
|
3.1
|
25.9
|
1.0
|
|
C4A
|
A:HEM201
|
3.1
|
30.8
|
1.0
|
|
CHD
|
A:HEM201
|
3.4
|
26.9
|
1.0
|
|
CHA
|
A:HEM201
|
3.4
|
31.6
|
1.0
|
|
CHB
|
A:HEM201
|
3.4
|
28.7
|
1.0
|
|
CHC
|
A:HEM201
|
3.5
|
27.4
|
1.0
|
|
ND1
|
A:HIS87
|
4.1
|
27.5
|
1.0
|
|
CG
|
A:HIS87
|
4.2
|
29.8
|
1.0
|
|
NE2
|
A:HIS58
|
4.2
|
25.6
|
1.0
|
|
C3D
|
A:HEM201
|
4.2
|
33.9
|
1.0
|
|
C2D
|
A:HEM201
|
4.2
|
32.3
|
1.0
|
|
C2A
|
A:HEM201
|
4.3
|
35.1
|
1.0
|
|
C2C
|
A:HEM201
|
4.3
|
28.6
|
1.0
|
|
C3B
|
A:HEM201
|
4.3
|
25.2
|
1.0
|
|
C2B
|
A:HEM201
|
4.3
|
23.0
|
1.0
|
|
C3C
|
A:HEM201
|
4.3
|
27.4
|
1.0
|
|
C3A
|
A:HEM201
|
4.4
|
33.7
|
1.0
|
|
CE1
|
A:HIS58
|
4.7
|
25.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 3w4u
Go back to
Iron Binding Sites List in 3w4u
Iron binding site 2 out
of 6 in the Human Zeta-2 Beta-2-S Hemoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Human Zeta-2 Beta-2-S Hemoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:23.8
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
23.8
|
1.0
|
|
C
|
B:CMO202
|
1.6
|
22.8
|
1.0
|
|
NC
|
B:HEM201
|
2.0
|
19.0
|
1.0
|
|
ND
|
B:HEM201
|
2.0
|
21.5
|
1.0
|
|
NE2
|
B:HIS92
|
2.0
|
18.7
|
1.0
|
|
NA
|
B:HEM201
|
2.0
|
23.6
|
1.0
|
|
NB
|
B:HEM201
|
2.1
|
22.0
|
1.0
|
|
O
|
B:CMO202
|
2.8
|
27.3
|
1.0
|
|
CD2
|
B:HIS92
|
3.0
|
18.5
|
1.0
|
|
C1C
|
B:HEM201
|
3.0
|
20.2
|
1.0
|
|
C1D
|
B:HEM201
|
3.0
|
20.3
|
1.0
|
|
C4B
|
B:HEM201
|
3.0
|
21.1
|
1.0
|
|
C4C
|
B:HEM201
|
3.0
|
18.4
|
1.0
|
|
CE1
|
B:HIS92
|
3.0
|
22.1
|
1.0
|
|
C4A
|
B:HEM201
|
3.0
|
22.4
|
1.0
|
|
C1A
|
B:HEM201
|
3.1
|
24.0
|
1.0
|
|
C4D
|
B:HEM201
|
3.1
|
24.4
|
1.0
|
|
C1B
|
B:HEM201
|
3.1
|
22.5
|
1.0
|
|
CHC
|
B:HEM201
|
3.3
|
19.9
|
1.0
|
|
CHD
|
B:HEM201
|
3.4
|
20.5
|
1.0
|
|
CHB
|
B:HEM201
|
3.4
|
22.3
|
1.0
|
|
CHA
|
B:HEM201
|
3.5
|
23.2
|
1.0
|
|
ND1
|
B:HIS92
|
4.1
|
20.4
|
1.0
|
|
CG
|
B:HIS92
|
4.1
|
20.4
|
1.0
|
|
C2D
|
B:HEM201
|
4.3
|
22.2
|
1.0
|
|
C2C
|
B:HEM201
|
4.3
|
19.9
|
1.0
|
|
C3D
|
B:HEM201
|
4.3
|
24.4
|
1.0
|
|
C3C
|
B:HEM201
|
4.3
|
20.9
|
1.0
|
|
NE2
|
B:HIS63
|
4.3
|
25.7
|
1.0
|
|
C2A
|
B:HEM201
|
4.3
|
25.9
|
1.0
|
|
C3B
|
B:HEM201
|
4.3
|
21.8
|
1.0
|
|
C3A
|
B:HEM201
|
4.3
|
23.9
|
1.0
|
|
C2B
|
B:HEM201
|
4.4
|
20.7
|
1.0
|
|
CE1
|
B:HIS63
|
4.7
|
26.2
|
1.0
|
|
CD1
|
B:LEU96
|
4.9
|
21.4
|
1.0
|
|
Iron binding site 3 out
of 6 in 3w4u
Go back to
Iron Binding Sites List in 3w4u
Iron binding site 3 out
of 6 in the Human Zeta-2 Beta-2-S Hemoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Human Zeta-2 Beta-2-S Hemoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:21.2
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
21.2
|
1.0
|
|
C
|
C:CMO202
|
1.6
|
22.5
|
1.0
|
|
ND
|
C:HEM201
|
1.9
|
19.4
|
1.0
|
|
NB
|
C:HEM201
|
1.9
|
17.9
|
1.0
|
|
NC
|
C:HEM201
|
2.0
|
18.7
|
1.0
|
|
NE2
|
C:HIS87
|
2.1
|
21.6
|
1.0
|
|
NA
|
C:HEM201
|
2.1
|
22.9
|
1.0
|
|
O
|
C:CMO202
|
2.8
|
28.4
|
1.0
|
|
C4B
|
C:HEM201
|
2.9
|
17.9
|
1.0
|
|
CE1
|
C:HIS87
|
3.0
|
20.5
|
1.0
|
|
C1D
|
C:HEM201
|
3.0
|
20.3
|
1.0
|
|
C1B
|
C:HEM201
|
3.0
|
19.1
|
1.0
|
|
C4A
|
C:HEM201
|
3.0
|
20.3
|
1.0
|
|
C4D
|
C:HEM201
|
3.0
|
22.7
|
1.0
|
|
C4C
|
C:HEM201
|
3.0
|
17.6
|
1.0
|
|
C1C
|
C:HEM201
|
3.0
|
16.5
|
1.0
|
|
C1A
|
C:HEM201
|
3.1
|
22.3
|
1.0
|
|
CD2
|
C:HIS87
|
3.1
|
18.4
|
1.0
|
|
CHC
|
C:HEM201
|
3.4
|
16.1
|
1.0
|
|
CHB
|
C:HEM201
|
3.4
|
20.9
|
1.0
|
|
CHD
|
C:HEM201
|
3.5
|
17.3
|
1.0
|
|
CHA
|
C:HEM201
|
3.5
|
21.2
|
1.0
|
|
ND1
|
C:HIS87
|
4.1
|
22.3
|
1.0
|
|
C3D
|
C:HEM201
|
4.2
|
21.4
|
1.0
|
|
C2B
|
C:HEM201
|
4.2
|
19.3
|
1.0
|
|
C3B
|
C:HEM201
|
4.2
|
19.5
|
1.0
|
|
CG
|
C:HIS87
|
4.2
|
21.8
|
1.0
|
|
C2D
|
C:HEM201
|
4.2
|
21.5
|
1.0
|
|
NE2
|
C:HIS58
|
4.3
|
17.9
|
1.0
|
|
C2C
|
C:HEM201
|
4.3
|
15.7
|
1.0
|
|
C3A
|
C:HEM201
|
4.3
|
22.5
|
1.0
|
|
C2A
|
C:HEM201
|
4.4
|
26.9
|
1.0
|
|
C3C
|
C:HEM201
|
4.4
|
15.9
|
1.0
|
|
O
|
C:HOH546
|
4.6
|
61.9
|
1.0
|
|
CE1
|
C:HIS58
|
4.8
|
21.5
|
1.0
|
|
CG2
|
C:VAL62
|
4.9
|
22.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 3w4u
Go back to
Iron Binding Sites List in 3w4u
Iron binding site 4 out
of 6 in the Human Zeta-2 Beta-2-S Hemoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Human Zeta-2 Beta-2-S Hemoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:32.3
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
32.3
|
1.0
|
|
C
|
D:CMO202
|
1.7
|
33.0
|
1.0
|
|
NC
|
D:HEM201
|
2.0
|
29.9
|
1.0
|
|
NB
|
D:HEM201
|
2.0
|
30.6
|
1.0
|
|
NA
|
D:HEM201
|
2.0
|
34.7
|
1.0
|
|
ND
|
D:HEM201
|
2.1
|
33.2
|
1.0
|
|
NE2
|
D:HIS92
|
2.1
|
29.9
|
1.0
|
|
O
|
D:CMO202
|
2.9
|
39.6
|
1.0
|
|
C1B
|
D:HEM201
|
3.0
|
32.5
|
1.0
|
|
C4C
|
D:HEM201
|
3.0
|
30.1
|
1.0
|
|
C1C
|
D:HEM201
|
3.0
|
30.2
|
1.0
|
|
C4B
|
D:HEM201
|
3.0
|
30.7
|
1.0
|
|
C1D
|
D:HEM201
|
3.1
|
31.6
|
1.0
|
|
C4A
|
D:HEM201
|
3.1
|
34.1
|
1.0
|
|
CE1
|
D:HIS92
|
3.1
|
28.4
|
1.0
|
|
C1A
|
D:HEM201
|
3.1
|
35.2
|
1.0
|
|
C4D
|
D:HEM201
|
3.1
|
32.1
|
1.0
|
|
CD2
|
D:HIS92
|
3.1
|
26.2
|
1.0
|
|
CHD
|
D:HEM201
|
3.4
|
30.3
|
1.0
|
|
CHB
|
D:HEM201
|
3.4
|
33.6
|
1.0
|
|
CHC
|
D:HEM201
|
3.4
|
29.5
|
1.0
|
|
CHA
|
D:HEM201
|
3.4
|
33.7
|
1.0
|
|
ND1
|
D:HIS92
|
4.2
|
27.3
|
1.0
|
|
C3C
|
D:HEM201
|
4.2
|
29.8
|
1.0
|
|
CG
|
D:HIS92
|
4.2
|
27.5
|
1.0
|
|
C2B
|
D:HEM201
|
4.3
|
32.1
|
1.0
|
|
C3D
|
D:HEM201
|
4.3
|
34.9
|
1.0
|
|
C2C
|
D:HEM201
|
4.3
|
29.7
|
1.0
|
|
C2A
|
D:HEM201
|
4.3
|
36.5
|
1.0
|
|
C3A
|
D:HEM201
|
4.3
|
35.3
|
1.0
|
|
C2D
|
D:HEM201
|
4.3
|
32.5
|
1.0
|
|
C3B
|
D:HEM201
|
4.3
|
32.1
|
1.0
|
|
NE2
|
D:HIS63
|
4.4
|
32.1
|
1.0
|
|
CE1
|
D:HIS63
|
4.7
|
34.3
|
1.0
|
|
CG2
|
D:VAL67
|
4.9
|
32.5
|
1.0
|
|
CD1
|
D:LEU96
|
4.9
|
27.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 3w4u
Go back to
Iron Binding Sites List in 3w4u
Iron binding site 5 out
of 6 in the Human Zeta-2 Beta-2-S Hemoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Human Zeta-2 Beta-2-S Hemoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:25.0
occ:1.00
|
FE
|
E:HEM201
|
0.0
|
25.0
|
1.0
|
|
C
|
E:CMO202
|
1.7
|
24.2
|
1.0
|
|
ND
|
E:HEM201
|
2.0
|
22.3
|
1.0
|
|
NA
|
E:HEM201
|
2.0
|
24.0
|
1.0
|
|
NC
|
E:HEM201
|
2.0
|
22.3
|
1.0
|
|
NE2
|
E:HIS87
|
2.0
|
23.2
|
1.0
|
|
NB
|
E:HEM201
|
2.1
|
22.9
|
1.0
|
|
O
|
E:CMO202
|
2.8
|
31.3
|
1.0
|
|
CE1
|
E:HIS87
|
2.9
|
24.4
|
1.0
|
|
C1A
|
E:HEM201
|
3.0
|
24.4
|
1.0
|
|
C1C
|
E:HEM201
|
3.0
|
21.3
|
1.0
|
|
C1D
|
E:HEM201
|
3.0
|
24.0
|
1.0
|
|
C4D
|
E:HEM201
|
3.0
|
24.4
|
1.0
|
|
C4A
|
E:HEM201
|
3.0
|
23.8
|
1.0
|
|
C4C
|
E:HEM201
|
3.1
|
19.4
|
1.0
|
|
C1B
|
E:HEM201
|
3.1
|
21.7
|
1.0
|
|
C4B
|
E:HEM201
|
3.1
|
21.8
|
1.0
|
|
CD2
|
E:HIS87
|
3.1
|
23.5
|
1.0
|
|
CHC
|
E:HEM201
|
3.4
|
19.5
|
1.0
|
|
CHA
|
E:HEM201
|
3.4
|
25.1
|
1.0
|
|
CHB
|
E:HEM201
|
3.4
|
22.8
|
1.0
|
|
CHD
|
E:HEM201
|
3.4
|
20.8
|
1.0
|
|
ND1
|
E:HIS87
|
4.1
|
22.2
|
1.0
|
|
CG
|
E:HIS87
|
4.2
|
21.7
|
1.0
|
|
C2A
|
E:HEM201
|
4.2
|
27.7
|
1.0
|
|
C2B
|
E:HEM201
|
4.3
|
21.3
|
1.0
|
|
NE2
|
E:HIS58
|
4.3
|
21.6
|
1.0
|
|
C3D
|
E:HEM201
|
4.3
|
25.3
|
1.0
|
|
C3A
|
E:HEM201
|
4.3
|
25.1
|
1.0
|
|
C2C
|
E:HEM201
|
4.3
|
21.9
|
1.0
|
|
C2D
|
E:HEM201
|
4.3
|
22.7
|
1.0
|
|
C3B
|
E:HEM201
|
4.3
|
21.5
|
1.0
|
|
C3C
|
E:HEM201
|
4.3
|
22.3
|
1.0
|
|
CE1
|
E:HIS58
|
4.7
|
22.0
|
1.0
|
|
CD1
|
E:LEU91
|
5.0
|
34.1
|
1.0
|
|
CG2
|
E:VAL62
|
5.0
|
21.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 3w4u
Go back to
Iron Binding Sites List in 3w4u
Iron binding site 6 out
of 6 in the Human Zeta-2 Beta-2-S Hemoglobin
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Human Zeta-2 Beta-2-S Hemoglobin within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:29.2
occ:1.00
|
FE
|
F:HEM201
|
0.0
|
29.2
|
1.0
|
|
C
|
F:CMO202
|
1.7
|
29.6
|
1.0
|
|
NA
|
F:HEM201
|
2.0
|
29.8
|
1.0
|
|
ND
|
F:HEM201
|
2.0
|
27.9
|
1.0
|
|
NE2
|
F:HIS92
|
2.0
|
26.8
|
1.0
|
|
NC
|
F:HEM201
|
2.0
|
27.0
|
1.0
|
|
NB
|
F:HEM201
|
2.1
|
27.6
|
1.0
|
|
O
|
F:CMO202
|
2.9
|
35.9
|
1.0
|
|
CE1
|
F:HIS92
|
3.0
|
25.1
|
1.0
|
|
C4D
|
F:HEM201
|
3.0
|
28.2
|
1.0
|
|
C4A
|
F:HEM201
|
3.0
|
28.3
|
1.0
|
|
C1A
|
F:HEM201
|
3.0
|
29.9
|
1.0
|
|
C4B
|
F:HEM201
|
3.1
|
24.8
|
1.0
|
|
CD2
|
F:HIS92
|
3.1
|
25.7
|
1.0
|
|
C1C
|
F:HEM201
|
3.1
|
25.1
|
1.0
|
|
C4C
|
F:HEM201
|
3.1
|
25.1
|
1.0
|
|
C1B
|
F:HEM201
|
3.1
|
25.9
|
1.0
|
|
C1D
|
F:HEM201
|
3.1
|
27.4
|
1.0
|
|
CHA
|
F:HEM201
|
3.4
|
29.2
|
1.0
|
|
CHC
|
F:HEM201
|
3.4
|
24.2
|
1.0
|
|
CHB
|
F:HEM201
|
3.4
|
28.4
|
1.0
|
|
CHD
|
F:HEM201
|
3.5
|
24.8
|
1.0
|
|
ND1
|
F:HIS92
|
4.1
|
25.3
|
1.0
|
|
CG
|
F:HIS92
|
4.2
|
26.0
|
1.0
|
|
C3A
|
F:HEM201
|
4.2
|
31.4
|
1.0
|
|
C2A
|
F:HEM201
|
4.2
|
32.1
|
1.0
|
|
C3D
|
F:HEM201
|
4.2
|
28.7
|
1.0
|
|
NE2
|
F:HIS63
|
4.3
|
37.9
|
1.0
|
|
C2C
|
F:HEM201
|
4.3
|
25.2
|
1.0
|
|
C3B
|
F:HEM201
|
4.3
|
25.5
|
1.0
|
|
C2B
|
F:HEM201
|
4.3
|
26.1
|
1.0
|
|
C2D
|
F:HEM201
|
4.3
|
28.5
|
1.0
|
|
C3C
|
F:HEM201
|
4.3
|
24.7
|
1.0
|
|
CE1
|
F:HIS63
|
4.6
|
38.7
|
1.0
|
|
CG2
|
F:VAL67
|
4.9
|
24.3
|
1.0
|
|
CD1
|
F:LEU96
|
4.9
|
29.4
|
1.0
|
|
Reference:
M.K.Safo,
T.-P.Ko,
O.Abdulmalik,
Z.He,
A.H.Wang,
E.R.Schreiter,
J.E.Russell.
Structure of Fully Liganded Hb Zeta 2 Beta 2(S) Trapped in A Tense Conformation Acta Crystallogr.,Sect.D V. 69 2061 2013.
ISSN: ISSN 0907-4449
PubMed: 24100324
DOI: 10.1107/S0907444913019197
Page generated: Sun Aug 4 22:28:21 2024
|
