Iron in PDB 4fvc: Hmob Structure with Heme
Protein crystallography data
The structure of Hmob Structure with Heme, PDB code: 4fvc
was solved by
S.Park,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.58 /
1.75
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.821,
117.519,
70.847,
90.00,
91.22,
90.00
|
|
R / Rfree (%)
|
19.9 /
23.3
|
Iron Binding Sites:
The binding sites of Iron atom in the Hmob Structure with Heme
(pdb code 4fvc). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Hmob Structure with Heme, PDB code: 4fvc:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4fvc
Go back to
Iron Binding Sites List in 4fvc
Iron binding site 1 out
of 6 in the Hmob Structure with Heme
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Hmob Structure with Heme within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:27.0
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
27.0
|
1.0
|
|
NB
|
A:HEM201
|
2.0
|
23.6
|
1.0
|
|
NA
|
A:HEM201
|
2.0
|
24.5
|
1.0
|
|
ND
|
A:HEM201
|
2.1
|
28.6
|
1.0
|
|
NC
|
A:HEM201
|
2.1
|
27.7
|
1.0
|
|
OH
|
A:TYR134
|
2.3
|
39.0
|
1.0
|
|
C4A
|
A:HEM201
|
3.0
|
19.9
|
1.0
|
|
C1B
|
A:HEM201
|
3.0
|
21.8
|
1.0
|
|
C4B
|
A:HEM201
|
3.0
|
25.3
|
1.0
|
|
C1A
|
A:HEM201
|
3.1
|
25.5
|
1.0
|
|
C1C
|
A:HEM201
|
3.1
|
27.1
|
1.0
|
|
C4D
|
A:HEM201
|
3.1
|
30.8
|
1.0
|
|
C1D
|
A:HEM201
|
3.1
|
29.8
|
1.0
|
|
C4C
|
A:HEM201
|
3.1
|
27.5
|
1.0
|
|
CZ
|
A:TYR134
|
3.2
|
39.4
|
1.0
|
|
CHB
|
A:HEM201
|
3.4
|
20.9
|
1.0
|
|
CHC
|
A:HEM201
|
3.4
|
25.9
|
1.0
|
|
CHA
|
A:HEM201
|
3.4
|
27.4
|
1.0
|
|
CHD
|
A:HEM201
|
3.4
|
28.3
|
1.0
|
|
CD1
|
A:ILE115
|
3.5
|
22.7
|
1.0
|
|
CE1
|
A:TYR134
|
3.9
|
37.2
|
1.0
|
|
CE2
|
A:TYR134
|
4.0
|
39.8
|
1.0
|
|
C3A
|
A:HEM201
|
4.2
|
23.0
|
1.0
|
|
C3B
|
A:HEM201
|
4.2
|
25.5
|
1.0
|
|
C2B
|
A:HEM201
|
4.3
|
20.9
|
1.0
|
|
C2A
|
A:HEM201
|
4.3
|
24.4
|
1.0
|
|
C3C
|
A:HEM201
|
4.3
|
28.3
|
1.0
|
|
C2C
|
A:HEM201
|
4.3
|
27.3
|
1.0
|
|
C3D
|
A:HEM201
|
4.3
|
34.2
|
1.0
|
|
C2D
|
A:HEM201
|
4.3
|
33.7
|
1.0
|
|
CD1
|
A:ILE72
|
4.9
|
19.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 4fvc
Go back to
Iron Binding Sites List in 4fvc
Iron binding site 2 out
of 6 in the Hmob Structure with Heme
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Hmob Structure with Heme within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:29.1
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
29.1
|
1.0
|
|
ND
|
B:HEM201
|
2.0
|
33.2
|
1.0
|
|
NA
|
B:HEM201
|
2.0
|
26.7
|
1.0
|
|
NB
|
B:HEM201
|
2.0
|
24.9
|
1.0
|
|
NC
|
B:HEM201
|
2.1
|
30.3
|
1.0
|
|
OH
|
B:TYR134
|
2.2
|
43.0
|
1.0
|
|
C4D
|
B:HEM201
|
3.0
|
34.4
|
1.0
|
|
C1D
|
B:HEM201
|
3.0
|
33.7
|
1.0
|
|
C1A
|
B:HEM201
|
3.0
|
28.2
|
1.0
|
|
C4B
|
B:HEM201
|
3.0
|
25.8
|
1.0
|
|
C4A
|
B:HEM201
|
3.1
|
25.5
|
1.0
|
|
C1B
|
B:HEM201
|
3.1
|
24.9
|
1.0
|
|
C1C
|
B:HEM201
|
3.1
|
28.6
|
1.0
|
|
C4C
|
B:HEM201
|
3.1
|
29.1
|
1.0
|
|
CZ
|
B:TYR134
|
3.2
|
44.3
|
1.0
|
|
CHA
|
B:HEM201
|
3.3
|
32.1
|
1.0
|
|
CHC
|
B:HEM201
|
3.4
|
27.4
|
1.0
|
|
CHD
|
B:HEM201
|
3.4
|
33.3
|
1.0
|
|
CHB
|
B:HEM201
|
3.5
|
25.5
|
1.0
|
|
CD1
|
B:ILE115
|
3.5
|
25.9
|
1.0
|
|
CE1
|
B:TYR134
|
3.9
|
45.9
|
1.0
|
|
CE2
|
B:TYR134
|
4.0
|
44.7
|
1.0
|
|
O
|
B:HOH400
|
4.1
|
42.7
|
1.0
|
|
C3D
|
B:HEM201
|
4.2
|
37.1
|
1.0
|
|
C2D
|
B:HEM201
|
4.2
|
36.9
|
1.0
|
|
C2A
|
B:HEM201
|
4.3
|
27.3
|
1.0
|
|
C3B
|
B:HEM201
|
4.3
|
28.4
|
1.0
|
|
C3A
|
B:HEM201
|
4.3
|
26.6
|
1.0
|
|
C2B
|
B:HEM201
|
4.3
|
24.9
|
1.0
|
|
C2C
|
B:HEM201
|
4.3
|
29.2
|
1.0
|
|
C3C
|
B:HEM201
|
4.3
|
29.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 4fvc
Go back to
Iron Binding Sites List in 4fvc
Iron binding site 3 out
of 6 in the Hmob Structure with Heme
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Hmob Structure with Heme within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:26.3
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
26.3
|
1.0
|
|
NB
|
C:HEM201
|
2.0
|
24.0
|
1.0
|
|
NC
|
C:HEM201
|
2.0
|
29.7
|
1.0
|
|
NA
|
C:HEM201
|
2.0
|
25.1
|
1.0
|
|
ND
|
C:HEM201
|
2.1
|
30.1
|
1.0
|
|
OH
|
C:TYR134
|
2.2
|
36.9
|
1.0
|
|
C4B
|
C:HEM201
|
3.0
|
27.1
|
1.0
|
|
C1C
|
C:HEM201
|
3.0
|
28.9
|
1.0
|
|
C4C
|
C:HEM201
|
3.0
|
30.2
|
1.0
|
|
C4A
|
C:HEM201
|
3.0
|
21.8
|
1.0
|
|
C1B
|
C:HEM201
|
3.1
|
22.1
|
1.0
|
|
C1A
|
C:HEM201
|
3.1
|
26.8
|
1.0
|
|
C1D
|
C:HEM201
|
3.1
|
32.2
|
1.0
|
|
C4D
|
C:HEM201
|
3.1
|
32.9
|
1.0
|
|
CZ
|
C:TYR134
|
3.2
|
38.4
|
1.0
|
|
CHC
|
C:HEM201
|
3.4
|
27.0
|
1.0
|
|
CHA
|
C:HEM201
|
3.4
|
28.4
|
1.0
|
|
CHD
|
C:HEM201
|
3.4
|
31.3
|
1.0
|
|
CHB
|
C:HEM201
|
3.5
|
22.5
|
1.0
|
|
CD1
|
C:ILE115
|
3.5
|
25.5
|
1.0
|
|
CE1
|
C:TYR134
|
4.0
|
39.4
|
1.0
|
|
CE2
|
C:TYR134
|
4.0
|
35.9
|
1.0
|
|
C3B
|
C:HEM201
|
4.2
|
25.0
|
1.0
|
|
C3C
|
C:HEM201
|
4.2
|
30.3
|
1.0
|
|
C2C
|
C:HEM201
|
4.3
|
29.7
|
1.0
|
|
C3A
|
C:HEM201
|
4.3
|
23.4
|
1.0
|
|
C2B
|
C:HEM201
|
4.3
|
22.8
|
1.0
|
|
C2A
|
C:HEM201
|
4.3
|
26.1
|
1.0
|
|
C2D
|
C:HEM201
|
4.3
|
35.1
|
1.0
|
|
C3D
|
C:HEM201
|
4.3
|
36.5
|
1.0
|
|
CD1
|
C:ILE72
|
4.8
|
21.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 4fvc
Go back to
Iron Binding Sites List in 4fvc
Iron binding site 4 out
of 6 in the Hmob Structure with Heme
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Hmob Structure with Heme within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:21.7
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
21.7
|
1.0
|
|
NB
|
D:HEM201
|
2.0
|
20.4
|
1.0
|
|
ND
|
D:HEM201
|
2.0
|
21.0
|
1.0
|
|
NA
|
D:HEM201
|
2.1
|
20.2
|
1.0
|
|
NC
|
D:HEM201
|
2.1
|
22.5
|
1.0
|
|
OH
|
D:TYR134
|
2.1
|
28.8
|
1.0
|
|
C4B
|
D:HEM201
|
3.0
|
21.8
|
1.0
|
|
C4D
|
D:HEM201
|
3.0
|
22.3
|
1.0
|
|
C1B
|
D:HEM201
|
3.0
|
20.8
|
1.0
|
|
C1D
|
D:HEM201
|
3.0
|
21.9
|
1.0
|
|
C1A
|
D:HEM201
|
3.1
|
21.5
|
1.0
|
|
C1C
|
D:HEM201
|
3.1
|
22.4
|
1.0
|
|
C4A
|
D:HEM201
|
3.1
|
21.3
|
1.0
|
|
C4C
|
D:HEM201
|
3.1
|
24.1
|
1.0
|
|
CZ
|
D:TYR134
|
3.2
|
30.9
|
1.0
|
|
CHA
|
D:HEM201
|
3.4
|
23.2
|
1.0
|
|
CHC
|
D:HEM201
|
3.4
|
21.4
|
1.0
|
|
CHB
|
D:HEM201
|
3.4
|
20.8
|
1.0
|
|
CHD
|
D:HEM201
|
3.5
|
20.6
|
1.0
|
|
CD1
|
D:ILE115
|
3.5
|
20.2
|
1.0
|
|
O
|
D:HOH322
|
3.9
|
31.8
|
1.0
|
|
CE1
|
D:TYR134
|
3.9
|
31.9
|
1.0
|
|
O
|
D:HOH364
|
4.0
|
36.9
|
1.0
|
|
CE2
|
D:TYR134
|
4.1
|
32.2
|
1.0
|
|
C3B
|
D:HEM201
|
4.2
|
23.2
|
1.0
|
|
C2B
|
D:HEM201
|
4.2
|
22.8
|
1.0
|
|
C3D
|
D:HEM201
|
4.2
|
26.5
|
1.0
|
|
C2D
|
D:HEM201
|
4.3
|
22.1
|
1.0
|
|
C2A
|
D:HEM201
|
4.3
|
21.6
|
1.0
|
|
C3A
|
D:HEM201
|
4.3
|
21.4
|
1.0
|
|
C3C
|
D:HEM201
|
4.3
|
24.3
|
1.0
|
|
C2C
|
D:HEM201
|
4.3
|
24.2
|
1.0
|
|
CD1
|
D:ILE72
|
4.8
|
18.0
|
1.0
|
|
CG1
|
D:ILE115
|
5.0
|
17.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 4fvc
Go back to
Iron Binding Sites List in 4fvc
Iron binding site 5 out
of 6 in the Hmob Structure with Heme
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Hmob Structure with Heme within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:29.1
occ:1.00
|
FE
|
E:HEM201
|
0.0
|
29.1
|
1.0
|
|
ND
|
E:HEM201
|
2.0
|
33.1
|
1.0
|
|
NA
|
E:HEM201
|
2.0
|
26.8
|
1.0
|
|
NB
|
E:HEM201
|
2.1
|
26.8
|
1.0
|
|
NC
|
E:HEM201
|
2.1
|
30.0
|
1.0
|
|
OH
|
E:TYR134
|
2.1
|
38.9
|
1.0
|
|
C4D
|
E:HEM201
|
3.0
|
35.5
|
1.0
|
|
C1A
|
E:HEM201
|
3.0
|
29.5
|
1.0
|
|
C1D
|
E:HEM201
|
3.0
|
34.1
|
1.0
|
|
C4B
|
E:HEM201
|
3.0
|
26.3
|
1.0
|
|
C1C
|
E:HEM201
|
3.1
|
29.2
|
1.0
|
|
C4A
|
E:HEM201
|
3.1
|
26.4
|
1.0
|
|
C1B
|
E:HEM201
|
3.1
|
26.3
|
1.0
|
|
C4C
|
E:HEM201
|
3.1
|
30.2
|
1.0
|
|
CZ
|
E:TYR134
|
3.2
|
42.2
|
1.0
|
|
CHA
|
E:HEM201
|
3.3
|
32.0
|
1.0
|
|
CHC
|
E:HEM201
|
3.4
|
26.6
|
1.0
|
|
CHD
|
E:HEM201
|
3.4
|
33.3
|
1.0
|
|
CHB
|
E:HEM201
|
3.5
|
26.2
|
1.0
|
|
CD1
|
E:ILE115
|
3.5
|
24.5
|
1.0
|
|
CE2
|
E:TYR134
|
3.9
|
41.8
|
1.0
|
|
CE1
|
E:TYR134
|
4.0
|
43.9
|
1.0
|
|
C3D
|
E:HEM201
|
4.2
|
38.1
|
1.0
|
|
C2D
|
E:HEM201
|
4.2
|
37.3
|
1.0
|
|
C3B
|
E:HEM201
|
4.3
|
28.8
|
1.0
|
|
C2A
|
E:HEM201
|
4.3
|
27.3
|
1.0
|
|
C3A
|
E:HEM201
|
4.3
|
27.8
|
1.0
|
|
C2C
|
E:HEM201
|
4.3
|
29.8
|
1.0
|
|
C2B
|
E:HEM201
|
4.3
|
26.7
|
1.0
|
|
C3C
|
E:HEM201
|
4.3
|
31.1
|
1.0
|
|
CG1
|
E:ILE115
|
5.0
|
21.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 4fvc
Go back to
Iron Binding Sites List in 4fvc
Iron binding site 6 out
of 6 in the Hmob Structure with Heme
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Hmob Structure with Heme within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:21.7
occ:1.00
|
FE
|
F:HEM201
|
0.0
|
21.7
|
1.0
|
|
NB
|
F:HEM201
|
2.0
|
20.7
|
1.0
|
|
ND
|
F:HEM201
|
2.1
|
21.9
|
1.0
|
|
NA
|
F:HEM201
|
2.1
|
20.1
|
1.0
|
|
NC
|
F:HEM201
|
2.1
|
22.5
|
1.0
|
|
OH
|
F:TYR134
|
2.2
|
28.1
|
1.0
|
|
C4B
|
F:HEM201
|
3.0
|
21.4
|
1.0
|
|
C4D
|
F:HEM201
|
3.0
|
23.6
|
1.0
|
|
C1B
|
F:HEM201
|
3.0
|
20.9
|
1.0
|
|
C1A
|
F:HEM201
|
3.1
|
22.4
|
1.0
|
|
C4A
|
F:HEM201
|
3.1
|
20.4
|
1.0
|
|
C1D
|
F:HEM201
|
3.1
|
22.9
|
1.0
|
|
C1C
|
F:HEM201
|
3.1
|
21.2
|
1.0
|
|
CZ
|
F:TYR134
|
3.1
|
30.3
|
1.0
|
|
C4C
|
F:HEM201
|
3.1
|
23.6
|
1.0
|
|
CHA
|
F:HEM201
|
3.4
|
23.3
|
1.0
|
|
CHC
|
F:HEM201
|
3.4
|
21.8
|
1.0
|
|
CHB
|
F:HEM201
|
3.5
|
20.2
|
1.0
|
|
CD1
|
F:ILE115
|
3.5
|
18.4
|
1.0
|
|
CHD
|
F:HEM201
|
3.5
|
20.5
|
1.0
|
|
CE1
|
F:TYR134
|
3.8
|
32.5
|
1.0
|
|
O
|
F:HOH345
|
4.0
|
36.6
|
1.0
|
|
CE2
|
F:TYR134
|
4.0
|
32.1
|
1.0
|
|
C3B
|
F:HEM201
|
4.2
|
24.9
|
1.0
|
|
C2B
|
F:HEM201
|
4.2
|
20.2
|
1.0
|
|
C3D
|
F:HEM201
|
4.3
|
26.9
|
1.0
|
|
C2A
|
F:HEM201
|
4.3
|
22.0
|
1.0
|
|
C2D
|
F:HEM201
|
4.3
|
25.0
|
1.0
|
|
C3A
|
F:HEM201
|
4.3
|
21.3
|
1.0
|
|
C3C
|
F:HEM201
|
4.3
|
24.5
|
1.0
|
|
C2C
|
F:HEM201
|
4.3
|
22.4
|
1.0
|
|
O
|
F:HOH362
|
4.5
|
46.9
|
1.0
|
|
CD1
|
F:ILE72
|
4.8
|
19.3
|
1.0
|
|
CG1
|
F:ILE115
|
5.0
|
16.6
|
1.0
|
|
Reference:
S.Park,
S.Park.
N/A N/A.
Page generated: Mon Aug 5 02:28:30 2024
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