Iron in PDB 6tv9: Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
Protein crystallography data
The structure of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1, PDB code: 6tv9
was solved by
T.Kluenemann,
G.Layer,
W.Blankenfeldt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
100.09 /
1.89
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.197,
149.443,
110.174,
90.00,
98.48,
90.00
|
|
R / Rfree (%)
|
21.5 /
25.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
(pdb code 6tv9). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1, PDB code: 6tv9:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 1 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:21.2
occ:0.80
|
FE
|
A:DHE401
|
0.0
|
21.2
|
0.8
|
|
NA
|
A:DHE401
|
2.0
|
19.6
|
0.8
|
|
NE2
|
A:HIS48
|
2.1
|
34.0
|
1.0
|
|
NE2
|
A:HIS238
|
2.1
|
26.6
|
1.0
|
|
NC
|
A:DHE401
|
2.1
|
19.0
|
0.8
|
|
ND
|
A:DHE401
|
2.1
|
16.2
|
0.8
|
|
NB
|
A:DHE401
|
2.1
|
22.2
|
0.8
|
|
CE1
|
A:HIS48
|
2.8
|
34.6
|
1.0
|
|
HE1
|
A:HIS48
|
2.8
|
41.7
|
1.0
|
|
CE1
|
A:HIS238
|
3.0
|
23.0
|
1.0
|
|
C1A
|
A:DHE401
|
3.1
|
18.5
|
0.8
|
|
HE1
|
A:HIS238
|
3.1
|
27.8
|
1.0
|
|
C1C
|
A:DHE401
|
3.1
|
20.4
|
0.8
|
|
C4C
|
A:DHE401
|
3.1
|
18.7
|
0.8
|
|
C1D
|
A:DHE401
|
3.1
|
16.2
|
0.8
|
|
C4A
|
A:DHE401
|
3.1
|
20.5
|
0.8
|
|
CD2
|
A:HIS238
|
3.1
|
24.4
|
1.0
|
|
C1B
|
A:DHE401
|
3.1
|
24.4
|
0.8
|
|
C4D
|
A:DHE401
|
3.1
|
15.8
|
0.8
|
|
C4B
|
A:DHE401
|
3.2
|
23.3
|
0.8
|
|
CD2
|
A:HIS48
|
3.2
|
33.0
|
1.0
|
|
HD2
|
A:HIS238
|
3.4
|
29.5
|
1.0
|
|
CHA
|
A:DHE401
|
3.5
|
17.1
|
0.8
|
|
CHD
|
A:DHE401
|
3.5
|
17.7
|
0.8
|
|
CHC
|
A:DHE401
|
3.5
|
21.8
|
0.8
|
|
HD2
|
A:HIS48
|
3.5
|
39.7
|
1.0
|
|
CHB
|
A:DHE401
|
3.6
|
22.8
|
0.8
|
|
ND1
|
A:HIS48
|
4.0
|
35.4
|
1.0
|
|
ND1
|
A:HIS238
|
4.1
|
23.0
|
1.0
|
|
CG
|
A:HIS238
|
4.2
|
23.5
|
1.0
|
|
CG
|
A:HIS48
|
4.3
|
32.5
|
1.0
|
|
C2C
|
A:DHE401
|
4.3
|
20.3
|
0.8
|
|
C2A
|
A:DHE401
|
4.4
|
19.7
|
0.8
|
|
C2B
|
A:DHE401
|
4.4
|
27.1
|
0.8
|
|
C3A
|
A:DHE401
|
4.4
|
20.4
|
0.8
|
|
C2D
|
A:DHE401
|
4.4
|
14.6
|
0.8
|
|
C3D
|
A:DHE401
|
4.5
|
16.2
|
0.8
|
|
C3C
|
A:DHE401
|
4.5
|
20.9
|
0.8
|
|
C3B
|
A:DHE401
|
4.5
|
25.1
|
0.8
|
|
HHA
|
A:DHE401
|
4.6
|
20.6
|
0.8
|
|
HHD
|
A:DHE401
|
4.6
|
21.4
|
0.8
|
|
HHC
|
A:DHE401
|
4.6
|
26.3
|
0.8
|
|
HHB
|
A:DHE401
|
4.6
|
27.5
|
0.8
|
|
HZ
|
A:PHE281
|
4.6
|
25.6
|
1.0
|
|
HD1
|
A:HIS48
|
4.8
|
42.6
|
1.0
|
|
HD11
|
A:ILE90
|
4.8
|
34.1
|
1.0
|
|
HGC2
|
A:DHE401
|
4.9
|
26.6
|
0.8
|
|
HD1
|
A:HIS238
|
4.9
|
27.7
|
1.0
|
|
O2C
|
A:DHE401
|
4.9
|
29.3
|
0.8
|
|
HGB2
|
A:DHE401
|
5.0
|
28.0
|
0.8
|
|
Iron binding site 2 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 2 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:25.0
occ:0.75
|
FE
|
B:DHE401
|
0.0
|
25.0
|
0.8
|
|
NA
|
B:DHE401
|
2.0
|
21.7
|
0.8
|
|
NB
|
B:DHE401
|
2.1
|
25.8
|
0.8
|
|
NC
|
B:DHE401
|
2.1
|
20.6
|
0.8
|
|
NE2
|
B:HIS238
|
2.1
|
43.6
|
1.0
|
|
NE2
|
B:HIS48
|
2.1
|
55.6
|
1.0
|
|
ND
|
B:DHE401
|
2.1
|
17.7
|
0.8
|
|
HE1
|
B:HIS48
|
2.6
|
67.9
|
1.0
|
|
CE1
|
B:HIS48
|
2.7
|
56.4
|
1.0
|
|
CE1
|
B:HIS238
|
3.0
|
42.6
|
1.0
|
|
HE1
|
B:HIS238
|
3.1
|
51.2
|
1.0
|
|
C1A
|
B:DHE401
|
3.1
|
19.8
|
0.8
|
|
C4A
|
B:DHE401
|
3.1
|
23.2
|
0.8
|
|
C1C
|
B:DHE401
|
3.1
|
19.9
|
0.8
|
|
C1B
|
B:DHE401
|
3.1
|
27.1
|
0.8
|
|
C4B
|
B:DHE401
|
3.1
|
26.7
|
0.8
|
|
C4C
|
B:DHE401
|
3.1
|
20.1
|
0.8
|
|
C1D
|
B:DHE401
|
3.1
|
16.8
|
0.8
|
|
C4D
|
B:DHE401
|
3.1
|
16.3
|
0.8
|
|
CD2
|
B:HIS238
|
3.2
|
41.3
|
1.0
|
|
CD2
|
B:HIS48
|
3.4
|
56.2
|
1.0
|
|
HD2
|
B:HIS238
|
3.4
|
49.7
|
1.0
|
|
CHC
|
B:DHE401
|
3.5
|
22.4
|
0.8
|
|
CHD
|
B:DHE401
|
3.5
|
17.0
|
0.8
|
|
CHA
|
B:DHE401
|
3.5
|
18.0
|
0.8
|
|
CHB
|
B:DHE401
|
3.5
|
25.4
|
0.8
|
|
HD2
|
B:HIS48
|
3.8
|
67.6
|
1.0
|
|
ND1
|
B:HIS48
|
3.9
|
56.7
|
1.0
|
|
ND1
|
B:HIS238
|
4.1
|
41.5
|
1.0
|
|
CG
|
B:HIS238
|
4.3
|
38.8
|
1.0
|
|
CG
|
B:HIS48
|
4.3
|
55.3
|
1.0
|
|
C2C
|
B:DHE401
|
4.3
|
23.0
|
0.8
|
|
C2B
|
B:DHE401
|
4.3
|
29.8
|
0.8
|
|
C2A
|
B:DHE401
|
4.4
|
22.9
|
0.8
|
|
C3A
|
B:DHE401
|
4.4
|
22.4
|
0.8
|
|
C3D
|
B:DHE401
|
4.5
|
17.7
|
0.8
|
|
C3B
|
B:DHE401
|
4.5
|
30.3
|
0.8
|
|
C2D
|
B:DHE401
|
4.5
|
15.6
|
0.8
|
|
C3C
|
B:DHE401
|
4.5
|
24.5
|
0.8
|
|
HD11
|
B:ILE90
|
4.5
|
48.2
|
1.0
|
|
HHD
|
B:DHE401
|
4.6
|
20.5
|
0.8
|
|
HHC
|
B:DHE401
|
4.6
|
27.1
|
0.8
|
|
HHA
|
B:DHE401
|
4.6
|
21.7
|
0.8
|
|
HHB
|
B:DHE401
|
4.6
|
30.6
|
0.8
|
|
HD1
|
B:HIS48
|
4.6
|
68.2
|
1.0
|
|
HGB2
|
B:DHE401
|
4.9
|
37.3
|
0.8
|
|
O1B
|
B:DHE401
|
4.9
|
41.2
|
0.8
|
|
HD1
|
B:HIS238
|
4.9
|
49.9
|
1.0
|
|
O2C
|
B:DHE401
|
4.9
|
37.9
|
0.8
|
|
Iron binding site 3 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 3 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:13.9
occ:0.75
|
FE
|
C:DHE401
|
0.0
|
13.9
|
0.8
|
|
NA
|
C:DHE401
|
2.0
|
11.7
|
0.8
|
|
NC
|
C:DHE401
|
2.1
|
15.1
|
0.8
|
|
ND
|
C:DHE401
|
2.1
|
12.8
|
0.8
|
|
NB
|
C:DHE401
|
2.1
|
15.5
|
0.8
|
|
NE2
|
C:HIS238
|
2.1
|
16.9
|
1.0
|
|
NE2
|
C:HIS48
|
2.1
|
21.1
|
1.0
|
|
HE1
|
C:HIS48
|
2.6
|
27.9
|
1.0
|
|
CE1
|
C:HIS48
|
2.7
|
23.2
|
1.0
|
|
CE1
|
C:HIS238
|
3.0
|
18.7
|
1.0
|
|
HE1
|
C:HIS238
|
3.1
|
22.6
|
1.0
|
|
C1A
|
C:DHE401
|
3.1
|
11.4
|
0.8
|
|
C1C
|
C:DHE401
|
3.1
|
17.8
|
0.8
|
|
C4A
|
C:DHE401
|
3.1
|
13.8
|
0.8
|
|
C4C
|
C:DHE401
|
3.1
|
15.9
|
0.8
|
|
C4D
|
C:DHE401
|
3.1
|
11.6
|
0.8
|
|
C1D
|
C:DHE401
|
3.1
|
13.1
|
0.8
|
|
C4B
|
C:DHE401
|
3.1
|
17.5
|
0.8
|
|
C1B
|
C:DHE401
|
3.1
|
17.0
|
0.8
|
|
CD2
|
C:HIS238
|
3.2
|
17.9
|
1.0
|
|
CD2
|
C:HIS48
|
3.4
|
18.8
|
1.0
|
|
HD2
|
C:HIS238
|
3.5
|
21.6
|
1.0
|
|
CHD
|
C:DHE401
|
3.5
|
14.3
|
0.8
|
|
CHA
|
C:DHE401
|
3.5
|
12.2
|
0.8
|
|
CHC
|
C:DHE401
|
3.5
|
17.7
|
0.8
|
|
CHB
|
C:DHE401
|
3.5
|
16.7
|
0.8
|
|
HD2
|
C:HIS48
|
3.8
|
22.7
|
1.0
|
|
ND1
|
C:HIS48
|
4.0
|
22.7
|
1.0
|
|
ND1
|
C:HIS238
|
4.2
|
17.1
|
1.0
|
|
CG
|
C:HIS238
|
4.3
|
16.5
|
1.0
|
|
CG
|
C:HIS48
|
4.3
|
19.0
|
1.0
|
|
C2C
|
C:DHE401
|
4.3
|
20.2
|
0.8
|
|
C2A
|
C:DHE401
|
4.3
|
12.9
|
0.8
|
|
C2B
|
C:DHE401
|
4.3
|
18.4
|
0.8
|
|
C3A
|
C:DHE401
|
4.4
|
14.1
|
0.8
|
|
C3D
|
C:DHE401
|
4.4
|
10.7
|
0.8
|
|
C2D
|
C:DHE401
|
4.4
|
9.9
|
0.8
|
|
C3C
|
C:DHE401
|
4.5
|
15.8
|
0.8
|
|
HD11
|
C:ILE90
|
4.5
|
15.6
|
1.0
|
|
C3B
|
C:DHE401
|
4.5
|
16.4
|
0.8
|
|
HHD
|
C:DHE401
|
4.5
|
17.4
|
0.8
|
|
HHA
|
C:DHE401
|
4.5
|
14.7
|
0.8
|
|
HHC
|
C:DHE401
|
4.5
|
21.3
|
0.8
|
|
HHB
|
C:DHE401
|
4.6
|
20.2
|
0.8
|
|
O2B
|
C:DHE401
|
4.6
|
31.7
|
0.8
|
|
HD1
|
C:HIS48
|
4.7
|
27.3
|
1.0
|
|
HZ
|
C:PHE281
|
4.7
|
21.4
|
1.0
|
|
O2C
|
C:DHE401
|
4.7
|
20.9
|
0.8
|
|
HGC2
|
C:DHE401
|
4.9
|
15.5
|
0.8
|
|
HD1
|
C:HIS238
|
4.9
|
20.7
|
1.0
|
|
HGB2
|
C:DHE401
|
5.0
|
16.7
|
0.8
|
|
Iron binding site 4 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 4 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:18.8
occ:0.75
|
FE
|
D:DHE401
|
0.0
|
18.8
|
0.8
|
|
NA
|
D:DHE401
|
2.0
|
15.1
|
0.8
|
|
NE2
|
D:HIS48
|
2.0
|
25.8
|
1.0
|
|
NC
|
D:DHE401
|
2.1
|
18.2
|
0.8
|
|
NB
|
D:DHE401
|
2.1
|
16.8
|
0.8
|
|
NE2
|
D:HIS238
|
2.1
|
22.9
|
1.0
|
|
ND
|
D:DHE401
|
2.1
|
11.9
|
0.8
|
|
CE1
|
D:HIS48
|
2.8
|
27.3
|
1.0
|
|
HE1
|
D:HIS48
|
2.9
|
32.9
|
1.0
|
|
CE1
|
D:HIS238
|
3.0
|
20.5
|
1.0
|
|
HE1
|
D:HIS238
|
3.0
|
24.8
|
1.0
|
|
C1A
|
D:DHE401
|
3.1
|
13.9
|
0.8
|
|
C4A
|
D:DHE401
|
3.1
|
15.7
|
0.8
|
|
C1C
|
D:DHE401
|
3.1
|
18.6
|
0.8
|
|
C1B
|
D:DHE401
|
3.1
|
17.8
|
0.8
|
|
C4C
|
D:DHE401
|
3.1
|
18.6
|
0.8
|
|
C4B
|
D:DHE401
|
3.1
|
15.9
|
0.8
|
|
C4D
|
D:DHE401
|
3.1
|
11.5
|
0.8
|
|
C1D
|
D:DHE401
|
3.1
|
13.1
|
0.8
|
|
CD2
|
D:HIS48
|
3.2
|
26.6
|
1.0
|
|
CD2
|
D:HIS238
|
3.2
|
20.5
|
1.0
|
|
HD2
|
D:HIS238
|
3.5
|
24.8
|
1.0
|
|
HD2
|
D:HIS48
|
3.5
|
32.0
|
1.0
|
|
CHA
|
D:DHE401
|
3.5
|
14.0
|
0.8
|
|
CHD
|
D:DHE401
|
3.5
|
14.6
|
0.8
|
|
CHB
|
D:DHE401
|
3.5
|
16.4
|
0.8
|
|
CHC
|
D:DHE401
|
3.5
|
15.3
|
0.8
|
|
ND1
|
D:HIS48
|
4.0
|
26.6
|
1.0
|
|
ND1
|
D:HIS238
|
4.1
|
18.2
|
1.0
|
|
CG
|
D:HIS48
|
4.2
|
25.1
|
1.0
|
|
CG
|
D:HIS238
|
4.3
|
18.0
|
1.0
|
|
C2C
|
D:DHE401
|
4.3
|
21.8
|
0.8
|
|
C2B
|
D:DHE401
|
4.3
|
18.4
|
0.8
|
|
C2A
|
D:DHE401
|
4.3
|
14.1
|
0.8
|
|
C3A
|
D:DHE401
|
4.3
|
17.5
|
0.8
|
|
C3D
|
D:DHE401
|
4.5
|
14.2
|
0.8
|
|
C2D
|
D:DHE401
|
4.5
|
13.3
|
0.8
|
|
C3B
|
D:DHE401
|
4.5
|
18.2
|
0.8
|
|
C3C
|
D:DHE401
|
4.5
|
21.4
|
0.8
|
|
HHA
|
D:DHE401
|
4.6
|
17.0
|
0.8
|
|
HHD
|
D:DHE401
|
4.6
|
17.7
|
0.8
|
|
HHB
|
D:DHE401
|
4.6
|
19.8
|
0.8
|
|
HHC
|
D:DHE401
|
4.6
|
18.4
|
0.8
|
|
O1B
|
D:DHE401
|
4.8
|
25.3
|
0.8
|
|
HD11
|
D:ILE90
|
4.8
|
12.8
|
1.0
|
|
HD1
|
D:HIS48
|
4.8
|
32.1
|
1.0
|
|
HZ
|
D:PHE281
|
4.8
|
24.1
|
1.0
|
|
HH22
|
D:ARG65
|
4.8
|
42.8
|
1.0
|
|
O1C
|
D:DHE401
|
4.9
|
30.2
|
0.8
|
|
HD1
|
D:HIS238
|
4.9
|
21.9
|
1.0
|
|
HGB2
|
D:DHE401
|
4.9
|
22.9
|
0.8
|
|
HGC2
|
D:DHE401
|
4.9
|
27.1
|
0.8
|
|
Iron binding site 5 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 5 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe401
b:25.6
occ:0.95
|
FE
|
E:DHE401
|
0.0
|
25.6
|
0.9
|
|
NA
|
E:DHE401
|
2.0
|
21.5
|
0.9
|
|
NE2
|
E:HIS48
|
2.0
|
35.5
|
1.0
|
|
NE2
|
E:HIS238
|
2.1
|
35.3
|
1.0
|
|
NC
|
E:DHE401
|
2.1
|
23.6
|
0.9
|
|
ND
|
E:DHE401
|
2.1
|
23.6
|
0.9
|
|
NB
|
E:DHE401
|
2.1
|
28.4
|
0.9
|
|
CE1
|
E:HIS48
|
2.8
|
33.6
|
1.0
|
|
HE1
|
E:HIS48
|
2.9
|
40.5
|
1.0
|
|
CE1
|
E:HIS238
|
2.9
|
33.0
|
1.0
|
|
HE1
|
E:HIS238
|
2.9
|
39.7
|
1.0
|
|
C1A
|
E:DHE401
|
3.1
|
21.2
|
0.9
|
|
C4A
|
E:DHE401
|
3.1
|
20.9
|
0.9
|
|
C1C
|
E:DHE401
|
3.1
|
24.6
|
0.9
|
|
C4C
|
E:DHE401
|
3.1
|
23.7
|
0.9
|
|
C1D
|
E:DHE401
|
3.1
|
22.6
|
0.9
|
|
C4B
|
E:DHE401
|
3.1
|
29.6
|
0.9
|
|
C4D
|
E:DHE401
|
3.1
|
23.0
|
0.9
|
|
C1B
|
E:DHE401
|
3.1
|
29.1
|
0.9
|
|
CD2
|
E:HIS48
|
3.2
|
34.0
|
1.0
|
|
CD2
|
E:HIS238
|
3.2
|
32.2
|
1.0
|
|
HD2
|
E:HIS48
|
3.5
|
41.0
|
1.0
|
|
CHA
|
E:DHE401
|
3.5
|
22.2
|
0.9
|
|
CHD
|
E:DHE401
|
3.5
|
24.1
|
0.9
|
|
CHC
|
E:DHE401
|
3.5
|
26.2
|
0.9
|
|
HD2
|
E:HIS238
|
3.5
|
38.7
|
1.0
|
|
CHB
|
E:DHE401
|
3.5
|
25.2
|
0.9
|
|
ND1
|
E:HIS48
|
4.0
|
32.8
|
1.0
|
|
ND1
|
E:HIS238
|
4.1
|
33.1
|
1.0
|
|
CG
|
E:HIS48
|
4.2
|
31.7
|
1.0
|
|
CG
|
E:HIS238
|
4.3
|
31.5
|
1.0
|
|
C2A
|
E:DHE401
|
4.3
|
19.1
|
0.9
|
|
C2C
|
E:DHE401
|
4.3
|
23.1
|
0.9
|
|
C2B
|
E:DHE401
|
4.4
|
31.0
|
0.9
|
|
C3A
|
E:DHE401
|
4.4
|
19.2
|
0.9
|
|
C2D
|
E:DHE401
|
4.4
|
22.1
|
0.9
|
|
C3D
|
E:DHE401
|
4.4
|
23.8
|
0.9
|
|
C3B
|
E:DHE401
|
4.5
|
29.6
|
0.9
|
|
C3C
|
E:DHE401
|
4.5
|
22.4
|
0.9
|
|
HHA
|
E:DHE401
|
4.5
|
26.8
|
0.9
|
|
HHD
|
E:DHE401
|
4.5
|
29.1
|
0.9
|
|
HHC
|
E:DHE401
|
4.6
|
31.6
|
0.9
|
|
HHB
|
E:DHE401
|
4.6
|
30.4
|
0.9
|
|
O1C
|
E:DHE401
|
4.7
|
24.8
|
0.9
|
|
HD1
|
E:HIS48
|
4.7
|
39.5
|
1.0
|
|
HD11
|
E:ILE90
|
4.7
|
20.3
|
1.0
|
|
HD1
|
E:HIS238
|
4.8
|
39.9
|
1.0
|
|
HZ
|
E:PHE281
|
4.8
|
27.4
|
1.0
|
|
O1B
|
E:DHE401
|
4.9
|
31.8
|
0.9
|
|
HGC2
|
E:DHE401
|
4.9
|
24.4
|
0.9
|
|
HGB2
|
E:DHE401
|
4.9
|
35.7
|
0.9
|
|
Iron binding site 6 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 6 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe401
b:17.9
occ:0.75
|
FE
|
F:DHE401
|
0.0
|
17.9
|
0.8
|
|
NA
|
F:DHE401
|
2.0
|
14.6
|
0.8
|
|
NE2
|
F:HIS48
|
2.1
|
25.3
|
1.0
|
|
NC
|
F:DHE401
|
2.1
|
13.9
|
0.8
|
|
NB
|
F:DHE401
|
2.1
|
19.7
|
0.8
|
|
ND
|
F:DHE401
|
2.1
|
13.6
|
0.8
|
|
NE2
|
F:HIS238
|
2.1
|
18.6
|
1.0
|
|
CE1
|
F:HIS48
|
2.9
|
27.0
|
1.0
|
|
HE1
|
F:HIS48
|
2.9
|
32.5
|
1.0
|
|
CE1
|
F:HIS238
|
3.0
|
17.4
|
1.0
|
|
C1A
|
F:DHE401
|
3.1
|
13.5
|
0.8
|
|
C4A
|
F:DHE401
|
3.1
|
16.9
|
0.8
|
|
HE1
|
F:HIS238
|
3.1
|
21.0
|
1.0
|
|
C1C
|
F:DHE401
|
3.1
|
17.0
|
0.8
|
|
C4D
|
F:DHE401
|
3.1
|
12.1
|
0.8
|
|
C1B
|
F:DHE401
|
3.1
|
21.4
|
0.8
|
|
C4B
|
F:DHE401
|
3.1
|
20.8
|
0.8
|
|
C4C
|
F:DHE401
|
3.1
|
15.1
|
0.8
|
|
C1D
|
F:DHE401
|
3.1
|
12.4
|
0.8
|
|
CD2
|
F:HIS238
|
3.2
|
16.4
|
1.0
|
|
CD2
|
F:HIS48
|
3.2
|
24.7
|
1.0
|
|
HD2
|
F:HIS238
|
3.5
|
19.8
|
1.0
|
|
CHA
|
F:DHE401
|
3.5
|
13.3
|
0.8
|
|
CHB
|
F:DHE401
|
3.5
|
19.8
|
0.8
|
|
CHD
|
F:DHE401
|
3.5
|
11.3
|
0.8
|
|
CHC
|
F:DHE401
|
3.5
|
18.5
|
0.8
|
|
HD2
|
F:HIS48
|
3.5
|
29.8
|
1.0
|
|
ND1
|
F:HIS48
|
4.1
|
25.2
|
1.0
|
|
ND1
|
F:HIS238
|
4.2
|
16.2
|
1.0
|
|
CG
|
F:HIS48
|
4.3
|
23.3
|
1.0
|
|
CG
|
F:HIS238
|
4.3
|
14.4
|
1.0
|
|
C2A
|
F:DHE401
|
4.3
|
12.6
|
0.8
|
|
C2C
|
F:DHE401
|
4.3
|
17.2
|
0.8
|
|
C2B
|
F:DHE401
|
4.4
|
23.4
|
0.8
|
|
C3A
|
F:DHE401
|
4.4
|
15.2
|
0.8
|
|
C3D
|
F:DHE401
|
4.4
|
12.9
|
0.8
|
|
C2D
|
F:DHE401
|
4.5
|
11.4
|
0.8
|
|
C3B
|
F:DHE401
|
4.5
|
21.0
|
0.8
|
|
C3C
|
F:DHE401
|
4.5
|
16.1
|
0.8
|
|
HHA
|
F:DHE401
|
4.5
|
16.1
|
0.8
|
|
HHD
|
F:DHE401
|
4.6
|
13.7
|
0.8
|
|
HHC
|
F:DHE401
|
4.6
|
22.4
|
0.8
|
|
HHB
|
F:DHE401
|
4.6
|
23.9
|
0.8
|
|
HD11
|
F:ILE90
|
4.7
|
19.6
|
1.0
|
|
O1C
|
F:DHE401
|
4.8
|
19.9
|
0.8
|
|
HD1
|
F:HIS48
|
4.8
|
30.3
|
1.0
|
|
HGB2
|
F:DHE401
|
4.8
|
20.5
|
0.8
|
|
O2B
|
F:DHE401
|
4.9
|
24.7
|
0.8
|
|
HD1
|
F:HIS238
|
4.9
|
19.6
|
1.0
|
|
HGC2
|
F:DHE401
|
4.9
|
18.9
|
0.8
|
|
Iron binding site 7 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 7 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe401
b:23.4
occ:0.95
|
FE
|
G:DHE401
|
0.0
|
23.4
|
0.9
|
|
NE2
|
G:HIS48
|
2.0
|
19.6
|
1.0
|
|
NA
|
G:DHE401
|
2.0
|
19.6
|
0.9
|
|
NC
|
G:DHE401
|
2.0
|
18.6
|
0.9
|
|
ND
|
G:DHE401
|
2.1
|
16.8
|
0.9
|
|
NE2
|
G:HIS238
|
2.1
|
22.7
|
1.0
|
|
NB
|
G:DHE401
|
2.1
|
25.4
|
0.9
|
|
CE1
|
G:HIS48
|
2.8
|
18.4
|
1.0
|
|
HE1
|
G:HIS48
|
2.9
|
22.2
|
1.0
|
|
CE1
|
G:HIS238
|
3.0
|
20.7
|
1.0
|
|
HE1
|
G:HIS238
|
3.0
|
24.9
|
1.0
|
|
C4C
|
G:DHE401
|
3.1
|
18.3
|
0.9
|
|
C1D
|
G:DHE401
|
3.1
|
15.4
|
0.9
|
|
C1C
|
G:DHE401
|
3.1
|
20.7
|
0.9
|
|
C1A
|
G:DHE401
|
3.1
|
16.5
|
0.9
|
|
C4D
|
G:DHE401
|
3.1
|
14.9
|
0.9
|
|
C4A
|
G:DHE401
|
3.1
|
21.0
|
0.9
|
|
CD2
|
G:HIS48
|
3.1
|
16.6
|
1.0
|
|
C4B
|
G:DHE401
|
3.1
|
24.7
|
0.9
|
|
C1B
|
G:DHE401
|
3.2
|
27.1
|
0.9
|
|
CD2
|
G:HIS238
|
3.2
|
20.1
|
1.0
|
|
HD2
|
G:HIS48
|
3.4
|
20.1
|
1.0
|
|
CHD
|
G:DHE401
|
3.5
|
15.3
|
0.9
|
|
HD2
|
G:HIS238
|
3.5
|
24.3
|
1.0
|
|
CHA
|
G:DHE401
|
3.5
|
13.5
|
0.9
|
|
CHC
|
G:DHE401
|
3.5
|
20.4
|
0.9
|
|
CHB
|
G:DHE401
|
3.6
|
24.1
|
0.9
|
|
ND1
|
G:HIS48
|
4.0
|
19.4
|
1.0
|
|
ND1
|
G:HIS238
|
4.1
|
20.2
|
1.0
|
|
CG
|
G:HIS48
|
4.2
|
17.0
|
1.0
|
|
CG
|
G:HIS238
|
4.3
|
18.9
|
1.0
|
|
C2C
|
G:DHE401
|
4.3
|
19.7
|
0.9
|
|
C2A
|
G:DHE401
|
4.4
|
14.8
|
0.9
|
|
C2B
|
G:DHE401
|
4.4
|
26.4
|
0.9
|
|
C3A
|
G:DHE401
|
4.4
|
16.9
|
0.9
|
|
C2D
|
G:DHE401
|
4.4
|
15.6
|
0.9
|
|
C3D
|
G:DHE401
|
4.4
|
16.5
|
0.9
|
|
C3C
|
G:DHE401
|
4.5
|
18.0
|
0.9
|
|
HHD
|
G:DHE401
|
4.5
|
18.5
|
0.9
|
|
C3B
|
G:DHE401
|
4.5
|
24.5
|
0.9
|
|
HHA
|
G:DHE401
|
4.5
|
16.3
|
0.9
|
|
HHC
|
G:DHE401
|
4.6
|
24.6
|
0.9
|
|
HHB
|
G:DHE401
|
4.6
|
29.0
|
0.9
|
|
O1B
|
G:DHE401
|
4.7
|
29.9
|
0.9
|
|
HD1
|
G:HIS48
|
4.7
|
23.4
|
1.0
|
|
HGC2
|
G:DHE401
|
4.8
|
14.6
|
0.9
|
|
HD11
|
G:ILE90
|
4.8
|
18.9
|
1.0
|
|
HD1
|
G:HIS238
|
4.9
|
24.3
|
1.0
|
|
HZ
|
G:PHE281
|
5.0
|
26.8
|
1.0
|
|
O1C
|
G:DHE401
|
5.0
|
25.3
|
0.9
|
|
HGB2
|
G:DHE401
|
5.0
|
22.6
|
0.9
|
|
Iron binding site 8 out
of 8 in 6tv9
Go back to
Iron Binding Sites List in 6tv9
Iron binding site 8 out
of 8 in the Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Heme D1 Biosynthesis Associated Protein Nirf in Complex with Dihydro- Heme D1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe401
b:25.3
occ:1.00
|
FE
|
H:DHE401
|
0.0
|
25.3
|
1.0
|
|
NE2
|
H:HIS48
|
2.0
|
31.4
|
1.0
|
|
NA
|
H:DHE401
|
2.0
|
22.1
|
1.0
|
|
NC
|
H:DHE401
|
2.1
|
22.1
|
1.0
|
|
ND
|
H:DHE401
|
2.1
|
23.6
|
1.0
|
|
NB
|
H:DHE401
|
2.1
|
26.4
|
1.0
|
|
NE2
|
H:HIS238
|
2.1
|
34.8
|
1.0
|
|
CE1
|
H:HIS48
|
2.8
|
30.8
|
1.0
|
|
HE1
|
H:HIS48
|
2.9
|
37.1
|
1.0
|
|
CE1
|
H:HIS238
|
3.0
|
32.3
|
1.0
|
|
HE1
|
H:HIS238
|
3.0
|
38.9
|
1.0
|
|
C1D
|
H:DHE401
|
3.1
|
23.3
|
1.0
|
|
C4C
|
H:DHE401
|
3.1
|
22.6
|
1.0
|
|
C1A
|
H:DHE401
|
3.1
|
22.0
|
1.0
|
|
C1C
|
H:DHE401
|
3.1
|
24.2
|
1.0
|
|
C4B
|
H:DHE401
|
3.1
|
27.2
|
1.0
|
|
C4D
|
H:DHE401
|
3.1
|
24.2
|
1.0
|
|
C4A
|
H:DHE401
|
3.1
|
25.5
|
1.0
|
|
CD2
|
H:HIS48
|
3.1
|
29.6
|
1.0
|
|
C1B
|
H:DHE401
|
3.2
|
27.9
|
1.0
|
|
CD2
|
H:HIS238
|
3.3
|
30.9
|
1.0
|
|
HD2
|
H:HIS48
|
3.4
|
35.7
|
1.0
|
|
CHD
|
H:DHE401
|
3.5
|
23.2
|
1.0
|
|
CHA
|
H:DHE401
|
3.5
|
21.6
|
1.0
|
|
CHC
|
H:DHE401
|
3.5
|
25.9
|
1.0
|
|
HD2
|
H:HIS238
|
3.6
|
37.2
|
1.0
|
|
CHB
|
H:DHE401
|
3.6
|
27.9
|
1.0
|
|
ND1
|
H:HIS48
|
4.0
|
28.5
|
1.0
|
|
ND1
|
H:HIS238
|
4.1
|
31.2
|
1.0
|
|
CG
|
H:HIS48
|
4.2
|
26.0
|
1.0
|
|
CG
|
H:HIS238
|
4.3
|
29.4
|
1.0
|
|
C2C
|
H:DHE401
|
4.3
|
21.3
|
1.0
|
|
C2B
|
H:DHE401
|
4.4
|
27.5
|
1.0
|
|
C2A
|
H:DHE401
|
4.4
|
22.7
|
1.0
|
|
C2D
|
H:DHE401
|
4.4
|
24.7
|
1.0
|
|
C3A
|
H:DHE401
|
4.4
|
23.5
|
1.0
|
|
C3D
|
H:DHE401
|
4.4
|
25.7
|
1.0
|
|
C3C
|
H:DHE401
|
4.5
|
19.5
|
1.0
|
|
C3B
|
H:DHE401
|
4.5
|
26.8
|
1.0
|
|
HHD
|
H:DHE401
|
4.5
|
27.9
|
1.0
|
|
HHA
|
H:DHE401
|
4.6
|
26.1
|
1.0
|
|
HHC
|
H:DHE401
|
4.6
|
31.2
|
1.0
|
|
HHB
|
H:DHE401
|
4.7
|
33.7
|
1.0
|
|
HD1
|
H:HIS48
|
4.7
|
34.4
|
1.0
|
|
HGC2
|
H:DHE401
|
4.8
|
19.6
|
1.0
|
|
HD11
|
H:ILE90
|
4.8
|
31.8
|
1.0
|
|
O1C
|
H:DHE401
|
4.8
|
28.4
|
1.0
|
|
HD1
|
H:HIS238
|
4.9
|
37.6
|
1.0
|
|
O1B
|
H:DHE401
|
4.9
|
28.5
|
1.0
|
|
O
|
H:HOH616
|
4.9
|
33.0
|
1.0
|
|
HGB2
|
H:DHE401
|
4.9
|
31.2
|
1.0
|
|
Reference:
T.Klunemann,
M.Nimtz,
L.Jansch,
G.Layer,
W.Blankenfeldt.
Crystal Structure of Nirf: Insights Into Its Role in Heme D1BIOSYNTHESIS. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32255259
DOI: 10.1111/FEBS.15323
Page generated: Wed Aug 6 14:21:06 2025
|
