Iron in PDB 5d8o: 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Enzymatic activity of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
All present enzymatic activity of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa:
1.16.3.1;
Protein crystallography data
The structure of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa, PDB code: 5d8o
was solved by
S.Lovell,
K.P.Battaile,
Y.Wang,
H.Yao,
M.Rivera,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.09 /
1.90
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.017,
195.279,
203.351,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.3 /
19.2
|
Other elements in 5d8o:
The structure of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
(pdb code 5d8o). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the
1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa, PDB code: 5d8o:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
Iron binding site 1 out
of 7 in 5d8o
Go back to
Iron Binding Sites List in 5d8o
Iron binding site 1 out
of 7 in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe205
b:18.2
occ:1.00
|
FE
|
A:HEM205
|
0.0
|
18.2
|
1.0
|
NB
|
A:HEM205
|
2.0
|
14.5
|
1.0
|
NC
|
A:HEM205
|
2.0
|
19.0
|
1.0
|
NA
|
A:HEM205
|
2.0
|
17.4
|
1.0
|
ND
|
A:HEM205
|
2.1
|
19.1
|
1.0
|
SD
|
A:MET52
|
2.4
|
15.5
|
1.0
|
C4B
|
A:HEM205
|
3.0
|
15.9
|
1.0
|
C1C
|
A:HEM205
|
3.0
|
17.8
|
1.0
|
C1A
|
A:HEM205
|
3.0
|
15.3
|
1.0
|
C1B
|
A:HEM205
|
3.1
|
15.9
|
1.0
|
C4D
|
A:HEM205
|
3.1
|
19.4
|
1.0
|
C4A
|
A:HEM205
|
3.1
|
20.6
|
1.0
|
C1D
|
A:HEM205
|
3.1
|
17.0
|
1.0
|
C4C
|
A:HEM205
|
3.1
|
20.7
|
1.0
|
CE
|
A:MET52
|
3.3
|
14.5
|
1.0
|
CHC
|
A:HEM205
|
3.3
|
18.3
|
1.0
|
CHA
|
A:HEM205
|
3.4
|
17.2
|
1.0
|
CHB
|
A:HEM205
|
3.5
|
19.5
|
1.0
|
CHD
|
A:HEM205
|
3.5
|
18.2
|
1.0
|
CG
|
A:MET52
|
3.5
|
14.6
|
1.0
|
C3B
|
A:HEM205
|
4.2
|
19.2
|
1.0
|
CB
|
A:MET52
|
4.2
|
18.6
|
1.0
|
C2C
|
A:HEM205
|
4.2
|
19.5
|
1.0
|
C2B
|
A:HEM205
|
4.3
|
20.3
|
1.0
|
C2A
|
A:HEM205
|
4.3
|
19.7
|
1.0
|
C3C
|
A:HEM205
|
4.3
|
20.8
|
1.0
|
C3A
|
A:HEM205
|
4.3
|
20.9
|
1.0
|
C3D
|
A:HEM205
|
4.3
|
16.4
|
1.0
|
C2D
|
A:HEM205
|
4.3
|
17.0
|
1.0
|
|
Iron binding site 2 out
of 7 in 5d8o
Go back to
Iron Binding Sites List in 5d8o
Iron binding site 2 out
of 7 in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe203
b:15.5
occ:1.00
|
FE
|
B:HEM203
|
0.0
|
15.5
|
1.0
|
NA
|
B:HEM203
|
2.0
|
18.7
|
1.0
|
NC
|
B:HEM203
|
2.0
|
16.7
|
1.0
|
ND
|
B:HEM203
|
2.0
|
12.8
|
1.0
|
NB
|
B:HEM203
|
2.1
|
13.9
|
1.0
|
SD
|
E:MET52
|
2.3
|
13.9
|
1.0
|
SD
|
B:MET52
|
2.4
|
13.2
|
1.0
|
C4C
|
B:HEM203
|
3.0
|
14.7
|
1.0
|
C1D
|
B:HEM203
|
3.0
|
11.7
|
1.0
|
C4B
|
B:HEM203
|
3.0
|
12.7
|
1.0
|
C1A
|
B:HEM203
|
3.0
|
15.0
|
1.0
|
C4D
|
B:HEM203
|
3.1
|
15.3
|
1.0
|
C4A
|
B:HEM203
|
3.1
|
15.3
|
1.0
|
C1C
|
B:HEM203
|
3.1
|
16.2
|
1.0
|
C1B
|
B:HEM203
|
3.1
|
16.4
|
1.0
|
CE
|
E:MET52
|
3.3
|
15.4
|
1.0
|
CHD
|
B:HEM203
|
3.4
|
12.0
|
1.0
|
CE
|
B:MET52
|
3.4
|
14.7
|
1.0
|
CHC
|
B:HEM203
|
3.4
|
15.4
|
1.0
|
CHA
|
B:HEM203
|
3.4
|
16.5
|
1.0
|
CHB
|
B:HEM203
|
3.5
|
12.9
|
1.0
|
CG
|
E:MET52
|
3.5
|
11.2
|
1.0
|
CG
|
B:MET52
|
3.6
|
13.2
|
1.0
|
CB
|
B:MET52
|
4.2
|
12.8
|
1.0
|
CB
|
E:MET52
|
4.2
|
11.8
|
1.0
|
C3C
|
B:HEM203
|
4.2
|
18.9
|
1.0
|
C2D
|
B:HEM203
|
4.3
|
14.8
|
1.0
|
C2A
|
B:HEM203
|
4.3
|
18.7
|
1.0
|
C3D
|
B:HEM203
|
4.3
|
13.4
|
1.0
|
C3A
|
B:HEM203
|
4.3
|
18.0
|
1.0
|
C3B
|
B:HEM203
|
4.3
|
12.0
|
1.0
|
C2C
|
B:HEM203
|
4.3
|
13.2
|
1.0
|
C2B
|
B:HEM203
|
4.3
|
16.5
|
1.0
|
|
Iron binding site 3 out
of 7 in 5d8o
Go back to
Iron Binding Sites List in 5d8o
Iron binding site 3 out
of 7 in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe203
b:20.0
occ:0.50
|
FE
|
D:HEM203
|
0.0
|
20.0
|
0.5
|
NA
|
D:HEM203
|
2.0
|
20.2
|
0.5
|
NB
|
D:HEM203
|
2.0
|
18.9
|
0.5
|
ND
|
D:HEM203
|
2.1
|
20.2
|
0.5
|
NC
|
D:HEM203
|
2.1
|
17.8
|
0.5
|
SD
|
D:MET52
|
2.4
|
18.4
|
1.0
|
C1A
|
D:HEM203
|
3.0
|
19.6
|
0.5
|
C4D
|
D:HEM203
|
3.0
|
19.1
|
0.5
|
C4A
|
D:HEM203
|
3.0
|
19.5
|
0.5
|
C4B
|
D:HEM203
|
3.0
|
19.6
|
0.5
|
C1B
|
D:HEM203
|
3.1
|
17.4
|
0.5
|
C1C
|
D:HEM203
|
3.1
|
19.2
|
0.5
|
C1D
|
D:HEM203
|
3.1
|
18.9
|
0.5
|
CE
|
D:MET52
|
3.1
|
19.1
|
1.0
|
C4C
|
D:HEM203
|
3.2
|
18.9
|
0.5
|
CHA
|
D:HEM203
|
3.4
|
16.3
|
0.5
|
CHC
|
D:HEM203
|
3.4
|
20.6
|
0.5
|
CHB
|
D:HEM203
|
3.4
|
18.2
|
0.5
|
CHD
|
D:HEM203
|
3.5
|
17.3
|
0.5
|
CG
|
D:MET52
|
3.6
|
16.7
|
1.0
|
C2A
|
D:HEM203
|
4.2
|
19.8
|
0.5
|
C3A
|
D:HEM203
|
4.2
|
18.8
|
0.5
|
C3B
|
D:HEM203
|
4.3
|
18.4
|
0.5
|
C3D
|
D:HEM203
|
4.3
|
20.0
|
0.5
|
C2B
|
D:HEM203
|
4.3
|
17.9
|
0.5
|
C2D
|
D:HEM203
|
4.3
|
18.7
|
0.5
|
C2C
|
D:HEM203
|
4.3
|
17.6
|
0.5
|
C3C
|
D:HEM203
|
4.4
|
18.8
|
0.5
|
CB
|
D:MET52
|
4.4
|
18.5
|
1.0
|
|
Iron binding site 4 out
of 7 in 5d8o
Go back to
Iron Binding Sites List in 5d8o
Iron binding site 4 out
of 7 in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe203
b:16.7
occ:1.00
|
FE
|
F:HEM203
|
0.0
|
16.7
|
1.0
|
NC
|
F:HEM203
|
2.0
|
14.0
|
1.0
|
NB
|
F:HEM203
|
2.0
|
17.5
|
1.0
|
ND
|
F:HEM203
|
2.1
|
15.0
|
1.0
|
NA
|
F:HEM203
|
2.1
|
19.6
|
1.0
|
SD
|
F:MET52
|
2.3
|
15.4
|
1.0
|
SD
|
K:MET52
|
2.4
|
16.4
|
1.0
|
C1C
|
F:HEM203
|
3.0
|
17.2
|
1.0
|
C4B
|
F:HEM203
|
3.0
|
14.7
|
1.0
|
C4C
|
F:HEM203
|
3.1
|
19.2
|
1.0
|
C4D
|
F:HEM203
|
3.1
|
13.1
|
1.0
|
C4A
|
F:HEM203
|
3.1
|
16.6
|
1.0
|
C1B
|
F:HEM203
|
3.1
|
14.2
|
1.0
|
C1A
|
F:HEM203
|
3.1
|
19.4
|
1.0
|
C1D
|
F:HEM203
|
3.1
|
14.4
|
1.0
|
CE
|
F:MET52
|
3.2
|
13.0
|
1.0
|
CE
|
K:MET52
|
3.4
|
13.3
|
1.0
|
CHC
|
F:HEM203
|
3.4
|
16.1
|
1.0
|
CHA
|
F:HEM203
|
3.4
|
16.5
|
1.0
|
CHB
|
F:HEM203
|
3.4
|
14.4
|
1.0
|
CHD
|
F:HEM203
|
3.4
|
15.1
|
1.0
|
CG
|
K:MET52
|
3.5
|
13.9
|
1.0
|
CG
|
F:MET52
|
3.6
|
11.3
|
1.0
|
CB
|
F:MET52
|
4.2
|
15.0
|
1.0
|
CB
|
K:MET52
|
4.2
|
13.2
|
1.0
|
C2C
|
F:HEM203
|
4.3
|
16.6
|
1.0
|
C3C
|
F:HEM203
|
4.3
|
16.3
|
1.0
|
C3B
|
F:HEM203
|
4.3
|
19.2
|
1.0
|
C3D
|
F:HEM203
|
4.3
|
16.0
|
1.0
|
C3A
|
F:HEM203
|
4.3
|
16.4
|
1.0
|
C2A
|
F:HEM203
|
4.3
|
19.0
|
1.0
|
C2B
|
F:HEM203
|
4.3
|
20.6
|
1.0
|
C2D
|
F:HEM203
|
4.3
|
16.4
|
1.0
|
CD1
|
K:ILE49
|
5.0
|
22.9
|
1.0
|
|
Iron binding site 5 out
of 7 in 5d8o
Go back to
Iron Binding Sites List in 5d8o
Iron binding site 5 out
of 7 in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe202
b:17.8
occ:1.00
|
FE
|
I:HEM202
|
0.0
|
17.8
|
1.0
|
NB
|
I:HEM202
|
2.0
|
19.3
|
1.0
|
NC
|
I:HEM202
|
2.1
|
17.1
|
1.0
|
NA
|
I:HEM202
|
2.1
|
17.4
|
1.0
|
ND
|
I:HEM202
|
2.1
|
18.3
|
1.0
|
SD
|
I:MET52
|
2.4
|
15.2
|
1.0
|
SD
|
C:MET52
|
2.4
|
15.4
|
1.0
|
C4B
|
I:HEM202
|
3.0
|
19.4
|
1.0
|
C1C
|
I:HEM202
|
3.0
|
19.8
|
1.0
|
C1A
|
I:HEM202
|
3.1
|
22.1
|
1.0
|
C4D
|
I:HEM202
|
3.1
|
15.0
|
1.0
|
C1B
|
I:HEM202
|
3.1
|
19.9
|
1.0
|
C4A
|
I:HEM202
|
3.1
|
14.1
|
1.0
|
C4C
|
I:HEM202
|
3.1
|
17.1
|
1.0
|
C1D
|
I:HEM202
|
3.1
|
16.6
|
1.0
|
CHC
|
I:HEM202
|
3.4
|
16.8
|
1.0
|
CE
|
I:MET52
|
3.4
|
16.6
|
1.0
|
CHA
|
I:HEM202
|
3.4
|
20.8
|
1.0
|
CE
|
C:MET52
|
3.4
|
13.9
|
1.0
|
CHB
|
I:HEM202
|
3.5
|
16.9
|
1.0
|
CHD
|
I:HEM202
|
3.5
|
21.7
|
1.0
|
CG
|
I:MET52
|
3.5
|
14.5
|
1.0
|
CG
|
C:MET52
|
3.5
|
12.9
|
1.0
|
CB
|
I:MET52
|
4.2
|
13.8
|
1.0
|
CB
|
C:MET52
|
4.2
|
12.3
|
1.0
|
C3B
|
I:HEM202
|
4.2
|
19.5
|
1.0
|
C2A
|
I:HEM202
|
4.3
|
16.1
|
1.0
|
C2B
|
I:HEM202
|
4.3
|
18.4
|
1.0
|
C2C
|
I:HEM202
|
4.3
|
20.5
|
1.0
|
C3A
|
I:HEM202
|
4.3
|
18.8
|
1.0
|
C3D
|
I:HEM202
|
4.3
|
13.2
|
1.0
|
C3C
|
I:HEM202
|
4.3
|
22.1
|
1.0
|
C2D
|
I:HEM202
|
4.3
|
20.7
|
1.0
|
|
Iron binding site 6 out
of 7 in 5d8o
Go back to
Iron Binding Sites List in 5d8o
Iron binding site 6 out
of 7 in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe204
b:18.5
occ:1.00
|
FE
|
J:HEM204
|
0.0
|
18.5
|
1.0
|
ND
|
J:HEM204
|
2.1
|
16.9
|
1.0
|
NC
|
J:HEM204
|
2.1
|
16.3
|
1.0
|
NB
|
J:HEM204
|
2.1
|
17.7
|
1.0
|
NA
|
J:HEM204
|
2.1
|
19.6
|
1.0
|
SD
|
H:MET52
|
2.4
|
17.2
|
1.0
|
SD
|
J:MET52
|
2.4
|
17.0
|
1.0
|
C4B
|
J:HEM204
|
3.0
|
22.1
|
1.0
|
C1C
|
J:HEM204
|
3.0
|
21.1
|
1.0
|
C1A
|
J:HEM204
|
3.0
|
17.2
|
1.0
|
C4D
|
J:HEM204
|
3.0
|
18.6
|
1.0
|
C1D
|
J:HEM204
|
3.1
|
16.3
|
1.0
|
C4C
|
J:HEM204
|
3.1
|
14.7
|
1.0
|
C4A
|
J:HEM204
|
3.1
|
20.2
|
1.0
|
C1B
|
J:HEM204
|
3.1
|
22.3
|
1.0
|
CE
|
J:MET52
|
3.3
|
14.2
|
1.0
|
CHC
|
J:HEM204
|
3.4
|
19.9
|
1.0
|
CHA
|
J:HEM204
|
3.4
|
14.2
|
1.0
|
CE
|
H:MET52
|
3.4
|
16.1
|
1.0
|
CHD
|
J:HEM204
|
3.5
|
14.7
|
1.0
|
CG
|
J:MET52
|
3.5
|
16.8
|
1.0
|
CHB
|
J:HEM204
|
3.5
|
15.2
|
1.0
|
CG
|
H:MET52
|
3.5
|
19.8
|
1.0
|
CB
|
J:MET52
|
4.2
|
12.7
|
1.0
|
CB
|
H:MET52
|
4.2
|
16.1
|
1.0
|
C3B
|
J:HEM204
|
4.3
|
20.7
|
1.0
|
C2A
|
J:HEM204
|
4.3
|
19.2
|
1.0
|
C3D
|
J:HEM204
|
4.3
|
15.8
|
1.0
|
C2D
|
J:HEM204
|
4.3
|
18.9
|
1.0
|
C2C
|
J:HEM204
|
4.3
|
20.4
|
1.0
|
C3A
|
J:HEM204
|
4.3
|
21.8
|
1.0
|
C2B
|
J:HEM204
|
4.3
|
21.8
|
1.0
|
C3C
|
J:HEM204
|
4.3
|
18.4
|
1.0
|
|
Iron binding site 7 out
of 7 in 5d8o
Go back to
Iron Binding Sites List in 5d8o
Iron binding site 7 out
of 7 in the 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of 1.90A Resolution Structure of Bfrb (Wild-Type, C2221 Form) From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe203
b:19.3
occ:0.50
|
FE
|
L:HEM203
|
0.0
|
19.3
|
0.5
|
NA
|
L:HEM203
|
2.0
|
19.9
|
0.5
|
NB
|
L:HEM203
|
2.0
|
16.7
|
0.5
|
ND
|
L:HEM203
|
2.0
|
19.8
|
0.5
|
NC
|
L:HEM203
|
2.1
|
16.9
|
0.5
|
SD
|
L:MET52
|
2.4
|
16.1
|
1.0
|
C1A
|
L:HEM203
|
3.0
|
21.0
|
0.5
|
C4A
|
L:HEM203
|
3.0
|
18.9
|
0.5
|
C1B
|
L:HEM203
|
3.0
|
17.7
|
0.5
|
C4D
|
L:HEM203
|
3.0
|
20.8
|
0.5
|
C1D
|
L:HEM203
|
3.1
|
18.9
|
0.5
|
C4B
|
L:HEM203
|
3.1
|
18.2
|
0.5
|
C1C
|
L:HEM203
|
3.1
|
18.3
|
0.5
|
C4C
|
L:HEM203
|
3.1
|
17.9
|
0.5
|
CE
|
L:MET52
|
3.3
|
16.0
|
1.0
|
CHB
|
L:HEM203
|
3.4
|
18.9
|
0.5
|
CHA
|
L:HEM203
|
3.4
|
17.5
|
0.5
|
CHD
|
L:HEM203
|
3.5
|
18.6
|
0.5
|
CHC
|
L:HEM203
|
3.5
|
19.2
|
0.5
|
CG
|
L:MET52
|
3.6
|
16.0
|
1.0
|
C2A
|
L:HEM203
|
4.2
|
19.5
|
0.5
|
C3A
|
L:HEM203
|
4.2
|
19.6
|
0.5
|
C3D
|
L:HEM203
|
4.3
|
19.4
|
0.5
|
C2B
|
L:HEM203
|
4.3
|
19.4
|
0.5
|
C2D
|
L:HEM203
|
4.3
|
19.4
|
0.5
|
CB
|
L:MET52
|
4.3
|
14.0
|
1.0
|
C3B
|
L:HEM203
|
4.3
|
18.3
|
0.5
|
C2C
|
L:HEM203
|
4.3
|
19.3
|
0.5
|
C3C
|
L:HEM203
|
4.3
|
19.2
|
0.5
|
|
Reference:
Y.Wang,
H.Yao,
Y.Cheng,
S.Lovell,
K.P.Battaile,
C.R.Midaugh,
M.Rivera.
Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots. Biochemistry V. 54 6162 2015.
ISSN: ISSN 0006-2960
PubMed: 26368531
DOI: 10.1021/ACS.BIOCHEM.5B00937
Page generated: Mon Aug 5 21:48:32 2024
|