Iron in PDB 3nmi: Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
Protein crystallography data
The structure of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmi
was solved by
R.J.Radford,
F.A.Tezcan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.05 /
2.01
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.290,
91.787,
130.637,
90.00,
107.99,
90.00
|
R / Rfree (%)
|
19.8 /
23.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
(pdb code 3nmi). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmi:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3nmi
Go back to
Iron Binding Sites List in 3nmi
Iron binding site 1 out
of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:13.0
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
13.0
|
1.0
|
NE2
|
A:HIS102
|
1.9
|
12.8
|
1.0
|
NC
|
A:HEM150
|
2.0
|
12.1
|
1.0
|
NB
|
A:HEM150
|
2.0
|
8.5
|
1.0
|
NA
|
A:HEM150
|
2.0
|
13.2
|
1.0
|
ND
|
A:HEM150
|
2.0
|
12.0
|
1.0
|
SD
|
A:MET7
|
2.3
|
13.2
|
1.0
|
CD2
|
A:HIS102
|
2.9
|
8.4
|
1.0
|
CE1
|
A:HIS102
|
2.9
|
14.0
|
1.0
|
C4B
|
A:HEM150
|
3.0
|
6.8
|
1.0
|
C1A
|
A:HEM150
|
3.0
|
12.4
|
1.0
|
C1B
|
A:HEM150
|
3.0
|
9.1
|
1.0
|
C4D
|
A:HEM150
|
3.0
|
10.4
|
1.0
|
C4C
|
A:HEM150
|
3.0
|
15.1
|
1.0
|
C1C
|
A:HEM150
|
3.1
|
11.6
|
1.0
|
C4A
|
A:HEM150
|
3.1
|
14.6
|
1.0
|
C1D
|
A:HEM150
|
3.1
|
8.4
|
1.0
|
CHA
|
A:HEM150
|
3.4
|
11.9
|
1.0
|
CG
|
A:MET7
|
3.4
|
9.9
|
1.0
|
CHB
|
A:HEM150
|
3.4
|
13.6
|
1.0
|
CHC
|
A:HEM150
|
3.4
|
7.9
|
1.0
|
CE
|
A:MET7
|
3.4
|
7.0
|
1.0
|
CHD
|
A:HEM150
|
3.4
|
7.6
|
1.0
|
ND1
|
A:HIS102
|
4.0
|
13.6
|
1.0
|
CG
|
A:HIS102
|
4.0
|
12.1
|
1.0
|
CB
|
A:MET7
|
4.2
|
9.8
|
1.0
|
C2A
|
A:HEM150
|
4.2
|
16.0
|
1.0
|
C3B
|
A:HEM150
|
4.2
|
12.8
|
1.0
|
C2B
|
A:HEM150
|
4.3
|
10.7
|
1.0
|
C3C
|
A:HEM150
|
4.3
|
8.0
|
1.0
|
C2C
|
A:HEM150
|
4.3
|
13.9
|
1.0
|
C3A
|
A:HEM150
|
4.3
|
16.3
|
1.0
|
C3D
|
A:HEM150
|
4.3
|
10.7
|
1.0
|
C2D
|
A:HEM150
|
4.3
|
12.1
|
1.0
|
CA
|
A:MET7
|
5.0
|
14.3
|
1.0
|
NH2
|
A:ARG106
|
5.0
|
28.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 3nmi
Go back to
Iron Binding Sites List in 3nmi
Iron binding site 2 out
of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:13.9
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
13.9
|
1.0
|
NE2
|
B:HIS102
|
1.9
|
12.0
|
1.0
|
NC
|
B:HEM150
|
2.0
|
12.4
|
1.0
|
ND
|
B:HEM150
|
2.0
|
12.4
|
1.0
|
NA
|
B:HEM150
|
2.1
|
13.5
|
1.0
|
NB
|
B:HEM150
|
2.1
|
9.8
|
1.0
|
SD
|
B:MET7
|
2.3
|
14.8
|
1.0
|
CE1
|
B:HIS102
|
2.9
|
11.5
|
1.0
|
CD2
|
B:HIS102
|
2.9
|
7.1
|
1.0
|
C4C
|
B:HEM150
|
3.0
|
11.2
|
1.0
|
C1C
|
B:HEM150
|
3.0
|
12.0
|
1.0
|
C1D
|
B:HEM150
|
3.0
|
15.2
|
1.0
|
C4D
|
B:HEM150
|
3.1
|
11.9
|
1.0
|
C4B
|
B:HEM150
|
3.1
|
11.5
|
1.0
|
C1A
|
B:HEM150
|
3.1
|
15.1
|
1.0
|
C1B
|
B:HEM150
|
3.1
|
11.5
|
1.0
|
C4A
|
B:HEM150
|
3.1
|
13.3
|
1.0
|
CE
|
B:MET7
|
3.4
|
13.1
|
1.0
|
CHD
|
B:HEM150
|
3.4
|
9.6
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
9.0
|
1.0
|
CHA
|
B:HEM150
|
3.4
|
11.2
|
1.0
|
CG
|
B:MET7
|
3.5
|
10.7
|
1.0
|
CHB
|
B:HEM150
|
3.5
|
14.4
|
1.0
|
ND1
|
B:HIS102
|
4.0
|
12.2
|
1.0
|
CG
|
B:HIS102
|
4.1
|
13.6
|
1.0
|
CB
|
B:MET7
|
4.2
|
14.2
|
1.0
|
C3C
|
B:HEM150
|
4.2
|
7.6
|
1.0
|
C2C
|
B:HEM150
|
4.2
|
10.3
|
1.0
|
C3D
|
B:HEM150
|
4.3
|
8.0
|
1.0
|
C2D
|
B:HEM150
|
4.3
|
10.8
|
1.0
|
C2B
|
B:HEM150
|
4.3
|
8.7
|
1.0
|
C2A
|
B:HEM150
|
4.3
|
16.2
|
1.0
|
C3B
|
B:HEM150
|
4.3
|
11.8
|
1.0
|
C3A
|
B:HEM150
|
4.3
|
13.7
|
1.0
|
NH1
|
B:ARG106
|
5.0
|
31.7
|
0.5
|
|
Iron binding site 3 out
of 6 in 3nmi
Go back to
Iron Binding Sites List in 3nmi
Iron binding site 3 out
of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:20.7
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
20.7
|
1.0
|
NE2
|
C:HIS102
|
1.9
|
18.1
|
1.0
|
NA
|
C:HEM150
|
2.0
|
23.3
|
1.0
|
ND
|
C:HEM150
|
2.0
|
16.4
|
1.0
|
NB
|
C:HEM150
|
2.0
|
18.9
|
1.0
|
NC
|
C:HEM150
|
2.1
|
20.2
|
1.0
|
SD
|
C:MET7
|
2.3
|
24.2
|
1.0
|
CE1
|
C:HIS102
|
2.8
|
14.7
|
1.0
|
CD2
|
C:HIS102
|
3.0
|
15.9
|
1.0
|
C1A
|
C:HEM150
|
3.0
|
25.2
|
1.0
|
C4D
|
C:HEM150
|
3.0
|
25.4
|
1.0
|
C4A
|
C:HEM150
|
3.1
|
29.7
|
1.0
|
C1C
|
C:HEM150
|
3.1
|
20.1
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
23.9
|
1.0
|
C1D
|
C:HEM150
|
3.1
|
23.0
|
1.0
|
C4B
|
C:HEM150
|
3.1
|
20.9
|
1.0
|
C4C
|
C:HEM150
|
3.1
|
18.3
|
1.0
|
CE
|
C:MET7
|
3.4
|
23.2
|
1.0
|
CHA
|
C:HEM150
|
3.4
|
21.4
|
1.0
|
CG
|
C:MET7
|
3.4
|
25.0
|
1.0
|
CHB
|
C:HEM150
|
3.4
|
23.8
|
1.0
|
CHC
|
C:HEM150
|
3.5
|
19.4
|
1.0
|
CHD
|
C:HEM150
|
3.5
|
17.0
|
1.0
|
ND1
|
C:HIS102
|
3.9
|
20.3
|
1.0
|
CG
|
C:HIS102
|
4.1
|
19.8
|
1.0
|
CB
|
C:MET7
|
4.2
|
23.3
|
1.0
|
NH2
|
C:ARG106
|
4.2
|
54.0
|
1.0
|
C2A
|
C:HEM150
|
4.3
|
27.2
|
1.0
|
C3A
|
C:HEM150
|
4.3
|
26.0
|
1.0
|
C3D
|
C:HEM150
|
4.3
|
18.8
|
1.0
|
C2C
|
C:HEM150
|
4.3
|
18.4
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
24.8
|
1.0
|
C2D
|
C:HEM150
|
4.3
|
19.9
|
1.0
|
C3B
|
C:HEM150
|
4.3
|
25.1
|
1.0
|
C3C
|
C:HEM150
|
4.3
|
16.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 3nmi
Go back to
Iron Binding Sites List in 3nmi
Iron binding site 4 out
of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:22.0
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
22.0
|
1.0
|
NE2
|
D:HIS102
|
1.9
|
23.0
|
1.0
|
NB
|
D:HEM150
|
2.0
|
17.2
|
1.0
|
NC
|
D:HEM150
|
2.0
|
18.7
|
1.0
|
NA
|
D:HEM150
|
2.0
|
20.8
|
1.0
|
ND
|
D:HEM150
|
2.1
|
21.1
|
1.0
|
SD
|
D:MET7
|
2.3
|
25.5
|
1.0
|
CE1
|
D:HIS102
|
2.8
|
23.6
|
1.0
|
CD2
|
D:HIS102
|
2.9
|
22.1
|
1.0
|
C4B
|
D:HEM150
|
3.0
|
19.3
|
1.0
|
C1C
|
D:HEM150
|
3.0
|
18.1
|
1.0
|
C1B
|
D:HEM150
|
3.0
|
18.9
|
1.0
|
C4C
|
D:HEM150
|
3.0
|
20.5
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
21.1
|
1.0
|
C1A
|
D:HEM150
|
3.1
|
25.8
|
1.0
|
C1D
|
D:HEM150
|
3.1
|
18.1
|
1.0
|
C4D
|
D:HEM150
|
3.1
|
20.9
|
1.0
|
CE
|
D:MET7
|
3.3
|
20.8
|
1.0
|
CG
|
D:MET7
|
3.3
|
18.6
|
1.0
|
CHC
|
D:HEM150
|
3.4
|
17.1
|
1.0
|
CHB
|
D:HEM150
|
3.4
|
18.8
|
1.0
|
CHD
|
D:HEM150
|
3.4
|
22.3
|
1.0
|
CHA
|
D:HEM150
|
3.5
|
24.0
|
1.0
|
ND1
|
D:HIS102
|
4.0
|
23.6
|
1.0
|
CG
|
D:HIS102
|
4.1
|
23.0
|
1.0
|
CB
|
D:MET7
|
4.2
|
23.2
|
1.0
|
C3B
|
D:HEM150
|
4.2
|
17.1
|
1.0
|
C2B
|
D:HEM150
|
4.2
|
18.4
|
1.0
|
C2C
|
D:HEM150
|
4.2
|
19.0
|
1.0
|
C3C
|
D:HEM150
|
4.2
|
18.1
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
18.4
|
1.0
|
C2A
|
D:HEM150
|
4.3
|
22.7
|
1.0
|
C2D
|
D:HEM150
|
4.3
|
20.5
|
1.0
|
C3D
|
D:HEM150
|
4.3
|
19.4
|
1.0
|
CA
|
D:MET7
|
5.0
|
22.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 3nmi
Go back to
Iron Binding Sites List in 3nmi
Iron binding site 5 out
of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe150
b:23.0
occ:1.00
|
FE
|
E:HEM150
|
0.0
|
23.0
|
1.0
|
NE2
|
E:HIS102
|
1.9
|
23.9
|
1.0
|
NB
|
E:HEM150
|
2.0
|
16.9
|
1.0
|
NA
|
E:HEM150
|
2.0
|
19.9
|
1.0
|
ND
|
E:HEM150
|
2.0
|
19.0
|
1.0
|
NC
|
E:HEM150
|
2.0
|
22.2
|
1.0
|
SD
|
E:MET7
|
2.3
|
22.5
|
1.0
|
CE1
|
E:HIS102
|
2.8
|
18.3
|
1.0
|
CD2
|
E:HIS102
|
2.9
|
18.6
|
1.0
|
C1B
|
E:HEM150
|
3.0
|
20.8
|
1.0
|
C1D
|
E:HEM150
|
3.0
|
20.8
|
1.0
|
C4B
|
E:HEM150
|
3.0
|
21.0
|
1.0
|
C4C
|
E:HEM150
|
3.0
|
21.2
|
1.0
|
C4A
|
E:HEM150
|
3.0
|
23.5
|
1.0
|
C1A
|
E:HEM150
|
3.0
|
23.2
|
1.0
|
C4D
|
E:HEM150
|
3.1
|
22.1
|
1.0
|
C1C
|
E:HEM150
|
3.1
|
22.1
|
1.0
|
CE
|
E:MET7
|
3.4
|
24.6
|
1.0
|
CHD
|
E:HEM150
|
3.4
|
21.6
|
1.0
|
CG
|
E:MET7
|
3.4
|
21.2
|
1.0
|
CHB
|
E:HEM150
|
3.4
|
21.6
|
1.0
|
CHA
|
E:HEM150
|
3.4
|
21.2
|
1.0
|
CHC
|
E:HEM150
|
3.5
|
23.6
|
1.0
|
ND1
|
E:HIS102
|
4.0
|
21.4
|
1.0
|
CG
|
E:HIS102
|
4.0
|
20.7
|
1.0
|
CB
|
E:MET7
|
4.2
|
20.3
|
1.0
|
C2B
|
E:HEM150
|
4.2
|
18.4
|
1.0
|
C3B
|
E:HEM150
|
4.2
|
17.4
|
1.0
|
C2A
|
E:HEM150
|
4.3
|
23.4
|
1.0
|
C3A
|
E:HEM150
|
4.3
|
24.4
|
1.0
|
C3C
|
E:HEM150
|
4.3
|
18.2
|
1.0
|
C2D
|
E:HEM150
|
4.3
|
22.8
|
1.0
|
C3D
|
E:HEM150
|
4.3
|
22.3
|
1.0
|
C2C
|
E:HEM150
|
4.3
|
18.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 3nmi
Go back to
Iron Binding Sites List in 3nmi
Iron binding site 6 out
of 6 in the Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of the Phenanthroline-Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe150
b:21.8
occ:1.00
|
FE
|
F:HEM150
|
0.0
|
21.8
|
1.0
|
NE2
|
F:HIS102
|
1.9
|
20.9
|
1.0
|
NB
|
F:HEM150
|
2.0
|
21.3
|
1.0
|
ND
|
F:HEM150
|
2.0
|
16.7
|
1.0
|
NA
|
F:HEM150
|
2.0
|
23.2
|
1.0
|
NC
|
F:HEM150
|
2.1
|
19.6
|
1.0
|
SD
|
F:MET7
|
2.3
|
27.0
|
1.0
|
CE1
|
F:HIS102
|
2.7
|
27.0
|
1.0
|
CD2
|
F:HIS102
|
3.0
|
17.0
|
1.0
|
C1B
|
F:HEM150
|
3.0
|
25.6
|
1.0
|
C4B
|
F:HEM150
|
3.0
|
23.2
|
1.0
|
C4A
|
F:HEM150
|
3.0
|
24.2
|
1.0
|
C1D
|
F:HEM150
|
3.1
|
23.4
|
1.0
|
C1A
|
F:HEM150
|
3.1
|
29.4
|
1.0
|
C4D
|
F:HEM150
|
3.1
|
26.6
|
1.0
|
C1C
|
F:HEM150
|
3.1
|
21.0
|
1.0
|
C4C
|
F:HEM150
|
3.1
|
20.4
|
1.0
|
CG
|
F:MET7
|
3.4
|
25.5
|
1.0
|
CE
|
F:MET7
|
3.4
|
24.3
|
1.0
|
CHB
|
F:HEM150
|
3.4
|
26.5
|
1.0
|
CHC
|
F:HEM150
|
3.4
|
21.8
|
1.0
|
CHD
|
F:HEM150
|
3.4
|
15.6
|
1.0
|
CHA
|
F:HEM150
|
3.5
|
23.1
|
1.0
|
ND1
|
F:HIS102
|
3.9
|
23.6
|
1.0
|
CG
|
F:HIS102
|
4.1
|
21.9
|
1.0
|
CB
|
F:MET7
|
4.2
|
27.4
|
1.0
|
C2B
|
F:HEM150
|
4.2
|
27.8
|
1.0
|
C3B
|
F:HEM150
|
4.3
|
27.9
|
1.0
|
C3A
|
F:HEM150
|
4.3
|
27.9
|
1.0
|
C2A
|
F:HEM150
|
4.3
|
24.9
|
1.0
|
C2D
|
F:HEM150
|
4.3
|
18.1
|
1.0
|
C3D
|
F:HEM150
|
4.3
|
20.7
|
1.0
|
C2C
|
F:HEM150
|
4.3
|
20.1
|
1.0
|
C3C
|
F:HEM150
|
4.3
|
17.0
|
1.0
|
NH2
|
F:ARG106
|
4.8
|
52.2
|
1.0
|
|
Reference:
R.J.Radford,
M.Lawrenz,
P.C.Nguyen,
J.A.Mccammon,
F.A.Tezcan.
Porous Protein Frameworks with Unsaturated Metal Centers in Sterically Encumbered Coordination Sites. Chem.Commun.(Camb.) V. 47 313 2011.
ISSN: ISSN 1359-7345
PubMed: 20740227
DOI: 10.1039/C0CC02168G
Page generated: Sun Aug 4 16:32:54 2024
|