Iron in PDB 2bc5: Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages
Protein crystallography data
The structure of Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages, PDB code: 2bc5
was solved by
J.Faraone-Mennella,
F.A.Tezcan,
H.B.Gray,
J.R.Winkler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.40 /
2.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.861,
68.158,
90.440,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.9 /
27.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages
(pdb code 2bc5). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages, PDB code: 2bc5:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2bc5
Go back to
Iron Binding Sites List in 2bc5
Iron binding site 1 out
of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages
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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:23.6
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
23.6
|
1.0
|
ND
|
A:HEM150
|
2.0
|
25.5
|
1.0
|
NC
|
A:HEM150
|
2.0
|
23.9
|
1.0
|
NE2
|
A:HIS102
|
2.0
|
28.9
|
1.0
|
NB
|
A:HEM150
|
2.0
|
17.5
|
1.0
|
NA
|
A:HEM150
|
2.1
|
24.4
|
1.0
|
SD
|
A:MET7
|
2.4
|
28.4
|
1.0
|
CD2
|
A:HIS102
|
2.9
|
27.5
|
1.0
|
C1C
|
A:HEM150
|
3.0
|
22.3
|
1.0
|
C4B
|
A:HEM150
|
3.0
|
20.3
|
1.0
|
C4D
|
A:HEM150
|
3.0
|
28.2
|
1.0
|
C1D
|
A:HEM150
|
3.0
|
26.5
|
1.0
|
C4C
|
A:HEM150
|
3.0
|
25.4
|
1.0
|
C1A
|
A:HEM150
|
3.1
|
25.9
|
1.0
|
CE1
|
A:HIS102
|
3.1
|
30.7
|
1.0
|
C1B
|
A:HEM150
|
3.2
|
20.9
|
1.0
|
C4A
|
A:HEM150
|
3.2
|
21.6
|
1.0
|
CHC
|
A:HEM150
|
3.3
|
21.3
|
1.0
|
CHA
|
A:HEM150
|
3.4
|
26.6
|
1.0
|
CHD
|
A:HEM150
|
3.4
|
23.3
|
1.0
|
CE
|
A:MET7
|
3.5
|
20.1
|
1.0
|
CHB
|
A:HEM150
|
3.6
|
18.4
|
1.0
|
CG
|
A:MET7
|
3.6
|
26.2
|
1.0
|
CG
|
A:HIS102
|
4.1
|
26.2
|
1.0
|
ND1
|
A:HIS102
|
4.2
|
29.4
|
1.0
|
C2C
|
A:HEM150
|
4.2
|
22.2
|
1.0
|
C3C
|
A:HEM150
|
4.2
|
22.7
|
1.0
|
C3D
|
A:HEM150
|
4.3
|
31.5
|
1.0
|
C2D
|
A:HEM150
|
4.3
|
25.6
|
1.0
|
C3B
|
A:HEM150
|
4.3
|
18.9
|
1.0
|
C2A
|
A:HEM150
|
4.4
|
31.4
|
1.0
|
C2B
|
A:HEM150
|
4.4
|
20.9
|
1.0
|
CB
|
A:MET7
|
4.4
|
28.7
|
1.0
|
C3A
|
A:HEM150
|
4.4
|
27.2
|
1.0
|
NH1
|
A:ARG106
|
5.0
|
40.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 2bc5
Go back to
Iron Binding Sites List in 2bc5
Iron binding site 2 out
of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages
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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:20.7
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
20.7
|
1.0
|
ND
|
B:HEM150
|
2.0
|
18.0
|
1.0
|
NE2
|
B:HIS102
|
2.0
|
20.2
|
1.0
|
NB
|
B:HEM150
|
2.0
|
16.2
|
1.0
|
NC
|
B:HEM150
|
2.1
|
14.1
|
1.0
|
NA
|
B:HEM150
|
2.1
|
19.5
|
1.0
|
SD
|
B:MET7
|
2.4
|
31.6
|
1.0
|
CD2
|
B:HIS102
|
3.0
|
18.2
|
1.0
|
C4D
|
B:HEM150
|
3.0
|
24.4
|
1.0
|
C1D
|
B:HEM150
|
3.0
|
22.8
|
1.0
|
C1A
|
B:HEM150
|
3.0
|
25.1
|
1.0
|
C4B
|
B:HEM150
|
3.0
|
18.1
|
1.0
|
CE1
|
B:HIS102
|
3.0
|
19.2
|
1.0
|
C1C
|
B:HEM150
|
3.0
|
12.8
|
1.0
|
C4C
|
B:HEM150
|
3.1
|
17.4
|
1.0
|
C1B
|
B:HEM150
|
3.1
|
22.8
|
1.0
|
C4A
|
B:HEM150
|
3.1
|
21.8
|
1.0
|
CHA
|
B:HEM150
|
3.3
|
17.4
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
16.3
|
1.0
|
CHD
|
B:HEM150
|
3.4
|
19.2
|
1.0
|
CHB
|
B:HEM150
|
3.5
|
20.3
|
1.0
|
CG
|
B:MET7
|
3.5
|
31.6
|
1.0
|
CE
|
B:MET7
|
3.6
|
35.6
|
1.0
|
CG
|
B:HIS102
|
4.1
|
19.1
|
1.0
|
ND1
|
B:HIS102
|
4.1
|
17.6
|
1.0
|
C3D
|
B:HEM150
|
4.2
|
23.1
|
1.0
|
C2D
|
B:HEM150
|
4.2
|
22.1
|
1.0
|
C3B
|
B:HEM150
|
4.3
|
13.7
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
16.1
|
1.0
|
C2A
|
B:HEM150
|
4.3
|
27.9
|
1.0
|
C3C
|
B:HEM150
|
4.3
|
13.7
|
1.0
|
CB
|
B:MET7
|
4.3
|
26.4
|
1.0
|
C2B
|
B:HEM150
|
4.3
|
18.5
|
1.0
|
C3A
|
B:HEM150
|
4.4
|
26.2
|
1.0
|
NH1
|
B:ARG106
|
4.8
|
39.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 2bc5
Go back to
Iron Binding Sites List in 2bc5
Iron binding site 3 out
of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages
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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:18.6
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
18.6
|
1.0
|
ND
|
C:HEM150
|
2.0
|
16.7
|
1.0
|
NE2
|
C:HIS102
|
2.0
|
22.5
|
1.0
|
NB
|
C:HEM150
|
2.0
|
17.1
|
1.0
|
NC
|
C:HEM150
|
2.1
|
15.0
|
1.0
|
NA
|
C:HEM150
|
2.1
|
23.4
|
1.0
|
SD
|
C:MET7
|
2.4
|
16.8
|
1.0
|
CD2
|
C:HIS102
|
2.9
|
16.3
|
1.0
|
C4D
|
C:HEM150
|
3.0
|
22.9
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
17.8
|
1.0
|
C4B
|
C:HEM150
|
3.0
|
18.2
|
1.0
|
C1D
|
C:HEM150
|
3.0
|
18.6
|
1.0
|
C1C
|
C:HEM150
|
3.0
|
16.3
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
18.3
|
1.0
|
C1A
|
C:HEM150
|
3.1
|
25.6
|
1.0
|
C4C
|
C:HEM150
|
3.1
|
17.3
|
1.0
|
C4A
|
C:HEM150
|
3.1
|
22.7
|
1.0
|
CHC
|
C:HEM150
|
3.3
|
17.1
|
1.0
|
CHA
|
C:HEM150
|
3.4
|
19.9
|
1.0
|
CHD
|
C:HEM150
|
3.4
|
14.7
|
1.0
|
CHB
|
C:HEM150
|
3.4
|
21.1
|
1.0
|
CE
|
C:MET7
|
3.5
|
23.5
|
1.0
|
CG
|
C:MET7
|
3.6
|
24.3
|
1.0
|
ND1
|
C:HIS102
|
4.1
|
20.5
|
1.0
|
CG
|
C:HIS102
|
4.1
|
16.0
|
1.0
|
C3D
|
C:HEM150
|
4.2
|
23.1
|
1.0
|
C2D
|
C:HEM150
|
4.3
|
18.1
|
1.0
|
C3B
|
C:HEM150
|
4.3
|
16.4
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
18.1
|
1.0
|
C2C
|
C:HEM150
|
4.3
|
17.3
|
1.0
|
C3C
|
C:HEM150
|
4.3
|
11.6
|
1.0
|
C2A
|
C:HEM150
|
4.4
|
28.9
|
1.0
|
C3A
|
C:HEM150
|
4.4
|
25.5
|
1.0
|
CB
|
C:MET7
|
4.4
|
22.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 2bc5
Go back to
Iron Binding Sites List in 2bc5
Iron binding site 4 out
of 4 in the Crystal Structure of E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages
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 E. Coli Cytochrome B562 with Engineered C-Type Heme Linkages within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:29.4
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
29.4
|
1.0
|
NA
|
D:HEM150
|
2.0
|
30.6
|
1.0
|
NE2
|
D:HIS102
|
2.0
|
33.6
|
1.0
|
ND
|
D:HEM150
|
2.0
|
31.2
|
1.0
|
NB
|
D:HEM150
|
2.0
|
25.9
|
1.0
|
NC
|
D:HEM150
|
2.1
|
24.3
|
1.0
|
SD
|
D:MET7
|
2.2
|
29.6
|
1.0
|
C1A
|
D:HEM150
|
3.0
|
32.8
|
1.0
|
CE1
|
D:HIS102
|
3.0
|
33.5
|
1.0
|
C4D
|
D:HEM150
|
3.0
|
33.3
|
1.0
|
CD2
|
D:HIS102
|
3.0
|
34.4
|
1.0
|
C4B
|
D:HEM150
|
3.0
|
26.5
|
1.0
|
C1C
|
D:HEM150
|
3.0
|
21.5
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
30.5
|
1.0
|
C1D
|
D:HEM150
|
3.1
|
32.6
|
1.0
|
C1B
|
D:HEM150
|
3.1
|
28.6
|
1.0
|
C4C
|
D:HEM150
|
3.1
|
27.7
|
1.0
|
CHA
|
D:HEM150
|
3.3
|
32.1
|
1.0
|
CHC
|
D:HEM150
|
3.3
|
23.6
|
1.0
|
CG
|
D:MET7
|
3.5
|
25.6
|
1.0
|
CHB
|
D:HEM150
|
3.5
|
28.1
|
1.0
|
CHD
|
D:HEM150
|
3.5
|
28.6
|
1.0
|
CE
|
D:MET7
|
3.5
|
25.5
|
1.0
|
ND1
|
D:HIS102
|
4.1
|
35.0
|
1.0
|
CG
|
D:HIS102
|
4.1
|
33.6
|
1.0
|
C2A
|
D:HEM150
|
4.2
|
37.3
|
1.0
|
C3D
|
D:HEM150
|
4.2
|
36.2
|
1.0
|
CB
|
D:MET7
|
4.3
|
26.8
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
36.5
|
1.0
|
C2D
|
D:HEM150
|
4.3
|
32.2
|
1.0
|
C3B
|
D:HEM150
|
4.3
|
25.8
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
23.8
|
1.0
|
C2B
|
D:HEM150
|
4.3
|
26.8
|
1.0
|
C3C
|
D:HEM150
|
4.4
|
25.1
|
1.0
|
NH1
|
D:ARG106
|
5.0
|
46.1
|
1.0
|
|
Reference:
J.Faraone-Mennella,
F.A.Tezcan,
H.B.Gray,
J.R.Winkler.
Stability and Folding Kinetics of Structurally Characterized Cytochrome C-B(562). Biochemistry V. 45 10504 2006.
ISSN: ISSN 0006-2960
PubMed: 16939202
DOI: 10.1021/BI060242X
Page generated: Sat Aug 3 19:32:57 2024
|