Iron in PDB 3tom: Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets
Protein crystallography data
The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets, PDB code: 3tom
was solved by
J.B.Brodin,
F.A.Tezcan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.80 /
2.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.690,
37.843,
138.489,
90.00,
112.61,
90.00
|
R / Rfree (%)
|
21 /
28.6
|
Other elements in 3tom:
The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets
(pdb code 3tom). 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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets, PDB code: 3tom:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3tom
Go back to
Iron Binding Sites List in 3tom
Iron binding site 1 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets
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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:22.6
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
22.6
|
1.0
|
NE2
|
A:HIS102
|
2.0
|
23.2
|
1.0
|
NC
|
A:HEM150
|
2.0
|
20.8
|
1.0
|
NB
|
A:HEM150
|
2.0
|
18.0
|
1.0
|
ND
|
A:HEM150
|
2.1
|
20.8
|
1.0
|
NA
|
A:HEM150
|
2.1
|
23.0
|
1.0
|
SD
|
A:MET7
|
2.4
|
21.4
|
1.0
|
CE1
|
A:HIS102
|
2.9
|
26.1
|
1.0
|
C1C
|
A:HEM150
|
3.0
|
22.4
|
1.0
|
CD2
|
A:HIS102
|
3.0
|
25.9
|
1.0
|
C4B
|
A:HEM150
|
3.0
|
20.3
|
1.0
|
C4C
|
A:HEM150
|
3.1
|
21.7
|
1.0
|
C1D
|
A:HEM150
|
3.1
|
22.2
|
1.0
|
C1B
|
A:HEM150
|
3.1
|
19.3
|
1.0
|
C4D
|
A:HEM150
|
3.1
|
21.7
|
1.0
|
C4A
|
A:HEM150
|
3.1
|
22.8
|
1.0
|
C1A
|
A:HEM150
|
3.1
|
24.1
|
1.0
|
CG
|
A:MET7
|
3.3
|
21.4
|
1.0
|
CHC
|
A:HEM150
|
3.4
|
21.5
|
1.0
|
CHD
|
A:HEM150
|
3.4
|
21.9
|
1.0
|
CE
|
A:MET7
|
3.4
|
20.1
|
1.0
|
CHA
|
A:HEM150
|
3.5
|
21.5
|
1.0
|
CHB
|
A:HEM150
|
3.5
|
21.5
|
1.0
|
ND1
|
A:HIS102
|
4.0
|
30.0
|
1.0
|
CB
|
A:MET7
|
4.1
|
22.3
|
1.0
|
CG
|
A:HIS102
|
4.1
|
28.8
|
1.0
|
C2C
|
A:HEM150
|
4.2
|
23.5
|
1.0
|
C3B
|
A:HEM150
|
4.3
|
18.8
|
1.0
|
C2B
|
A:HEM150
|
4.3
|
17.7
|
1.0
|
C3C
|
A:HEM150
|
4.3
|
21.3
|
1.0
|
C2D
|
A:HEM150
|
4.3
|
22.3
|
1.0
|
C3D
|
A:HEM150
|
4.3
|
23.0
|
1.0
|
C3A
|
A:HEM150
|
4.4
|
26.5
|
1.0
|
C2A
|
A:HEM150
|
4.4
|
27.7
|
1.0
|
NH1
|
A:ARG106
|
4.8
|
37.8
|
1.0
|
CA
|
A:MET7
|
5.0
|
22.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 3tom
Go back to
Iron Binding Sites List in 3tom
Iron binding site 2 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets
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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:27.9
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
27.9
|
1.0
|
NC
|
B:HEM150
|
2.0
|
24.8
|
1.0
|
NB
|
B:HEM150
|
2.0
|
26.8
|
1.0
|
NE2
|
B:HIS102
|
2.0
|
29.9
|
1.0
|
ND
|
B:HEM150
|
2.1
|
28.9
|
1.0
|
NA
|
B:HEM150
|
2.1
|
31.4
|
1.0
|
SD
|
B:MET7
|
2.4
|
28.6
|
1.0
|
C4B
|
B:HEM150
|
3.0
|
24.7
|
1.0
|
CE1
|
B:HIS102
|
3.0
|
33.1
|
1.0
|
CD2
|
B:HIS102
|
3.0
|
32.5
|
1.0
|
C1C
|
B:HEM150
|
3.0
|
24.1
|
1.0
|
C4C
|
B:HEM150
|
3.0
|
24.3
|
1.0
|
C1B
|
B:HEM150
|
3.1
|
26.0
|
1.0
|
C1D
|
B:HEM150
|
3.1
|
27.2
|
1.0
|
C4A
|
B:HEM150
|
3.1
|
32.0
|
1.0
|
C4D
|
B:HEM150
|
3.1
|
31.8
|
1.0
|
C1A
|
B:HEM150
|
3.1
|
34.4
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
24.0
|
1.0
|
CHD
|
B:HEM150
|
3.4
|
24.5
|
1.0
|
CHB
|
B:HEM150
|
3.4
|
30.1
|
1.0
|
CHA
|
B:HEM150
|
3.5
|
34.1
|
1.0
|
CE
|
B:MET7
|
3.5
|
26.4
|
1.0
|
CG
|
B:MET7
|
3.6
|
30.5
|
1.0
|
ND1
|
B:HIS102
|
4.1
|
36.3
|
1.0
|
CG
|
B:HIS102
|
4.2
|
35.5
|
1.0
|
C3B
|
B:HEM150
|
4.2
|
22.5
|
1.0
|
C3C
|
B:HEM150
|
4.2
|
23.1
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
23.1
|
1.0
|
C2B
|
B:HEM150
|
4.3
|
23.5
|
1.0
|
CB
|
B:MET7
|
4.3
|
31.8
|
1.0
|
C3A
|
B:HEM150
|
4.3
|
36.4
|
1.0
|
C2D
|
B:HEM150
|
4.4
|
28.6
|
1.0
|
C3D
|
B:HEM150
|
4.4
|
30.9
|
1.0
|
C2A
|
B:HEM150
|
4.4
|
38.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 3tom
Go back to
Iron Binding Sites List in 3tom
Iron binding site 3 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets
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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:30.7
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
30.7
|
1.0
|
NE2
|
C:HIS102
|
1.9
|
35.1
|
1.0
|
NA
|
C:HEM150
|
2.0
|
34.0
|
1.0
|
ND
|
C:HEM150
|
2.1
|
30.8
|
1.0
|
NB
|
C:HEM150
|
2.1
|
31.0
|
1.0
|
NC
|
C:HEM150
|
2.1
|
30.6
|
1.0
|
SD
|
C:MET7
|
2.4
|
31.8
|
1.0
|
CE1
|
C:HIS102
|
2.9
|
37.2
|
1.0
|
CD2
|
C:HIS102
|
3.0
|
36.2
|
1.0
|
C1A
|
C:HEM150
|
3.0
|
35.1
|
1.0
|
C4A
|
C:HEM150
|
3.0
|
36.3
|
1.0
|
C4D
|
C:HEM150
|
3.1
|
31.4
|
1.0
|
C4B
|
C:HEM150
|
3.1
|
30.7
|
1.0
|
C1D
|
C:HEM150
|
3.1
|
31.2
|
1.0
|
C1C
|
C:HEM150
|
3.1
|
30.9
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
32.2
|
1.0
|
C4C
|
C:HEM150
|
3.1
|
29.8
|
1.0
|
CHA
|
C:HEM150
|
3.4
|
33.7
|
1.0
|
CG
|
C:MET7
|
3.4
|
30.4
|
1.0
|
CHB
|
C:HEM150
|
3.4
|
35.4
|
1.0
|
CHC
|
C:HEM150
|
3.4
|
30.4
|
1.0
|
CE
|
C:MET7
|
3.5
|
28.6
|
1.0
|
CHD
|
C:HEM150
|
3.5
|
29.7
|
1.0
|
ND1
|
C:HIS102
|
4.0
|
39.8
|
1.0
|
CB
|
C:MET7
|
4.1
|
31.3
|
1.0
|
CG
|
C:HIS102
|
4.1
|
38.8
|
1.0
|
C2A
|
C:HEM150
|
4.2
|
37.8
|
1.0
|
C3A
|
C:HEM150
|
4.3
|
37.9
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
31.6
|
1.0
|
C3B
|
C:HEM150
|
4.3
|
30.2
|
1.0
|
C3D
|
C:HEM150
|
4.3
|
32.1
|
1.0
|
C2C
|
C:HEM150
|
4.3
|
30.2
|
1.0
|
C2D
|
C:HEM150
|
4.3
|
31.6
|
1.0
|
C3C
|
C:HEM150
|
4.3
|
29.7
|
1.0
|
CA
|
C:MET7
|
5.0
|
30.6
|
1.0
|
|
Iron binding site 4 out
of 4 in 3tom
Go back to
Iron Binding Sites List in 3tom
Iron binding site 4 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets
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 An Engineered Cytochrome CB562 That Forms 2D, Zn- Mediated Sheets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:29.7
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
29.7
|
1.0
|
NE2
|
D:HIS102
|
2.0
|
34.8
|
1.0
|
NC
|
D:HEM150
|
2.0
|
29.4
|
1.0
|
NA
|
D:HEM150
|
2.1
|
33.8
|
1.0
|
NB
|
D:HEM150
|
2.1
|
31.6
|
1.0
|
ND
|
D:HEM150
|
2.1
|
30.2
|
1.0
|
SD
|
D:MET7
|
2.3
|
32.9
|
1.0
|
CE1
|
D:HIS102
|
2.9
|
37.4
|
1.0
|
C4C
|
D:HEM150
|
3.0
|
28.7
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
35.2
|
1.0
|
C1C
|
D:HEM150
|
3.1
|
29.6
|
1.0
|
C1B
|
D:HEM150
|
3.1
|
32.1
|
1.0
|
CD2
|
D:HIS102
|
3.1
|
35.8
|
1.0
|
C1D
|
D:HEM150
|
3.1
|
27.3
|
1.0
|
C1A
|
D:HEM150
|
3.1
|
35.7
|
1.0
|
C4B
|
D:HEM150
|
3.1
|
31.3
|
1.0
|
C4D
|
D:HEM150
|
3.2
|
31.6
|
1.0
|
CG
|
D:MET7
|
3.4
|
31.1
|
1.0
|
CHB
|
D:HEM150
|
3.4
|
34.3
|
1.0
|
CHD
|
D:HEM150
|
3.4
|
27.4
|
1.0
|
CHC
|
D:HEM150
|
3.5
|
29.8
|
1.0
|
CE
|
D:MET7
|
3.5
|
28.7
|
1.0
|
CHA
|
D:HEM150
|
3.5
|
32.4
|
1.0
|
ND1
|
D:HIS102
|
4.0
|
40.2
|
1.0
|
CB
|
D:MET7
|
4.1
|
32.9
|
1.0
|
CG
|
D:HIS102
|
4.2
|
39.9
|
1.0
|
C3C
|
D:HEM150
|
4.3
|
29.4
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
29.1
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
39.3
|
1.0
|
C2B
|
D:HEM150
|
4.3
|
32.3
|
1.0
|
C2A
|
D:HEM150
|
4.3
|
39.8
|
1.0
|
C3B
|
D:HEM150
|
4.4
|
31.1
|
1.0
|
C2D
|
D:HEM150
|
4.4
|
26.9
|
1.0
|
C3D
|
D:HEM150
|
4.4
|
29.1
|
1.0
|
CA
|
D:MET7
|
4.9
|
32.7
|
1.0
|
|
Reference:
J.D.Brodin,
X.I.Ambroggio,
C.Tang,
K.N.Parent,
T.S.Baker,
F.A.Tezcan.
Metal-Directed, Chemically Tunable Assembly of One-, Two- and Three-Dimensional Crystalline Protein Arrays. Nat Chem V. 4 375 2012.
PubMed: 22522257
DOI: 10.1038/NCHEM.1290
Page generated: Sun Aug 4 20:33:03 2024
|