Iron in PDB 3tol: Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers
Protein crystallography data
The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers, PDB code: 3tol
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)
|
63.28 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.546,
69.506,
126.567,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
24.5
|
Other elements in 3tol:
The structure of Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers 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 1D, Zn- Mediated Coordination Polymers
(pdb code 3tol). 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 1D, Zn- Mediated Coordination Polymers, PDB code: 3tol:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3tol
Go back to
Iron Binding Sites List in 3tol
Iron binding site 1 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers
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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:22.3
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
22.3
|
1.0
|
NB
|
A:HEM150
|
2.1
|
22.3
|
1.0
|
ND
|
A:HEM150
|
2.1
|
23.1
|
1.0
|
NE2
|
A:HIS102
|
2.1
|
20.6
|
1.0
|
NA
|
A:HEM150
|
2.1
|
23.6
|
1.0
|
NC
|
A:HEM150
|
2.1
|
21.3
|
1.0
|
SD
|
A:MET7
|
2.3
|
22.1
|
1.0
|
CD2
|
A:HIS102
|
3.0
|
19.2
|
1.0
|
C4B
|
A:HEM150
|
3.1
|
22.1
|
1.0
|
C4D
|
A:HEM150
|
3.1
|
25.2
|
1.0
|
C1D
|
A:HEM150
|
3.1
|
24.7
|
1.0
|
C1C
|
A:HEM150
|
3.1
|
21.1
|
1.0
|
C1A
|
A:HEM150
|
3.1
|
25.0
|
1.0
|
CE1
|
A:HIS102
|
3.1
|
21.6
|
1.0
|
C1B
|
A:HEM150
|
3.1
|
22.9
|
1.0
|
C4A
|
A:HEM150
|
3.1
|
25.0
|
1.0
|
C4C
|
A:HEM150
|
3.1
|
21.5
|
1.0
|
CHC
|
A:HEM150
|
3.4
|
19.9
|
1.0
|
CHA
|
A:HEM150
|
3.4
|
26.1
|
1.0
|
CE
|
A:MET7
|
3.4
|
19.0
|
1.0
|
CHD
|
A:HEM150
|
3.4
|
22.8
|
1.0
|
CG
|
A:MET7
|
3.5
|
20.6
|
1.0
|
CHB
|
A:HEM150
|
3.5
|
22.5
|
1.0
|
ND1
|
A:HIS102
|
4.2
|
23.2
|
1.0
|
CG
|
A:HIS102
|
4.2
|
22.9
|
1.0
|
CB
|
A:MET7
|
4.2
|
22.1
|
1.0
|
C3B
|
A:HEM150
|
4.3
|
20.2
|
1.0
|
C3D
|
A:HEM150
|
4.3
|
25.2
|
1.0
|
C2B
|
A:HEM150
|
4.3
|
20.8
|
1.0
|
C2A
|
A:HEM150
|
4.3
|
28.4
|
1.0
|
C3A
|
A:HEM150
|
4.3
|
25.4
|
1.0
|
C2D
|
A:HEM150
|
4.3
|
24.6
|
1.0
|
C2C
|
A:HEM150
|
4.3
|
19.2
|
1.0
|
C3C
|
A:HEM150
|
4.4
|
21.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 3tol
Go back to
Iron Binding Sites List in 3tol
Iron binding site 2 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers
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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:23.1
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
23.1
|
1.0
|
ND
|
C:HEM150
|
1.9
|
20.2
|
1.0
|
NE2
|
C:HIS102
|
2.0
|
24.2
|
1.0
|
NB
|
C:HEM150
|
2.0
|
19.8
|
1.0
|
NC
|
C:HEM150
|
2.1
|
18.8
|
1.0
|
NA
|
C:HEM150
|
2.1
|
21.5
|
1.0
|
SD
|
C:MET7
|
2.4
|
26.0
|
1.0
|
C4D
|
C:HEM150
|
2.9
|
26.0
|
1.0
|
C4B
|
C:HEM150
|
2.9
|
22.7
|
1.0
|
CD2
|
C:HIS102
|
2.9
|
21.2
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
25.1
|
1.0
|
C1C
|
C:HEM150
|
3.0
|
19.0
|
1.0
|
C1A
|
C:HEM150
|
3.1
|
23.7
|
1.0
|
C1D
|
C:HEM150
|
3.1
|
23.0
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
23.4
|
1.0
|
C4C
|
C:HEM150
|
3.2
|
17.6
|
1.0
|
C4A
|
C:HEM150
|
3.2
|
22.9
|
1.0
|
CHC
|
C:HEM150
|
3.3
|
19.3
|
1.0
|
CHA
|
C:HEM150
|
3.3
|
22.8
|
1.0
|
CE
|
C:MET7
|
3.4
|
23.9
|
1.0
|
CG
|
C:MET7
|
3.5
|
26.2
|
1.0
|
CHD
|
C:HEM150
|
3.5
|
19.9
|
1.0
|
CHB
|
C:HEM150
|
3.6
|
22.4
|
1.0
|
ND1
|
C:HIS102
|
4.1
|
24.4
|
1.0
|
CG
|
C:HIS102
|
4.1
|
25.2
|
1.0
|
C3D
|
C:HEM150
|
4.2
|
25.9
|
1.0
|
C3B
|
C:HEM150
|
4.2
|
21.8
|
1.0
|
CB
|
C:MET7
|
4.2
|
27.3
|
1.0
|
C2D
|
C:HEM150
|
4.2
|
22.9
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
22.1
|
1.0
|
C2C
|
C:HEM150
|
4.3
|
17.6
|
1.0
|
C2A
|
C:HEM150
|
4.3
|
25.1
|
1.0
|
C3C
|
C:HEM150
|
4.4
|
18.2
|
1.0
|
C3A
|
C:HEM150
|
4.4
|
25.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 3tol
Go back to
Iron Binding Sites List in 3tol
Iron binding site 3 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers
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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:24.1
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
24.1
|
1.0
|
NE2
|
D:HIS102
|
1.9
|
25.8
|
1.0
|
NB
|
D:HEM150
|
2.1
|
23.4
|
1.0
|
ND
|
D:HEM150
|
2.1
|
26.6
|
1.0
|
NC
|
D:HEM150
|
2.1
|
23.4
|
1.0
|
NA
|
D:HEM150
|
2.1
|
25.2
|
1.0
|
SD
|
D:MET7
|
2.4
|
26.0
|
1.0
|
CE1
|
D:HIS102
|
2.9
|
27.6
|
1.0
|
CD2
|
D:HIS102
|
2.9
|
25.8
|
1.0
|
C4B
|
D:HEM150
|
3.0
|
23.0
|
1.0
|
C1C
|
D:HEM150
|
3.1
|
22.5
|
1.0
|
C4D
|
D:HEM150
|
3.1
|
27.9
|
1.0
|
C1A
|
D:HEM150
|
3.1
|
27.6
|
1.0
|
C1D
|
D:HEM150
|
3.1
|
27.4
|
1.0
|
C4C
|
D:HEM150
|
3.1
|
23.6
|
1.0
|
C1B
|
D:HEM150
|
3.1
|
25.3
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
26.6
|
1.0
|
CHC
|
D:HEM150
|
3.4
|
22.2
|
1.0
|
CHA
|
D:HEM150
|
3.4
|
27.4
|
1.0
|
CG
|
D:MET7
|
3.5
|
26.1
|
1.0
|
CE
|
D:MET7
|
3.5
|
22.7
|
1.0
|
CHD
|
D:HEM150
|
3.5
|
25.2
|
1.0
|
CHB
|
D:HEM150
|
3.5
|
25.2
|
1.0
|
ND1
|
D:HIS102
|
4.0
|
28.4
|
1.0
|
CG
|
D:HIS102
|
4.0
|
29.6
|
1.0
|
C3B
|
D:HEM150
|
4.3
|
22.8
|
1.0
|
CB
|
D:MET7
|
4.3
|
27.3
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
23.9
|
1.0
|
C3D
|
D:HEM150
|
4.3
|
30.1
|
1.0
|
C2A
|
D:HEM150
|
4.3
|
31.3
|
1.0
|
C2B
|
D:HEM150
|
4.3
|
24.0
|
1.0
|
C2D
|
D:HEM150
|
4.3
|
27.9
|
1.0
|
C3C
|
D:HEM150
|
4.3
|
23.1
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
29.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 3tol
Go back to
Iron Binding Sites List in 3tol
Iron binding site 4 out
of 4 in the Crystal Structure of An Engineered Cytochrome CB562 That Forms 1D, Zn- Mediated Coordination Polymers
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 1D, Zn- Mediated Coordination Polymers within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:19.9
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
19.9
|
1.0
|
NE2
|
B:HIS102
|
1.9
|
19.0
|
1.0
|
ND
|
B:HEM150
|
2.1
|
21.6
|
1.0
|
NB
|
B:HEM150
|
2.1
|
19.5
|
1.0
|
NC
|
B:HEM150
|
2.1
|
20.3
|
1.0
|
NA
|
B:HEM150
|
2.1
|
22.8
|
1.0
|
SD
|
B:MET7
|
2.2
|
20.3
|
1.0
|
CE1
|
B:HIS102
|
2.9
|
20.3
|
1.0
|
CD2
|
B:HIS102
|
2.9
|
18.4
|
1.0
|
C4B
|
B:HEM150
|
3.1
|
18.7
|
1.0
|
C1C
|
B:HEM150
|
3.1
|
21.6
|
1.0
|
C4D
|
B:HEM150
|
3.1
|
24.5
|
1.0
|
C1D
|
B:HEM150
|
3.1
|
22.4
|
1.0
|
C4C
|
B:HEM150
|
3.1
|
21.6
|
1.0
|
C1B
|
B:HEM150
|
3.1
|
21.8
|
1.0
|
C1A
|
B:HEM150
|
3.1
|
24.9
|
1.0
|
C4A
|
B:HEM150
|
3.2
|
24.1
|
1.0
|
CE
|
B:MET7
|
3.3
|
19.4
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
19.3
|
1.0
|
CG
|
B:MET7
|
3.4
|
19.6
|
1.0
|
CHA
|
B:HEM150
|
3.4
|
25.3
|
1.0
|
CHD
|
B:HEM150
|
3.5
|
21.1
|
1.0
|
CHB
|
B:HEM150
|
3.5
|
22.6
|
1.0
|
ND1
|
B:HIS102
|
4.0
|
22.0
|
1.0
|
CG
|
B:HIS102
|
4.1
|
21.6
|
1.0
|
CB
|
B:MET7
|
4.3
|
19.9
|
1.0
|
C3B
|
B:HEM150
|
4.3
|
18.7
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
19.1
|
1.0
|
C3D
|
B:HEM150
|
4.3
|
24.4
|
1.0
|
C2D
|
B:HEM150
|
4.3
|
23.9
|
1.0
|
C3C
|
B:HEM150
|
4.3
|
21.0
|
1.0
|
C2B
|
B:HEM150
|
4.3
|
20.1
|
1.0
|
C2A
|
B:HEM150
|
4.4
|
27.3
|
1.0
|
C3A
|
B:HEM150
|
4.4
|
25.7
|
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 20:33:00 2024
|