Iron in PDB 6ot7: Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Protein crystallography data
The structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562, PDB code: 6ot7
was solved by
E.Golub,
J.Esselborn,
J.B.Bailey,
F.A.Tezcan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
91.83 /
1.85
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.700,
126.700,
167.800,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.3 /
21.1
|
Other elements in 6ot7:
The structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
(pdb code 6ot7). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the
Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562, PDB code: 6ot7:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Iron binding site 1 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 1 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:32.0
occ:1.00
|
FE
|
D:HEC201
|
0.0
|
32.0
|
1.0
|
ND
|
D:HEC201
|
2.0
|
36.0
|
1.0
|
NB
|
D:HEC201
|
2.0
|
32.6
|
1.0
|
NA
|
D:HEC201
|
2.1
|
30.8
|
1.0
|
NC
|
D:HEC201
|
2.1
|
29.4
|
1.0
|
NE2
|
D:HIS102
|
2.2
|
32.6
|
1.0
|
SD
|
D:MET7
|
2.4
|
34.6
|
1.0
|
C4D
|
D:HEC201
|
3.0
|
34.2
|
1.0
|
C1A
|
D:HEC201
|
3.1
|
37.3
|
1.0
|
C1D
|
D:HEC201
|
3.1
|
35.1
|
1.0
|
C4B
|
D:HEC201
|
3.1
|
33.1
|
1.0
|
C1C
|
D:HEC201
|
3.1
|
33.6
|
1.0
|
CD2
|
D:HIS102
|
3.1
|
31.3
|
1.0
|
C4A
|
D:HEC201
|
3.1
|
36.2
|
1.0
|
C1B
|
D:HEC201
|
3.1
|
32.8
|
1.0
|
C4C
|
D:HEC201
|
3.1
|
32.3
|
1.0
|
CE1
|
D:HIS102
|
3.2
|
38.5
|
1.0
|
CE
|
D:MET7
|
3.2
|
38.7
|
1.0
|
CHA
|
D:HEC201
|
3.4
|
37.8
|
1.0
|
CHC
|
D:HEC201
|
3.4
|
30.5
|
1.0
|
CG
|
D:MET7
|
3.5
|
34.6
|
1.0
|
CHD
|
D:HEC201
|
3.5
|
33.2
|
1.0
|
CHB
|
D:HEC201
|
3.5
|
31.2
|
1.0
|
CB
|
D:MET7
|
4.2
|
32.9
|
1.0
|
C3D
|
D:HEC201
|
4.2
|
35.4
|
1.0
|
CG
|
D:HIS102
|
4.3
|
35.6
|
1.0
|
C2D
|
D:HEC201
|
4.3
|
35.7
|
1.0
|
ND1
|
D:HIS102
|
4.3
|
36.3
|
1.0
|
C3B
|
D:HEC201
|
4.3
|
37.6
|
1.0
|
C2A
|
D:HEC201
|
4.3
|
37.6
|
1.0
|
C2C
|
D:HEC201
|
4.3
|
33.3
|
1.0
|
C2B
|
D:HEC201
|
4.3
|
35.6
|
1.0
|
C3A
|
D:HEC201
|
4.3
|
33.8
|
1.0
|
C3C
|
D:HEC201
|
4.3
|
29.6
|
1.0
|
|
Iron binding site 2 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 2 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe204
b:88.7
occ:0.33
|
O
|
D:HAE206
|
2.0
|
96.1
|
1.0
|
O2
|
D:HAE206
|
2.1
|
92.4
|
1.0
|
C2
|
D:HAE206
|
2.7
|
84.7
|
1.0
|
N
|
D:HAE206
|
2.7
|
92.1
|
1.0
|
HN
|
D:HAE206
|
3.5
|
0.5
|
1.0
|
C1
|
D:HAE206
|
4.2
|
75.8
|
1.0
|
SG
|
D:CYS82
|
4.6
|
83.5
|
1.0
|
|
Iron binding site 3 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 3 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe207
b:46.8
occ:1.00
|
O
|
C:HAE203
|
2.0
|
61.2
|
1.0
|
O2
|
A:HAE203
|
2.1
|
44.9
|
1.0
|
O
|
A:HAE203
|
2.1
|
55.0
|
1.0
|
O2
|
C:HAE203
|
2.1
|
49.4
|
1.0
|
O2
|
D:HAE205
|
2.2
|
51.5
|
1.0
|
O
|
D:HAE205
|
2.2
|
49.2
|
1.0
|
C2
|
A:HAE203
|
2.8
|
48.0
|
1.0
|
N
|
C:HAE203
|
2.8
|
52.2
|
1.0
|
C2
|
C:HAE203
|
2.8
|
39.7
|
1.0
|
N
|
A:HAE203
|
2.8
|
52.0
|
1.0
|
C2
|
D:HAE205
|
2.9
|
52.9
|
1.0
|
N
|
D:HAE205
|
3.0
|
56.5
|
1.0
|
HN
|
C:HAE203
|
3.6
|
62.6
|
1.0
|
HN
|
A:HAE203
|
3.7
|
62.4
|
1.0
|
HN
|
D:HAE205
|
3.8
|
67.8
|
1.0
|
C1
|
A:HAE203
|
4.3
|
56.4
|
1.0
|
C1
|
C:HAE203
|
4.3
|
47.7
|
1.0
|
O
|
C:HOH370
|
4.3
|
42.4
|
1.0
|
C1
|
D:HAE205
|
4.4
|
49.0
|
1.0
|
O
|
A:HOH349
|
4.6
|
48.7
|
1.0
|
O
|
D:HOH321
|
4.6
|
48.0
|
1.0
|
SG
|
C:CYS63
|
4.8
|
50.8
|
1.0
|
SG
|
A:CYS63
|
4.9
|
50.1
|
1.0
|
SG
|
D:CYS63
|
5.0
|
49.7
|
1.0
|
|
Iron binding site 4 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 4 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:27.5
occ:1.00
|
FE
|
A:HEC201
|
0.0
|
27.5
|
1.0
|
ND
|
A:HEC201
|
2.0
|
24.8
|
1.0
|
NA
|
A:HEC201
|
2.0
|
24.1
|
1.0
|
NC
|
A:HEC201
|
2.0
|
24.5
|
1.0
|
NB
|
A:HEC201
|
2.0
|
28.5
|
1.0
|
NE2
|
A:HIS102
|
2.2
|
27.6
|
1.0
|
SD
|
A:MET7
|
2.4
|
29.3
|
1.0
|
C1C
|
A:HEC201
|
3.0
|
27.2
|
1.0
|
C1A
|
A:HEC201
|
3.0
|
27.9
|
1.0
|
C4D
|
A:HEC201
|
3.0
|
32.1
|
1.0
|
C1D
|
A:HEC201
|
3.0
|
25.6
|
1.0
|
C4A
|
A:HEC201
|
3.0
|
28.2
|
1.0
|
C4B
|
A:HEC201
|
3.1
|
29.0
|
1.0
|
C4C
|
A:HEC201
|
3.1
|
27.0
|
1.0
|
C1B
|
A:HEC201
|
3.1
|
28.3
|
1.0
|
CD2
|
A:HIS102
|
3.1
|
28.3
|
1.0
|
CE1
|
A:HIS102
|
3.2
|
29.8
|
1.0
|
CE
|
A:MET7
|
3.3
|
27.4
|
1.0
|
CHC
|
A:HEC201
|
3.4
|
27.4
|
1.0
|
CHA
|
A:HEC201
|
3.4
|
33.2
|
1.0
|
CHB
|
A:HEC201
|
3.4
|
25.5
|
1.0
|
CHD
|
A:HEC201
|
3.5
|
25.4
|
1.0
|
CG
|
A:MET7
|
3.5
|
24.6
|
1.0
|
CB
|
A:MET7
|
4.2
|
30.3
|
1.0
|
C2D
|
A:HEC201
|
4.2
|
33.5
|
1.0
|
C3D
|
A:HEC201
|
4.2
|
27.5
|
1.0
|
C2A
|
A:HEC201
|
4.2
|
28.0
|
1.0
|
C3A
|
A:HEC201
|
4.3
|
28.4
|
1.0
|
ND1
|
A:HIS102
|
4.3
|
30.5
|
1.0
|
C2C
|
A:HEC201
|
4.3
|
25.2
|
1.0
|
CG
|
A:HIS102
|
4.3
|
30.2
|
1.0
|
C3B
|
A:HEC201
|
4.3
|
30.3
|
1.0
|
C2B
|
A:HEC201
|
4.3
|
31.0
|
1.0
|
C3C
|
A:HEC201
|
4.3
|
22.6
|
1.0
|
NH2
|
A:ARG106
|
4.9
|
36.9
|
1.0
|
|
Iron binding site 5 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 5 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe206
b:0.5
occ:0.66
|
O
|
C:HAE204
|
2.0
|
0.4
|
1.0
|
O2
|
C:HAE204
|
2.1
|
0.7
|
1.0
|
O2
|
B:HAE203
|
2.2
|
96.2
|
1.0
|
O
|
B:HAE203
|
2.2
|
0.1
|
1.0
|
C2
|
C:HAE204
|
2.7
|
0.5
|
1.0
|
N
|
C:HAE204
|
2.7
|
0.5
|
1.0
|
C2
|
B:HAE203
|
2.8
|
93.7
|
1.0
|
N
|
B:HAE203
|
2.9
|
99.5
|
1.0
|
HN
|
C:HAE204
|
3.5
|
0.8
|
1.0
|
HN
|
B:HAE203
|
3.7
|
0.3
|
1.0
|
C1
|
C:HAE204
|
4.2
|
74.0
|
1.0
|
SG
|
C:CYS82
|
4.3
|
79.2
|
1.0
|
C1
|
B:HAE203
|
4.3
|
81.8
|
1.0
|
|
Iron binding site 6 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 6 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe206
b:0.1
occ:0.33
|
O2
|
A:HAE204
|
2.1
|
95.8
|
1.0
|
O
|
A:HAE204
|
2.2
|
0.1
|
1.0
|
C2
|
A:HAE204
|
2.8
|
93.1
|
1.0
|
N
|
A:HAE204
|
2.9
|
92.4
|
1.0
|
HN
|
A:HAE204
|
3.7
|
0.8
|
1.0
|
C1
|
A:HAE204
|
4.3
|
75.2
|
1.0
|
SG
|
A:CYS82
|
4.8
|
73.8
|
1.0
|
|
Iron binding site 7 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 7 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:32.7
occ:1.00
|
FE
|
B:HEC201
|
0.0
|
32.7
|
1.0
|
NA
|
B:HEC201
|
2.0
|
34.9
|
1.0
|
ND
|
B:HEC201
|
2.0
|
30.1
|
1.0
|
NB
|
B:HEC201
|
2.0
|
30.3
|
1.0
|
NC
|
B:HEC201
|
2.1
|
35.9
|
1.0
|
NE2
|
B:HIS102
|
2.2
|
40.3
|
1.0
|
SD
|
B:MET7
|
2.4
|
34.4
|
1.0
|
C1B
|
B:HEC201
|
3.0
|
35.2
|
1.0
|
C4A
|
B:HEC201
|
3.0
|
32.8
|
1.0
|
C1A
|
B:HEC201
|
3.0
|
32.7
|
1.0
|
C4D
|
B:HEC201
|
3.0
|
38.5
|
1.0
|
C4B
|
B:HEC201
|
3.1
|
35.4
|
1.0
|
C1D
|
B:HEC201
|
3.1
|
32.1
|
1.0
|
CD2
|
B:HIS102
|
3.1
|
36.2
|
1.0
|
C1C
|
B:HEC201
|
3.1
|
32.0
|
1.0
|
C4C
|
B:HEC201
|
3.1
|
35.7
|
1.0
|
CE
|
B:MET7
|
3.2
|
40.6
|
1.0
|
CE1
|
B:HIS102
|
3.2
|
39.2
|
1.0
|
CHB
|
B:HEC201
|
3.4
|
29.7
|
1.0
|
CHA
|
B:HEC201
|
3.4
|
35.4
|
1.0
|
CHD
|
B:HEC201
|
3.5
|
34.3
|
1.0
|
CHC
|
B:HEC201
|
3.5
|
28.9
|
1.0
|
CG
|
B:MET7
|
3.5
|
32.4
|
1.0
|
C2A
|
B:HEC201
|
4.2
|
32.0
|
1.0
|
C3A
|
B:HEC201
|
4.2
|
33.6
|
1.0
|
C2B
|
B:HEC201
|
4.2
|
31.9
|
1.0
|
CB
|
B:MET7
|
4.3
|
32.8
|
1.0
|
C3D
|
B:HEC201
|
4.3
|
38.6
|
1.0
|
C3B
|
B:HEC201
|
4.3
|
30.8
|
1.0
|
C2D
|
B:HEC201
|
4.3
|
34.4
|
1.0
|
CG
|
B:HIS102
|
4.3
|
37.4
|
1.0
|
ND1
|
B:HIS102
|
4.3
|
34.7
|
1.0
|
C2C
|
B:HEC201
|
4.3
|
33.6
|
1.0
|
C3C
|
B:HEC201
|
4.3
|
30.9
|
1.0
|
|
Iron binding site 8 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 8 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:52.2
occ:0.33
|
O
|
B:HAE204
|
2.2
|
52.6
|
1.0
|
O2
|
B:HAE204
|
2.3
|
58.9
|
1.0
|
N
|
B:HAE204
|
2.9
|
56.8
|
1.0
|
C2
|
B:HAE204
|
2.9
|
60.6
|
1.0
|
HN
|
B:HAE204
|
3.7
|
68.1
|
1.0
|
O
|
B:HOH304
|
4.1
|
57.6
|
1.0
|
C1
|
B:HAE204
|
4.4
|
58.2
|
1.0
|
|
Iron binding site 9 out
of 9 in 6ot7
Go back to
Iron Binding Sites List in 6ot7
Iron binding site 9 out
of 9 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:26.8
occ:1.00
|
FE
|
C:HEC201
|
0.0
|
26.8
|
1.0
|
ND
|
C:HEC201
|
2.0
|
25.7
|
1.0
|
NB
|
C:HEC201
|
2.0
|
24.9
|
1.0
|
NA
|
C:HEC201
|
2.0
|
26.7
|
1.0
|
NC
|
C:HEC201
|
2.0
|
25.1
|
1.0
|
NE2
|
C:HIS102
|
2.1
|
26.8
|
1.0
|
SD
|
C:MET7
|
2.4
|
27.8
|
1.0
|
C1B
|
C:HEC201
|
3.0
|
26.2
|
1.0
|
C4D
|
C:HEC201
|
3.0
|
31.9
|
1.0
|
C1D
|
C:HEC201
|
3.0
|
27.6
|
1.0
|
C4B
|
C:HEC201
|
3.0
|
22.2
|
1.0
|
CD2
|
C:HIS102
|
3.1
|
28.2
|
1.0
|
C1A
|
C:HEC201
|
3.1
|
26.3
|
1.0
|
C4A
|
C:HEC201
|
3.1
|
27.9
|
1.0
|
C1C
|
C:HEC201
|
3.1
|
25.8
|
1.0
|
C4C
|
C:HEC201
|
3.1
|
27.3
|
1.0
|
CE1
|
C:HIS102
|
3.2
|
28.4
|
1.0
|
CE
|
C:MET7
|
3.3
|
27.8
|
1.0
|
CHB
|
C:HEC201
|
3.4
|
26.6
|
1.0
|
CG
|
C:MET7
|
3.4
|
28.5
|
1.0
|
CHA
|
C:HEC201
|
3.4
|
29.4
|
1.0
|
CHC
|
C:HEC201
|
3.4
|
24.6
|
1.0
|
CHD
|
C:HEC201
|
3.5
|
27.7
|
1.0
|
C2B
|
C:HEC201
|
4.2
|
23.3
|
1.0
|
CG
|
C:HIS102
|
4.2
|
28.2
|
1.0
|
ND1
|
C:HIS102
|
4.2
|
25.8
|
1.0
|
C3B
|
C:HEC201
|
4.2
|
21.7
|
1.0
|
C3D
|
C:HEC201
|
4.2
|
30.6
|
1.0
|
CB
|
C:MET7
|
4.3
|
26.9
|
1.0
|
C2D
|
C:HEC201
|
4.3
|
32.6
|
1.0
|
C2A
|
C:HEC201
|
4.3
|
29.9
|
1.0
|
C3A
|
C:HEC201
|
4.3
|
32.1
|
1.0
|
C2C
|
C:HEC201
|
4.3
|
25.6
|
1.0
|
C3C
|
C:HEC201
|
4.3
|
24.8
|
1.0
|
NH2
|
C:ARG106
|
5.0
|
40.5
|
1.0
|
|
Reference:
E.Golub,
R.H.Subramanian,
J.Esselborn,
R.G.Alberstein,
J.B.Bailey,
J.A.Chiong,
X.Yan,
T.Booth,
T.S.Baker,
F.A.Tezcan.
Constructing Protein Polyhedra Via Orthogonal Chemical Interactions Nature 2020.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-019-1928-2
Page generated: Wed Aug 7 05:20:03 2024
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