Iron in PDB 6ot9: Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562
Protein crystallography data
The structure of Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562, PDB code: 6ot9
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)
|
36.27 /
2.40
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.640,
125.640,
166.350,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.7 /
27.2
|
Other elements in 6ot9:
The structure of Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562
(pdb code 6ot9). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562, PDB code: 6ot9:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 6ot9
Go back to
Iron Binding Sites List in 6ot9
Iron binding site 1 out
of 6 in the Bimetallic Dodecameric Cage Design 1 (BMC1) 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 1 (BMC1) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe204
b:58.7
occ:1.00
|
FE
|
C:HEC204
|
0.0
|
58.7
|
1.0
|
NA
|
C:HEC204
|
2.0
|
62.6
|
1.0
|
ND
|
C:HEC204
|
2.0
|
61.0
|
1.0
|
NB
|
C:HEC204
|
2.1
|
53.2
|
1.0
|
NC
|
C:HEC204
|
2.1
|
58.8
|
1.0
|
NE2
|
C:HIS102
|
2.3
|
62.5
|
1.0
|
SD
|
C:MET7
|
2.9
|
0.6
|
1.0
|
C4A
|
C:HEC204
|
3.0
|
57.8
|
1.0
|
C1D
|
C:HEC204
|
3.0
|
56.2
|
1.0
|
C1B
|
C:HEC204
|
3.1
|
51.8
|
1.0
|
C4D
|
C:HEC204
|
3.1
|
58.7
|
1.0
|
C1A
|
C:HEC204
|
3.1
|
59.5
|
1.0
|
C4B
|
C:HEC204
|
3.1
|
55.6
|
1.0
|
C4C
|
C:HEC204
|
3.1
|
61.9
|
1.0
|
C1C
|
C:HEC204
|
3.1
|
59.1
|
1.0
|
CD2
|
C:HIS102
|
3.2
|
61.7
|
1.0
|
CE1
|
C:HIS102
|
3.3
|
59.0
|
1.0
|
CE
|
C:MET7
|
3.4
|
77.9
|
1.0
|
CHB
|
C:HEC204
|
3.4
|
54.8
|
1.0
|
CHD
|
C:HEC204
|
3.4
|
59.8
|
1.0
|
CHC
|
C:HEC204
|
3.5
|
55.8
|
1.0
|
CHA
|
C:HEC204
|
3.5
|
54.2
|
1.0
|
CG
|
C:MET7
|
3.5
|
62.4
|
1.0
|
CB
|
C:MET7
|
4.1
|
69.0
|
1.0
|
C3A
|
C:HEC204
|
4.2
|
62.9
|
1.0
|
C2D
|
C:HEC204
|
4.3
|
62.9
|
1.0
|
C2A
|
C:HEC204
|
4.3
|
61.8
|
1.0
|
C3D
|
C:HEC204
|
4.3
|
59.6
|
1.0
|
C2B
|
C:HEC204
|
4.3
|
60.3
|
1.0
|
C3B
|
C:HEC204
|
4.3
|
60.5
|
1.0
|
C2C
|
C:HEC204
|
4.3
|
54.8
|
1.0
|
C3C
|
C:HEC204
|
4.3
|
60.9
|
1.0
|
CG
|
C:HIS102
|
4.3
|
63.1
|
1.0
|
ND1
|
C:HIS102
|
4.4
|
69.5
|
1.0
|
|
Iron binding site 2 out
of 6 in 6ot9
Go back to
Iron Binding Sites List in 6ot9
Iron binding site 2 out
of 6 in the Bimetallic Dodecameric Cage Design 1 (BMC1) 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 1 (BMC1) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe206
b:94.6
occ:1.00
|
O2
|
A:HAE201
|
2.0
|
97.9
|
1.0
|
O
|
C:HAE203
|
2.0
|
98.3
|
1.0
|
O
|
D:HAE202
|
2.1
|
97.7
|
1.0
|
O
|
A:HAE201
|
2.1
|
88.8
|
1.0
|
O2
|
C:HAE203
|
2.1
|
96.9
|
1.0
|
O2
|
D:HAE202
|
2.1
|
96.8
|
1.0
|
N
|
C:HAE203
|
2.7
|
90.5
|
1.0
|
C2
|
A:HAE201
|
2.7
|
91.5
|
1.0
|
C2
|
C:HAE203
|
2.7
|
94.1
|
1.0
|
N
|
A:HAE201
|
2.8
|
86.1
|
1.0
|
C2
|
D:HAE202
|
2.9
|
96.4
|
1.0
|
N
|
D:HAE202
|
2.9
|
90.7
|
1.0
|
C1
|
A:HAE201
|
4.2
|
92.5
|
1.0
|
C1
|
C:HAE203
|
4.2
|
93.5
|
1.0
|
C1
|
D:HAE202
|
4.3
|
96.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 6ot9
Go back to
Iron Binding Sites List in 6ot9
Iron binding site 3 out
of 6 in the Bimetallic Dodecameric Cage Design 1 (BMC1) 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 1 (BMC1) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe203
b:59.9
occ:1.00
|
FE
|
D:HEC203
|
0.0
|
59.9
|
1.0
|
NB
|
D:HEC203
|
2.0
|
68.5
|
1.0
|
NC
|
D:HEC203
|
2.0
|
69.5
|
1.0
|
ND
|
D:HEC203
|
2.1
|
68.3
|
1.0
|
NA
|
D:HEC203
|
2.1
|
71.7
|
1.0
|
NE2
|
D:HIS102
|
2.3
|
63.1
|
1.0
|
SD
|
D:MET7
|
2.6
|
66.3
|
1.0
|
C4B
|
D:HEC203
|
3.0
|
66.2
|
1.0
|
C1C
|
D:HEC203
|
3.0
|
71.1
|
1.0
|
C1B
|
D:HEC203
|
3.0
|
70.4
|
1.0
|
C4A
|
D:HEC203
|
3.1
|
72.4
|
1.0
|
C1D
|
D:HEC203
|
3.1
|
71.3
|
1.0
|
C4C
|
D:HEC203
|
3.1
|
66.2
|
1.0
|
C4D
|
D:HEC203
|
3.1
|
70.5
|
1.0
|
C1A
|
D:HEC203
|
3.1
|
66.3
|
1.0
|
CE1
|
D:HIS102
|
3.2
|
66.1
|
1.0
|
CD2
|
D:HIS102
|
3.2
|
64.0
|
1.0
|
CHC
|
D:HEC203
|
3.4
|
68.6
|
1.0
|
CHB
|
D:HEC203
|
3.4
|
65.0
|
1.0
|
CHD
|
D:HEC203
|
3.4
|
63.7
|
1.0
|
CE
|
D:MET7
|
3.5
|
68.4
|
1.0
|
CHA
|
D:HEC203
|
3.5
|
65.0
|
1.0
|
CG
|
D:MET7
|
3.5
|
63.6
|
1.0
|
CB
|
D:MET7
|
4.2
|
58.8
|
1.0
|
C3B
|
D:HEC203
|
4.2
|
69.0
|
1.0
|
C2C
|
D:HEC203
|
4.3
|
66.6
|
1.0
|
C2B
|
D:HEC203
|
4.3
|
70.7
|
1.0
|
C3C
|
D:HEC203
|
4.3
|
67.7
|
1.0
|
C2D
|
D:HEC203
|
4.3
|
64.6
|
1.0
|
C3A
|
D:HEC203
|
4.3
|
71.8
|
1.0
|
C3D
|
D:HEC203
|
4.3
|
68.2
|
1.0
|
ND1
|
D:HIS102
|
4.3
|
70.8
|
1.0
|
C2A
|
D:HEC203
|
4.4
|
73.4
|
1.0
|
CG
|
D:HIS102
|
4.4
|
73.0
|
1.0
|
CA
|
D:MET7
|
4.9
|
65.7
|
1.0
|
|
Iron binding site 4 out
of 6 in 6ot9
Go back to
Iron Binding Sites List in 6ot9
Iron binding site 4 out
of 6 in the Bimetallic Dodecameric Cage Design 1 (BMC1) 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 1 (BMC1) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:97.2
occ:0.33
|
O
|
B:HAE203
|
2.0
|
1.0
|
1.0
|
O2
|
B:HAE203
|
2.1
|
92.0
|
1.0
|
C2
|
B:HAE203
|
2.8
|
94.7
|
1.0
|
N
|
B:HAE203
|
2.8
|
89.7
|
1.0
|
C1
|
B:HAE203
|
4.3
|
94.7
|
1.0
|
|
Iron binding site 5 out
of 6 in 6ot9
Go back to
Iron Binding Sites List in 6ot9
Iron binding site 5 out
of 6 in the Bimetallic Dodecameric Cage Design 1 (BMC1) 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 1 (BMC1) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe204
b:59.9
occ:1.00
|
FE
|
B:HEC204
|
0.0
|
59.9
|
1.0
|
NB
|
B:HEC204
|
2.0
|
64.4
|
1.0
|
NC
|
B:HEC204
|
2.0
|
75.8
|
1.0
|
NA
|
B:HEC204
|
2.0
|
67.5
|
1.0
|
ND
|
B:HEC204
|
2.1
|
65.3
|
1.0
|
NE2
|
B:HIS102
|
2.3
|
69.0
|
1.0
|
SD
|
B:MET7
|
2.6
|
64.0
|
1.0
|
C4A
|
B:HEC204
|
3.0
|
69.5
|
1.0
|
C1C
|
B:HEC204
|
3.0
|
76.1
|
1.0
|
C1B
|
B:HEC204
|
3.0
|
62.5
|
1.0
|
C4B
|
B:HEC204
|
3.0
|
62.7
|
1.0
|
CE
|
B:MET7
|
3.0
|
66.3
|
1.0
|
C4C
|
B:HEC204
|
3.1
|
68.3
|
1.0
|
C1D
|
B:HEC204
|
3.1
|
67.9
|
1.0
|
C4D
|
B:HEC204
|
3.1
|
70.0
|
1.0
|
C1A
|
B:HEC204
|
3.1
|
68.5
|
1.0
|
CE1
|
B:HIS102
|
3.2
|
66.6
|
1.0
|
CG
|
B:MET7
|
3.3
|
63.6
|
1.0
|
CD2
|
B:HIS102
|
3.3
|
71.1
|
1.0
|
CHB
|
B:HEC204
|
3.4
|
59.5
|
1.0
|
CHC
|
B:HEC204
|
3.4
|
70.1
|
1.0
|
CHD
|
B:HEC204
|
3.4
|
69.7
|
1.0
|
CHA
|
B:HEC204
|
3.5
|
67.3
|
1.0
|
CB
|
B:MET7
|
4.1
|
63.4
|
1.0
|
C2C
|
B:HEC204
|
4.3
|
69.8
|
1.0
|
C2B
|
B:HEC204
|
4.3
|
60.6
|
1.0
|
C3B
|
B:HEC204
|
4.3
|
60.0
|
1.0
|
C3C
|
B:HEC204
|
4.3
|
70.7
|
1.0
|
C3A
|
B:HEC204
|
4.3
|
72.2
|
1.0
|
C2D
|
B:HEC204
|
4.3
|
75.3
|
1.0
|
C3D
|
B:HEC204
|
4.3
|
73.3
|
1.0
|
C2A
|
B:HEC204
|
4.3
|
73.9
|
1.0
|
ND1
|
B:HIS102
|
4.3
|
67.7
|
1.0
|
CG
|
B:HIS102
|
4.4
|
73.3
|
1.0
|
CA
|
B:MET7
|
4.9
|
59.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 6ot9
Go back to
Iron Binding Sites List in 6ot9
Iron binding site 6 out
of 6 in the Bimetallic Dodecameric Cage Design 1 (BMC1) 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 1 (BMC1) From Cytochrome CB562 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:53.6
occ:1.00
|
FE
|
A:HEC202
|
0.0
|
53.6
|
1.0
|
ND
|
A:HEC202
|
2.0
|
55.2
|
1.0
|
NA
|
A:HEC202
|
2.0
|
51.8
|
1.0
|
NC
|
A:HEC202
|
2.1
|
55.3
|
1.0
|
NB
|
A:HEC202
|
2.1
|
57.8
|
1.0
|
NE2
|
A:HIS102
|
2.3
|
56.4
|
1.0
|
SD
|
A:MET7
|
2.5
|
62.3
|
1.0
|
C4D
|
A:HEC202
|
3.0
|
54.6
|
1.0
|
C4A
|
A:HEC202
|
3.0
|
54.4
|
1.0
|
C1C
|
A:HEC202
|
3.1
|
56.5
|
1.0
|
C1D
|
A:HEC202
|
3.1
|
47.1
|
1.0
|
C4B
|
A:HEC202
|
3.1
|
56.6
|
1.0
|
C1A
|
A:HEC202
|
3.1
|
54.6
|
1.0
|
C4C
|
A:HEC202
|
3.1
|
52.8
|
1.0
|
C1B
|
A:HEC202
|
3.1
|
53.2
|
1.0
|
CD2
|
A:HIS102
|
3.2
|
55.9
|
1.0
|
CG
|
A:MET7
|
3.4
|
58.6
|
1.0
|
CE1
|
A:HIS102
|
3.4
|
63.0
|
1.0
|
CHC
|
A:HEC202
|
3.4
|
53.9
|
1.0
|
CE
|
A:MET7
|
3.4
|
52.3
|
1.0
|
CHB
|
A:HEC202
|
3.4
|
53.3
|
1.0
|
CHA
|
A:HEC202
|
3.4
|
53.1
|
1.0
|
CHD
|
A:HEC202
|
3.4
|
53.7
|
1.0
|
CB
|
A:MET7
|
4.1
|
57.4
|
1.0
|
C3D
|
A:HEC202
|
4.2
|
62.2
|
1.0
|
C2D
|
A:HEC202
|
4.3
|
56.5
|
1.0
|
C3A
|
A:HEC202
|
4.3
|
52.1
|
1.0
|
C2A
|
A:HEC202
|
4.3
|
57.0
|
1.0
|
C2C
|
A:HEC202
|
4.3
|
61.3
|
1.0
|
C3C
|
A:HEC202
|
4.3
|
53.0
|
1.0
|
C3B
|
A:HEC202
|
4.3
|
58.7
|
1.0
|
C2B
|
A:HEC202
|
4.3
|
58.4
|
1.0
|
CG
|
A:HIS102
|
4.4
|
65.2
|
1.0
|
ND1
|
A:HIS102
|
4.4
|
65.0
|
1.0
|
CA
|
A:MET7
|
4.9
|
59.4
|
1.0
|
|
Reference:
E.Golub,
R.H.Subramanian,
J.Esselborn,
R.G.Alberstein,
J.B.Bailey,
J.A.Chiong,
X.Yan,
T.Booth,
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ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-019-1928-2
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