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:

Zinc (Zn) 6 atoms

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

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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

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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

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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

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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

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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, 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: Sun Dec 13 16:48:11 2020

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