Iron in PDB 6ot9: Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562

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

The structure of Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562 also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

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 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 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 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 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 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 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

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