Iron in PDB 6ot7: Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562

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

The structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

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 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 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 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 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 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 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 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 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 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

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