Zinc 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:

Iron

(Fe)

9 atoms

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc where determined in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562, PDB code: 6ot7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn202 b:32.8 occ:1.00 NE2 D:HIS16 2.0 36.4 1.0 OD1 D:ASP12 2.0 35.1 1.0 CG D:ASP12 2.8 37.2 1.0 CD2 D:HIS16 2.8 32.3 1.0 OD2 D:ASP12 2.9 38.2 1.0 CE1 D:HIS16 3.1 40.4 1.0 O D:HOH333 3.6 37.2 1.0 CG D:HIS16 4.0 38.1 1.0 ND1 D:HIS16 4.1 37.9 1.0 CB D:ASP12 4.3 31.8 1.0 O D:ASP12 4.5 30.4 1.0 C D:ASP12 4.7 32.2 1.0 CA D:ASP12 4.9 31.2 1.0

Zinc binding site 2 out of 7 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn203 b:42.8 occ:0.68 O D:HOH335 2.0 47.8 1.0 OD2 D:ASP39 2.0 45.5 1.0 N D:ALA1 2.1 46.0 1.0 NE2 A:HIS77 2.2 53.1 1.0 O D:ALA1 2.3 48.1 1.0 CG D:ASP39 2.7 52.4 1.0 OD1 D:ASP39 2.8 46.2 1.0 C D:ALA1 3.0 53.9 1.0 CA D:ALA1 3.0 48.7 1.0 CE1 A:HIS77 3.0 50.7 1.0 CD2 A:HIS77 3.3 50.2 1.0 CB D:ALA1 3.8 46.4 1.0 CB D:ASP39 4.2 41.2 1.0 ND1 A:HIS77 4.2 48.5 1.0 N D:ASP2 4.3 44.6 1.0 O D:HOH336 4.3 50.6 1.0 CG A:HIS77 4.4 55.0 1.0 ND2 D:ASN6 4.7 42.4 1.0 O D:HOH325 5.0 51.1 1.0

Zinc binding site 3 out of 7 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn208 b:40.7 occ:0.76 O C:HOH353 2.1 42.7 1.0 OD2 C:ASP39 2.1 38.7 1.0 N C:ALA1 2.1 43.5 1.0 NE2 D:HIS77 2.1 48.2 1.0 O C:ALA1 2.3 45.0 1.0 OD1 C:ASP39 2.6 48.8 1.0 CG C:ASP39 2.6 44.6 1.0 CE1 D:HIS77 3.0 47.4 1.0 C C:ALA1 3.0 48.3 1.0 CA C:ALA1 3.0 48.1 1.0 CD2 D:HIS77 3.2 43.2 1.0 CB C:ALA1 3.8 42.5 1.0 CB C:ASP39 4.1 35.0 1.0 ND1 D:HIS77 4.1 48.0 1.0 O C:HOH361 4.2 44.0 1.0 O C:HOH359 4.2 56.6 1.0 CG D:HIS77 4.3 39.8 1.0 N C:ASP2 4.3 39.1 1.0 ND2 C:ASN6 4.4 35.8 1.0

Zinc binding site 4 out of 7 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn202 b:35.2 occ:0.69 OD2 A:ASP39 2.0 34.8 1.0 NE2 C:HIS77 2.1 41.6 1.0 N A:ALA1 2.1 35.6 1.0 O A:HOH357 2.1 43.9 1.0 O A:ALA1 2.3 40.2 1.0 CG A:ASP39 2.7 44.5 1.0 OD1 A:ASP39 2.9 43.0 1.0 CE1 C:HIS77 3.0 44.8 1.0 C A:ALA1 3.0 33.2 1.0 CA A:ALA1 3.0 40.3 1.0 CD2 C:HIS77 3.1 36.6 1.0 CB A:ALA1 3.8 34.6 1.0 O A:HOH334 4.1 38.9 1.0 ND1 C:HIS77 4.1 45.1 1.0 CB A:ASP39 4.2 32.7 1.0 O A:HOH358 4.2 51.5 1.0 CG C:HIS77 4.2 39.6 1.0 O C:HOH377 4.3 54.2 1.0 N A:ASP2 4.3 33.5 1.0 ND2 A:ASN6 4.6 41.6 1.0 O A:HOH302 4.8 45.2 1.0 OD1 A:ASN6 4.8 38.2 1.0

Zinc binding site 5 out of 7 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn205 b:32.9 occ:1.00 ND1 A:HIS5 2.0 28.8 1.0 ND1 A:HIS8 2.1 31.7 1.0 NE2 B:HIS16 2.1 32.6 1.0 OD2 B:ASP12 2.1 48.0 1.0 OD1 B:ASP12 2.5 46.4 1.0 CG B:ASP12 2.6 35.8 1.0 CD2 B:HIS16 2.9 31.8 1.0 CE1 A:HIS5 2.9 37.5 1.0 CE1 A:HIS8 3.0 36.2 1.0 CG A:HIS8 3.1 31.4 1.0 CG A:HIS5 3.1 32.9 1.0 CE1 B:HIS16 3.1 35.7 1.0 CB A:HIS8 3.5 29.6 1.0 CB A:HIS5 3.6 33.9 1.0 CA A:HIS5 3.8 30.5 1.0 NE2 A:HIS5 4.1 35.7 1.0 CG B:HIS16 4.1 37.8 1.0 CB B:ASP12 4.1 32.9 1.0 NE2 A:HIS8 4.1 35.8 1.0 ND1 B:HIS16 4.2 35.4 1.0 CD2 A:HIS8 4.2 29.1 1.0 CD2 A:HIS5 4.2 38.1 1.0 O A:HIS5 4.5 29.2 1.0 O B:HOH314 4.5 48.6 1.0 C A:HIS5 4.7 33.0 1.0 O B:ASP12 4.7 32.3 1.0 N A:HIS5 4.8 28.9 1.0 C B:ASP12 4.9 32.5 1.0 O A:GLU4 5.0 29.2 0.4 CA A:HIS8 5.0 29.6 1.0

Zinc binding site 6 out of 7 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn207 b:37.0 occ:1.00 ND1 B:HIS5 1.8 31.0 1.0 ND1 B:HIS8 2.0 27.9 1.0 OD1 A:ASP12 2.0 39.0 1.0 NE2 A:HIS16 2.1 37.3 1.0 CE1 B:HIS5 2.7 40.4 1.0 CG A:ASP12 2.7 39.1 1.0 OD2 A:ASP12 2.8 39.7 1.0 CD2 A:HIS16 2.9 39.5 1.0 CG B:HIS5 2.9 41.5 1.0 CE1 B:HIS8 3.0 37.5 1.0 CG B:HIS8 3.0 30.7 1.0 CE1 A:HIS16 3.2 45.5 1.0 CB B:HIS8 3.4 34.6 1.0 CB B:HIS5 3.4 32.1 1.0 O A:HOH316 3.4 39.6 1.0 CA B:HIS5 3.6 37.6 1.0 NE2 B:HIS5 3.9 38.0 1.0 CD2 B:HIS5 4.0 38.3 1.0 NE2 B:HIS8 4.1 35.3 1.0 CG A:HIS16 4.1 38.8 1.0 CD2 B:HIS8 4.1 29.3 1.0 ND1 A:HIS16 4.2 40.7 1.0 CB A:ASP12 4.2 33.9 1.0 O A:HOH372 4.3 44.8 1.0 O B:HIS5 4.3 31.4 1.0 O A:ASP12 4.4 31.4 1.0 C B:HIS5 4.5 38.3 1.0 C A:ASP12 4.6 33.6 1.0 N B:HIS5 4.6 37.0 1.0 CA A:ASP12 4.8 33.4 1.0 CA B:HIS8 4.9 35.9 1.0 O B:GLU4 5.0 31.8 1.0

Zinc binding site 7 out of 7 in the Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 C:Zn202 b:32.3 occ:1.00 NE2 C:HIS16 2.0 32.4 1.0 OD1 C:ASP12 2.1 33.7 1.0 CG C:ASP12 2.9 37.8 1.0 CD2 C:HIS16 2.9 29.1 1.0 OD2 C:ASP12 3.0 38.3 1.0 CE1 C:HIS16 3.1 38.8 1.0 O C:HOH366 3.7 36.1 1.0 CG C:HIS16 4.1 28.6 1.0 ND1 C:HIS16 4.1 34.2 1.0 CB C:ASP12 4.4 31.8 1.0 O C:ASP12 4.6 26.1 1.0 C C:ASP12 4.8 27.6 1.0 CA C:ASP12 4.9 27.8 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