Zinc 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:

Iron

(Fe)

6 atoms

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Bimetallic Dodecameric Cage Design 1 (BMC1) From Cytochrome CB562, PDB code: 6ot9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc 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 Zinc with other atoms in the Zn 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:Zn201 b:68.9 occ:1.00 NE2 D:HIS77 2.1 69.7 1.0 OD2 C:ASP39 2.1 65.2 1.0 N C:ALA1 2.2 64.7 1.0 O C:ALA1 2.5 60.5 1.0 OD1 C:ASP39 2.7 60.0 1.0 CG C:ASP39 2.8 60.9 1.0 CE1 D:HIS77 2.9 67.1 1.0 CA C:ALA1 3.0 65.3 1.0 C C:ALA1 3.1 63.5 1.0 CD2 D:HIS77 3.2 62.7 1.0 CB C:ALA1 3.5 54.1 1.0 ND1 D:HIS77 4.1 69.6 1.0 CG D:HIS77 4.3 67.3 1.0 CB C:ASP39 4.3 62.3 1.0 ND2 C:ASN6 4.4 62.5 1.0 N C:ASP2 4.4 60.2 1.0 O C:ASP39 4.9 69.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn202 b:69.8 occ:1.00 OD2 C:ASP12 1.9 72.8 1.0 NE2 C:HIS8 2.2 67.9 1.0 CG C:ASP12 2.7 67.5 1.0 CD2 C:HIS8 2.8 67.2 1.0 OD1 C:ASP12 2.9 65.5 1.0 CE1 C:HIS8 3.2 65.2 1.0 CG C:HIS8 3.9 70.9 1.0 ND1 C:HIS8 4.1 77.6 1.0 CB C:ASP12 4.1 66.5 1.0 O C:HIS8 4.7 63.3 1.0

Zinc 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 Zinc with other atoms in the Zn 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 C:Zn205 b:65.8 occ:1.00 OD2 A:ASP39 1.7 68.7 1.0 NE2 C:HIS77 2.1 73.3 1.0 O A:ALA1 2.3 62.6 1.0 N A:ALA1 2.5 56.2 1.0 CG A:ASP39 2.8 68.0 1.0 CE1 C:HIS77 3.0 66.8 1.0 C A:ALA1 3.0 66.4 1.0 CA A:ALA1 3.1 55.2 1.0 OD1 A:ASP39 3.2 71.5 1.0 CD2 C:HIS77 3.2 62.8 1.0 CB A:ALA1 3.3 48.0 1.0 CB A:ASP39 4.1 58.1 1.0 ND1 C:HIS77 4.2 70.4 1.0 CG C:HIS77 4.3 67.3 1.0 O C:HOH301 4.3 54.7 1.0 N A:ASP2 4.3 62.1 1.0 ND2 A:ASN6 4.4 56.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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 D:Zn201 b:69.7 occ:0.88 OD2 D:ASP39 1.9 66.7 1.0 NE2 A:HIS77 2.1 75.5 1.0 N D:ALA1 2.2 68.6 1.0 O D:ALA1 2.6 62.7 1.0 CE1 A:HIS77 2.7 70.7 1.0 CG D:ASP39 2.8 72.9 1.0 CA D:ALA1 3.0 71.3 1.0 OD1 D:ASP39 3.1 74.2 1.0 C D:ALA1 3.1 71.0 1.0 CD2 A:HIS77 3.4 67.0 1.0 CB D:ALA1 3.4 58.4 1.0 ND1 A:HIS77 3.9 72.7 1.0 CB D:ASP39 4.2 71.8 1.0 CG A:HIS77 4.3 68.1 1.0 N D:ASP2 4.3 66.1 1.0 ND2 D:ASN6 4.3 63.3 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn201 b:68.9 occ:0.91 OD2 B:ASP39 2.1 63.4 1.0 N B:ALA1 2.1 68.4 1.0 O B:HOH302 2.1 65.6 1.0 O B:ALA1 2.5 58.5 1.0 CA B:ALA1 2.9 66.7 1.0 CG B:ASP39 3.0 76.4 1.0 C B:ALA1 3.0 61.6 1.0 CB B:ALA1 3.3 55.6 1.0 OD1 B:ASP39 3.3 81.8 1.0 CB B:ASP39 4.3 64.2 1.0 N B:ASP2 4.4 65.0 1.0 O B:HOH303 4.4 62.4 1.0 ND2 B:ASN6 4.6 65.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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 B:Zn205 b:65.3 occ:1.00 OD2 A:ASP12 2.0 66.5 1.0 OD2 B:ASP12 2.0 60.2 1.0 NE2 A:HIS8 2.1 63.1 1.0 NE2 B:HIS8 2.1 59.3 1.0 CD2 B:HIS8 2.6 59.8 1.0 CG A:ASP12 2.7 64.2 1.0 OD1 A:ASP12 2.8 59.7 1.0 CG B:ASP12 2.9 58.8 1.0 CE1 A:HIS8 2.9 61.6 1.0 CD2 A:HIS8 3.1 56.8 1.0 OD1 B:ASP12 3.1 56.2 1.0 CE1 B:HIS8 3.4 54.6 1.0 CG B:HIS8 3.9 66.9 1.0 ND1 A:HIS8 3.9 56.3 1.0 CG A:HIS8 4.0 58.4 1.0 CB A:ASP12 4.1 65.2 1.0 ND1 B:HIS8 4.2 64.3 1.0 CB B:ASP12 4.3 56.6 1.0 O A:HIS8 4.6 60.8 1.0 O B:HIS8 4.9 59.6 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