Zinc in PDB 6ovh: Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562

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

Iron

(Fe)

20 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 (pdb code 6ovh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562, PDB code: 6ovh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Cryo-Em Structure of 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 Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:65.6 occ:0.75 OD2 A:ASP39 2.1 43.8 1.0 N A:ALA1 2.2 45.8 1.0 OD1 A:ASP39 2.3 43.8 1.0 CG A:ASP39 2.5 43.8 1.0 NE2 C:HIS77 2.6 44.6 1.0 O A:ALA1 3.4 45.8 1.0 CD2 C:HIS77 3.5 44.6 1.0 CA A:ALA1 3.5 45.8 1.0 CE1 C:HIS77 3.5 44.6 1.0 C A:ALA1 3.9 45.8 1.0 CB A:ASP39 3.9 43.8 1.0 CB A:ALA1 4.4 45.8 1.0 ND1 C:HIS77 4.7 44.6 1.0 CG C:HIS77 4.7 44.6 1.0 O A:HOH308 4.7 48.9 1.0 ND2 A:ASN6 4.9 39.3 1.0 O A:ASP39 4.9 43.8 1.0 CA A:ASP39 5.0 43.8 1.0

Zinc binding site 2 out of 24 in the Cryo-Em Structure of 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 Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:58.9 occ:1.00 OD2 A:ASP12 2.2 39.4 1.0 ND1 B:HIS5 2.2 40.4 1.0 NE2 A:HIS16 2.3 42.6 1.0 ND1 B:HIS8 2.3 38.6 1.0 CG A:ASP12 3.0 39.4 1.0 CE1 B:HIS5 3.0 40.4 1.0 OD1 A:ASP12 3.1 39.4 1.0 CD2 A:HIS16 3.2 42.6 1.0 CE1 B:HIS8 3.3 38.6 1.0 CE1 A:HIS16 3.3 42.6 1.0 CG B:HIS8 3.3 38.6 1.0 CG B:HIS5 3.3 40.4 1.0 CB B:HIS8 3.6 38.6 1.0 CB B:HIS5 3.8 40.4 1.0 CA B:HIS5 3.9 40.4 1.0 O A:HOH310 4.1 44.0 1.0 NE2 B:HIS5 4.2 40.4 1.0 CG A:HIS16 4.4 42.6 1.0 CD2 B:HIS5 4.4 40.4 1.0 ND1 A:HIS16 4.4 42.6 1.0 CB A:ASP12 4.4 39.4 1.0 NE2 B:HIS8 4.4 38.6 1.0 CD2 B:HIS8 4.5 38.6 1.0 O B:HIS5 4.6 40.4 1.0 O A:ASP12 4.7 39.4 1.0 C B:HIS5 4.8 40.4 1.0 O A:HOH306 4.8 40.9 1.0 N B:HIS5 4.9 40.4 1.0

Zinc binding site 3 out of 24 in the Cryo-Em Structure of 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 Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:58.6 occ:1.00 OD2 B:ASP12 2.2 39.3 1.0 ND1 A:HIS5 2.2 39.9 1.0 NE2 B:HIS16 2.3 42.6 1.0 ND1 A:HIS8 2.3 38.6 1.0 CG B:ASP12 3.0 39.3 1.0 CE1 A:HIS5 3.1 39.9 1.0 OD1 B:ASP12 3.1 39.3 1.0 CD2 B:HIS16 3.2 42.6 1.0 CE1 A:HIS8 3.2 38.6 1.0 CE1 B:HIS16 3.3 42.6 1.0 CG A:HIS8 3.3 38.6 1.0 CG A:HIS5 3.3 39.9 1.0 CB A:HIS8 3.6 38.6 1.0 CB A:HIS5 3.7 39.9 1.0 CA A:HIS5 3.9 39.9 1.0 O B:HOH308 4.1 43.6 1.0 NE2 A:HIS5 4.2 39.9 1.0 CG B:HIS16 4.3 42.6 1.0 NE2 A:HIS8 4.4 38.6 1.0 ND1 B:HIS16 4.4 42.6 1.0 CD2 A:HIS5 4.4 39.9 1.0 CB B:ASP12 4.4 39.3 1.0 CD2 A:HIS8 4.4 38.6 1.0 O A:HIS5 4.5 39.9 1.0 O B:ASP12 4.7 39.3 1.0 C A:HIS5 4.8 39.9 1.0 N A:HIS5 4.9 39.9 1.0

Zinc binding site 4 out of 24 in the Cryo-Em Structure of 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 Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn206 b:79.5 occ:1.00 OD2 B:ASP39 2.1 45.8 1.0 N B:ALA1 2.2 48.5 1.0 OD1 B:ASP39 2.3 45.8 1.0 CG B:ASP39 2.5 45.8 1.0 NE2 F:HIS77 2.5 41.5 0.5 O B:ALA1 3.4 48.5 1.0 CD2 F:HIS77 3.4 41.5 0.5 CE1 F:HIS77 3.5 41.5 0.5 CA B:ALA1 3.5 48.5 1.0 CB B:ASP39 3.9 45.8 1.0 C B:ALA1 3.9 48.5 1.0 CB B:ALA1 4.3 48.5 1.0 ND1 F:HIS77 4.6 41.5 0.5 CG F:HIS77 4.6 41.5 0.5 O B:HOH305 4.6 48.9 1.0 ND2 B:ASN6 4.9 39.4 1.0 CA B:ASP39 5.0 45.8 1.0 O B:ASP39 5.0 45.8 1.0

Zinc binding site 5 out of 24 in the Cryo-Em Structure of 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 Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn205 b:67.5 occ:0.76 OD2 C:ASP39 2.1 44.8 1.0 N C:ALA1 2.2 48.1 1.0 OD1 C:ASP39 2.3 44.8 1.0 CG C:ASP39 2.5 44.8 1.0 NE2 D:HIS77 2.6 44.4 1.0 O C:ALA1 3.3 48.1 1.0 CD2 D:HIS77 3.4 44.4 1.0 CA C:ALA1 3.5 48.1 1.0 CE1 D:HIS77 3.6 44.4 1.0 C C:ALA1 3.8 48.1 1.0 CB C:ASP39 3.9 44.8 1.0 CB C:ALA1 4.3 48.1 1.0 CG D:HIS77 4.6 44.4 1.0 O C:HOH306 4.7 48.7 1.0 ND1 D:HIS77 4.7 44.4 1.0 ND2 C:ASN6 4.9 40.3 1.0 O C:ASP39 4.9 44.8 1.0 CA C:ASP39 5.0 44.8 1.0

Zinc binding site 6 out of 24 in the Cryo-Em Structure of 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 Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn206 b:61.2 occ:1.00 OD2 L:ASP12 2.1 38.2 1.0 NE2 L:HIS16 2.2 41.5 1.0 ND1 C:HIS5 2.2 41.2 1.0 ND1 C:HIS8 2.2 39.4 1.0 CG L:ASP12 3.0 38.2 1.0 CE1 C:HIS5 3.0 41.2 1.0 CD2 L:HIS16 3.1 41.5 1.0 OD1 L:ASP12 3.1 38.2 1.0 CG C:HIS8 3.2 39.4 1.0 CE1 C:HIS8 3.2 39.4 1.0 CE1 L:HIS16 3.3 41.5 1.0 CG C:HIS5 3.4 41.2 1.0 CB C:HIS8 3.5 39.4 1.0 CB C:HIS5 3.8 41.2 1.0 CA C:HIS5 3.9 41.2 1.0 NE2 C:HIS5 4.2 41.2 1.0 CG L:HIS16 4.3 41.5 1.0 NE2 C:HIS8 4.3 39.4 1.0 ND1 L:HIS16 4.3 41.5 1.0 CD2 C:HIS8 4.3 39.4 1.0 CB L:ASP12 4.4 38.2 1.0 CD2 C:HIS5 4.4 41.2 1.0 O C:HIS5 4.5 41.2 1.0 O L:ASP12 4.6 38.2 1.0 C C:HIS5 4.7 41.2 1.0 N C:HIS5 4.9 41.2 1.0 CA C:HIS8 5.0 39.4 1.0 C L:ASP12 5.0 38.2 1.0

Zinc binding site 7 out of 24 in the Cryo-Em Structure of 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 Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn205 b:64.9 occ:0.72 OD2 D:ASP39 2.1 43.8 1.0 N D:ALA1 2.2 46.1 1.0 OD1 D:ASP39 2.3 43.8 1.0 CG D:ASP39 2.5 43.8 1.0 NE2 A:HIS77 2.6 43.9 1.0 O D:ALA1 3.4 46.1 1.0 CD2 A:HIS77 3.5 43.9 1.0 CA D:ALA1 3.5 46.1 1.0 CE1 A:HIS77 3.6 43.9 1.0 CB D:ASP39 3.9 43.8 1.0 C D:ALA1 3.9 46.1 1.0 CB D:ALA1 4.3 46.1 1.0 CG A:HIS77 4.7 43.9 1.0 ND1 A:HIS77 4.7 43.9 1.0 O D:HOH305 4.7 49.3 1.0 ND2 D:ASN6 4.9 40.1 1.0 CA D:ASP39 5.0 43.8 1.0 O D:ASP39 5.0 43.8 1.0

Zinc binding site 8 out of 24 in the Cryo-Em Structure of 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 8 of Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn206 b:58.5 occ:1.00 OD2 D:ASP12 2.1 39.2 1.0 ND1 G:HIS5 2.2 41.0 1.0 NE2 D:HIS16 2.2 41.9 1.0 ND1 G:HIS8 2.3 38.4 1.0 CG D:ASP12 2.9 39.2 1.0 CE1 G:HIS5 3.0 41.0 1.0 OD1 D:ASP12 3.1 39.2 1.0 CD2 D:HIS16 3.1 41.9 1.0 CE1 D:HIS16 3.2 41.9 1.0 CE1 G:HIS8 3.2 38.4 1.0 CG G:HIS8 3.3 38.4 1.0 CG G:HIS5 3.3 41.0 1.0 CB G:HIS8 3.6 38.4 1.0 CB G:HIS5 3.8 41.0 1.0 CA G:HIS5 3.9 41.0 1.0 NE2 G:HIS5 4.2 41.0 1.0 CG D:HIS16 4.3 41.9 1.0 ND1 D:HIS16 4.3 41.9 1.0 CB D:ASP12 4.4 39.2 1.0 NE2 G:HIS8 4.4 38.4 1.0 CD2 G:HIS5 4.4 41.0 1.0 CD2 G:HIS8 4.4 38.4 1.0 O G:HIS5 4.5 41.0 1.0 O D:ASP12 4.6 39.2 1.0 C G:HIS5 4.8 41.0 1.0 N G:HIS5 4.9 41.0 1.0 C D:ASP12 5.0 39.2 1.0

Zinc binding site 9 out of 24 in the Cryo-Em Structure of 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 9 of Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn207 b:57.3 occ:1.00 OD2 G:ASP12 2.2 39.8 1.0 ND1 D:HIS5 2.2 41.2 1.0 NE2 G:HIS16 2.2 44.1 1.0 ND1 D:HIS8 2.3 39.4 1.0 CG G:ASP12 3.0 39.8 1.0 CE1 D:HIS5 3.1 41.2 1.0 CD2 G:HIS16 3.1 44.1 1.0 OD1 G:ASP12 3.2 39.8 1.0 CE1 D:HIS8 3.2 39.4 1.0 CE1 G:HIS16 3.3 44.1 1.0 CG D:HIS8 3.3 39.4 1.0 CG D:HIS5 3.3 41.2 1.0 CB D:HIS8 3.6 39.4 1.0 CB D:HIS5 3.8 41.2 1.0 CA D:HIS5 3.9 41.2 1.0 O G:HOH308 4.2 43.8 1.0 NE2 D:HIS5 4.2 41.2 1.0 CG G:HIS16 4.3 44.1 1.0 ND1 G:HIS16 4.3 44.1 1.0 NE2 D:HIS8 4.4 39.4 1.0 CD2 D:HIS5 4.4 41.2 1.0 CD2 D:HIS8 4.4 39.4 1.0 CB G:ASP12 4.4 39.8 1.0 O D:HIS5 4.5 41.2 1.0 O G:ASP12 4.7 39.8 1.0 C D:HIS5 4.8 41.2 1.0 N D:HIS5 4.9 41.2 1.0

Zinc binding site 10 out of 24 in the Cryo-Em Structure of 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 10 of Cryo-Em Structure of Bimetallic Dodecameric Cage Design 3 (BMC3) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn204 b:61.1 occ:0.75 OD2 E:ASP39 2.1 44.1 1.0 N E:ALA1 2.2 45.6 1.0 OD1 E:ASP39 2.4 44.1 1.0 CG E:ASP39 2.5 44.1 1.0 NE2 G:HIS77 2.5 45.2 1.0 O E:ALA1 3.3 45.6 1.0 CD2 G:HIS77 3.5 45.2 1.0 CA E:ALA1 3.5 45.6 1.0 CE1 G:HIS77 3.5 45.2 1.0 C E:ALA1 3.8 45.6 1.0 CB E:ASP39 4.0 44.1 1.0 CB E:ALA1 4.4 45.6 1.0 O E:HOH308 4.6 48.1 1.0 ND1 G:HIS77 4.6 45.2 1.0 CG G:HIS77 4.6 45.2 1.0 ND2 E:ASN6 4.9 39.0 1.0 O E:ASP39 4.9 44.1 1.0 CA E:ASP39 5.0 44.1 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