Zinc in PDB 6ot8: Bimetallic Hexameric Cage Design 4 (BMC4) From Cytochrome CB562

The structure of Bimetallic Hexameric Cage Design 4 (BMC4) From Cytochrome CB562, PDB code: 6ot8 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)	48.47 / 1.50
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.000, 87.000, 63.300, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 21.8

The structure of Bimetallic Hexameric Cage Design 4 (BMC4) From Cytochrome CB562 also contains other interesting chemical elements:

Iron

(Fe)

3 atoms

The binding sites of Zinc atom in the Bimetallic Hexameric Cage Design 4 (BMC4) From Cytochrome CB562 (pdb code 6ot8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Bimetallic Hexameric Cage Design 4 (BMC4) From Cytochrome CB562, PDB code: 6ot8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Bimetallic Hexameric Cage Design 4 (BMC4) 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 Hexameric Cage Design 4 (BMC4) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:40.2 occ:0.50 OE1 A:GLU5 1.9 34.9 1.0 ND1 A:HIS8 2.0 34.2 1.0 CD A:GLU5 2.7 30.6 1.0 OE2 A:GLU5 2.8 35.2 1.0 CE1 A:HIS8 2.9 36.2 1.0 HE1 A:HIS8 3.0 43.5 1.0 CG A:HIS8 3.1 31.3 1.0 HB2 A:HIS8 3.2 35.4 1.0 HA A:GLU5 3.5 36.4 1.0 CB A:HIS8 3.5 29.5 1.0 HB3 A:HIS8 3.5 35.4 1.0 NE2 A:HIS8 4.0 37.4 1.0 CD2 A:HIS8 4.1 32.3 1.0 CG A:GLU5 4.2 49.9 1.0 CA A:GLU5 4.4 30.3 1.0 O A:HOH316 4.4 48.5 1.0 O A:HOH332 4.4 48.5 1.0 HB3 A:GLU5 4.5 37.6 1.0 CB A:GLU5 4.6 31.3 1.0 HG3 A:GLU5 4.6 59.9 1.0 HG2 A:GLU5 4.7 59.9 1.0 HG2 A:GLU4 4.7 43.3 0.5 HE2 A:HIS8 4.8 44.9 1.0 O A:GLU4 4.8 34.0 0.6 O A:HOH373 4.9 60.7 1.0 CA A:HIS8 5.0 29.8 1.0

Zinc binding site 2 out of 3 in the Bimetallic Hexameric Cage Design 4 (BMC4) 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 Hexameric Cage Design 4 (BMC4) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:33.8 occ:0.74 OD1 A:ASP21 1.8 37.1 1.0 OE1 A:GLU25 1.9 32.0 1.0 O A:HOH367 2.1 35.9 1.0 CD A:GLU25 2.7 44.4 1.0 CG A:ASP21 2.8 40.2 1.0 OE2 A:GLU25 2.9 38.2 1.0 OD2 A:ASP21 3.1 78.4 1.0 HD21 A:ASN22 3.4 44.0 1.0 H A:ASP21 3.6 38.9 1.0 HD22 A:ASN22 3.8 44.0 1.0 ND2 A:ASN22 3.9 36.6 1.0 CG A:GLU25 4.1 33.4 1.0 O A:HOH330 4.1 53.4 1.0 CB A:ASP21 4.1 39.1 1.0 HB3 A:ASP21 4.3 47.0 1.0 HG2 A:GLU25 4.3 40.1 1.0 N A:ASP21 4.4 32.4 1.0 HG3 A:GLU25 4.4 40.1 1.0 HA A:ALA20 4.6 37.1 1.0 HB2 A:ASP21 4.8 47.0 1.0 CA A:ASP21 4.8 36.3 1.0 CG A:ASN22 5.0 34.8 1.0

Zinc binding site 3 out of 3 in the Bimetallic Hexameric Cage Design 4 (BMC4) 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 Hexameric Cage Design 4 (BMC4) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:78.9 occ:0.55 NE2 A:HIS16 1.9 44.4 1.0 CD2 A:HIS16 2.7 54.2 1.0 HD2 A:HIS16 2.8 65.1 1.0 CE1 A:HIS16 3.1 93.2 1.0 HB3 A:ASP12 3.3 41.9 1.0 O A:HOH327 3.4 45.6 1.0 HE1 A:HIS16 3.4 0.9 1.0 CG A:HIS16 3.9 39.3 1.0 ND1 A:HIS16 4.1 81.2 1.0 CB A:ASP12 4.2 34.9 1.0 HB2 A:ASP12 4.5 41.9 1.0 O A:ASP12 4.6 28.6 1.0 OD2 A:ASP12 4.6 41.5 1.0 C A:ASP12 4.9 28.6 1.0 CG A:ASP12 4.9 0.8 1.0 HD1 A:HIS16 4.9 97.5 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