Zinc in PDB 6ot4: Bimetallic Dodecameric Cage Design 2 (BMC2) From Cytochrome CB562

The structure of Bimetallic Dodecameric Cage Design 2 (BMC2) From Cytochrome CB562, PDB code: 6ot4 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)	31.54 / 1.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	126.140, 126.140, 168.210, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 19.1

The structure of Bimetallic Dodecameric Cage Design 2 (BMC2) From Cytochrome CB562 also contains other interesting chemical elements:

Iron

(Fe)

10 atoms

The binding sites of Zinc atom in the Bimetallic Dodecameric Cage Design 2 (BMC2) From Cytochrome CB562 (pdb code 6ot4). 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 2 (BMC2) From Cytochrome CB562, PDB code: 6ot4:
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 2 (BMC2) 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 2 (BMC2) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:21.2 occ:0.80 H3 A:ALA1 1.8 34.8 1.0 H2 A:ALA1 1.8 34.8 1.0 NE2 C:HIS77 2.0 23.6 1.0 OD2 A:ASP39 2.0 20.8 1.0 O C:HOH409 2.1 31.4 1.0 N A:ALA1 2.1 29.0 1.0 O A:ALA1 2.3 21.7 1.0 CG A:ASP39 2.8 22.9 1.0 H1 A:ALA1 2.9 34.8 1.0 CE1 C:HIS77 2.9 28.7 1.0 CD2 C:HIS77 3.0 23.7 1.0 C A:ALA1 3.0 20.1 1.0 CA A:ALA1 3.0 22.2 1.0 OD1 A:ASP39 3.0 27.4 1.0 HE1 C:HIS77 3.1 34.4 1.0 HD2 C:HIS77 3.2 28.4 1.0 HB3 A:ALA1 3.2 27.4 1.0 HD21 A:ASN6 3.4 31.6 1.0 CB A:ALA1 3.6 22.8 1.0 HA A:ALA1 3.9 26.6 1.0 HB2 A:ALA1 4.0 27.4 1.0 ND1 C:HIS77 4.1 26.0 1.0 O C:HOH448 4.1 34.2 1.0 CG C:HIS77 4.1 21.8 1.0 ND2 A:ASN6 4.2 26.3 1.0 O A:HOH469 4.2 55.4 1.0 CB A:ASP39 4.2 21.4 1.0 N A:ASP2 4.3 22.6 1.0 O A:HOH419 4.4 44.1 1.0 HB3 A:ASP39 4.4 25.7 1.0 HB1 A:ALA1 4.4 27.4 1.0 O A:HOH400 4.5 26.8 1.0 HB2 A:ASP39 4.5 25.7 1.0 O A:HOH424 4.6 37.6 1.0 HD22 A:ASN6 4.6 31.6 1.0 O C:HOH391 4.6 27.3 1.0 HA A:ASP2 4.7 24.7 0.6 HA A:ASP2 4.7 27.8 0.4 O A:HOH437 4.8 57.1 1.0 O B:HOH425 4.8 27.8 1.0 HD1 C:HIS77 4.8 31.2 1.0 H A:ASP2 4.9 27.1 0.4 H A:ASP2 4.9 27.1 0.6

Zinc binding site 2 out of 6 in the Bimetallic Dodecameric Cage Design 2 (BMC2) 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 2 (BMC2) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:19.0 occ:1.00 NE2 B:HIS8 1.9 19.6 1.0 NE2 A:HIS8 2.0 15.7 1.0 OD2 B:ASP12 2.0 18.8 1.0 OD2 A:ASP12 2.0 20.2 1.0 CG B:ASP12 2.7 16.1 1.0 CG A:ASP12 2.7 18.6 1.0 OD1 B:ASP12 2.7 17.7 1.0 OD1 A:ASP12 2.8 18.5 1.0 CD2 B:HIS8 2.8 18.5 1.0 CD2 A:HIS8 2.8 18.4 1.0 HD2 B:HIS8 2.9 22.2 1.0 CE1 B:HIS8 3.0 22.9 1.0 HD2 A:HIS8 3.0 22.1 1.0 CE1 A:HIS8 3.0 20.6 1.0 HE1 B:HIS8 3.2 27.5 1.0 HE1 A:HIS8 3.3 24.7 1.0 CG B:HIS8 3.9 18.8 1.0 ND1 B:HIS8 4.0 24.2 1.0 CG A:HIS8 4.0 17.0 1.0 ND1 A:HIS8 4.1 20.6 1.0 CB B:ASP12 4.1 14.2 1.0 CB A:ASP12 4.1 15.9 1.0 O A:HOH346 4.2 24.6 1.0 O B:HOH347 4.2 24.9 1.0 HB3 B:ASP12 4.4 17.0 1.0 HB2 B:ASP12 4.4 17.0 1.0 HB3 A:ASP12 4.4 19.1 1.0 HB2 A:ASP12 4.4 19.1 1.0 O B:HOH386 4.5 27.5 1.0 O A:HOH412 4.5 38.1 1.0 O B:HOH319 4.7 28.7 1.0 HD1 B:HIS8 4.8 29.0 1.0 O A:HOH343 4.8 31.2 1.0 HD1 A:HIS8 4.9 24.8 1.0 O B:HIS8 5.0 17.2 1.0

Zinc binding site 3 out of 6 in the Bimetallic Dodecameric Cage Design 2 (BMC2) 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 2 (BMC2) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:24.7 occ:0.74 H3 D:ALA1 1.8 44.6 1.0 OD2 D:ASP39 1.9 24.8 1.0 H2 D:ALA1 2.0 44.6 1.0 NE2 A:HIS77 2.1 25.3 1.0 O D:HOH401 2.1 32.6 1.0 N D:ALA1 2.2 37.1 1.0 O D:ALA1 2.3 27.1 1.0 CG D:ASP39 2.8 29.4 1.0 OD1 D:ASP39 2.9 35.8 1.0 C D:ALA1 3.0 27.2 1.0 H1 D:ALA1 3.0 44.6 1.0 CA D:ALA1 3.0 28.9 1.0 CD2 A:HIS77 3.0 25.2 1.0 CE1 A:HIS77 3.0 31.9 1.0 HB3 D:ALA1 3.1 30.4 1.0 HD2 A:HIS77 3.2 30.3 1.0 HE1 A:HIS77 3.2 38.3 1.0 HD21 D:ASN6 3.4 38.1 1.0 CB D:ALA1 3.6 25.3 1.0 HA D:ALA1 3.9 34.7 1.0 O A:HOH314 3.9 60.3 1.0 HB2 D:ALA1 4.1 30.4 1.0 ND1 A:HIS77 4.2 33.8 1.0 O A:HOH454 4.2 36.6 1.0 CG A:HIS77 4.2 25.5 1.0 ND2 D:ASN6 4.2 31.7 1.0 CB D:ASP39 4.2 24.8 1.0 O D:HOH385 4.3 30.5 1.0 N D:ASP2 4.3 25.7 1.0 HB1 D:ALA1 4.3 30.4 1.0 O D:HOH397 4.3 48.3 1.0 HB3 D:ASP39 4.4 29.7 1.0 HB2 D:ASP39 4.6 29.7 1.0 HD22 D:ASN6 4.6 38.1 1.0 HA D:ASP2 4.7 41.4 0.6 HA D:ASP2 4.7 30.0 0.5 O A:HOH351 4.8 27.4 1.0 H D:ASP2 4.9 30.9 0.5 H D:ASP2 4.9 30.9 0.6 HD1 A:HIS77 4.9 40.5 1.0 OD1 D:ASN6 5.0 21.9 1.0

Zinc binding site 4 out of 6 in the Bimetallic Dodecameric Cage Design 2 (BMC2) 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 2 (BMC2) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:20.3 occ:0.81 H3 B:ALA1 1.6 29.9 1.0 H2 B:ALA1 1.7 29.9 1.0 OD2 B:ASP39 2.0 20.8 1.0 N B:ALA1 2.0 24.9 1.0 O B:HOH413 2.1 28.5 1.0 O B:ALA1 2.3 21.5 1.0 H1 B:ALA1 2.7 29.9 1.0 CG B:ASP39 2.8 21.6 1.0 CA B:ALA1 2.9 26.9 1.0 C B:ALA1 2.9 20.7 1.0 OD1 B:ASP39 3.1 27.7 1.0 HB3 B:ALA1 3.2 30.4 1.0 HD21 B:ASN6 3.4 26.1 1.0 CB B:ALA1 3.5 25.3 1.0 HA B:ALA1 3.7 32.3 1.0 HB2 B:ALA1 4.0 30.4 1.0 O B:HOH320 4.1 41.2 1.0 O B:HOH434 4.1 41.4 1.0 N B:ASP2 4.2 21.3 1.0 ND2 B:ASN6 4.2 21.7 1.0 CB B:ASP39 4.2 20.4 1.0 HB1 B:ALA1 4.3 30.4 1.0 HB3 B:ASP39 4.4 24.5 1.0 O B:HOH467 4.4 45.7 1.0 O B:HOH395 4.4 26.2 1.0 HB2 B:ASP39 4.6 24.5 1.0 HD22 B:ASN6 4.6 26.1 1.0 O B:HOH432 4.6 40.7 1.0 HA B:ASP2 4.7 22.4 1.0 H B:ASP2 4.8 25.6 1.0 O B:HOH428 4.9 43.7 1.0 CA B:ASP2 5.0 18.6 1.0

Zinc binding site 5 out of 6 in the Bimetallic Dodecameric Cage Design 2 (BMC2) 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 2 (BMC2) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn204 b:24.6 occ:0.84 H2 C:ALA1 1.6 35.2 1.0 H3 C:ALA1 1.8 35.2 1.0 NE2 D:HIS77 2.0 23.9 1.0 OD2 C:ASP39 2.0 24.5 1.0 N C:ALA1 2.0 29.3 1.0 O C:HOH405 2.2 31.1 1.0 O C:ALA1 2.3 22.9 1.0 H1 C:ALA1 2.8 35.2 1.0 CG C:ASP39 2.9 25.6 1.0 CA C:ALA1 2.9 26.6 1.0 C C:ALA1 2.9 25.8 1.0 CE1 D:HIS77 3.0 26.2 1.0 CD2 D:HIS77 3.0 22.6 1.0 OD1 C:ASP39 3.1 34.2 1.0 HE1 D:HIS77 3.1 31.4 1.0 HB3 C:ALA1 3.2 29.7 1.0 HD2 D:HIS77 3.3 27.2 1.0 HD21 C:ASN6 3.4 32.7 1.0 CB C:ALA1 3.6 24.8 1.0 HA C:ALA1 3.7 32.0 1.0 ND1 D:HIS77 4.1 27.4 1.0 O C:HOH460 4.1 47.1 1.0 HB2 C:ALA1 4.1 29.7 1.0 CG D:HIS77 4.2 22.2 1.0 O C:HOH407 4.2 47.9 1.0 ND2 C:ASN6 4.2 27.3 1.0 N C:ASP2 4.2 25.0 1.0 CB C:ASP39 4.3 24.7 1.0 HB1 C:ALA1 4.3 29.7 1.0 O C:HOH403 4.4 33.2 1.0 HB3 C:ASP39 4.5 29.6 1.0 HD22 C:ASN6 4.5 32.7 1.0 O D:HOH392 4.6 33.5 1.0 HB2 C:ASP39 4.6 29.6 1.0 HA C:ASP2 4.6 26.4 1.0 O C:HOH421 4.8 43.2 1.0 H C:ASP2 4.8 30.0 1.0 O C:HOH416 4.8 40.0 1.0 HD1 D:HIS77 4.9 32.8 1.0 CA C:ASP2 5.0 22.0 1.0

Zinc binding site 6 out of 6 in the Bimetallic Dodecameric Cage Design 2 (BMC2) 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 2 (BMC2) From Cytochrome CB562 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn205 b:20.4 occ:1.00 NE2 C:HIS8 2.0 21.2 1.0 OD2 C:ASP12 2.0 20.1 1.0 CG C:ASP12 2.7 17.7 1.0 OD1 C:ASP12 2.8 19.9 1.0 CD2 C:HIS8 2.8 20.3 1.0 HD2 C:HIS8 3.0 24.4 1.0 CE1 C:HIS8 3.0 23.8 1.0 HE1 C:HIS8 3.3 28.6 1.0 CG C:HIS8 4.0 19.6 1.0 ND1 C:HIS8 4.0 22.7 1.0 CB C:ASP12 4.1 16.0 1.0 O C:HOH372 4.2 24.5 1.0 O C:HOH462 4.4 45.5 1.0 HB3 C:ASP12 4.4 19.1 1.0 HB2 C:ASP12 4.4 19.1 1.0 O C:HOH364 4.5 40.6 1.0 HD1 C:HIS8 4.8 27.3 1.0 O C:HOH346 4.8 31.0 1.0 O C:HIS8 4.9 19.2 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