Zinc in PDB 5awi: Domain-Swapped Cytochrome CB562 Dimer

The structure of Domain-Swapped Cytochrome CB562 Dimer, PDB code: 5awi was solved by T.Miyamoto, M.Kuribayashi, S.Nagao, Y.Shomura, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.31 / 1.85
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	94.608, 94.608, 94.608, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.5

The structure of Domain-Swapped Cytochrome CB562 Dimer also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Domain-Swapped Cytochrome CB562 Dimer (pdb code 5awi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Domain-Swapped Cytochrome CB562 Dimer, PDB code: 5awi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:29.5 occ:1.00 OD2 A:ASP5 1.8 28.9 1.0 O1 A:SO4206 2.0 25.1 1.0 O3 A:SO4207 2.1 24.3 1.0 CG A:ASP5 2.7 28.2 1.0 OD1 A:ASP5 3.0 28.5 1.0 O3 A:SO4206 3.1 26.1 1.0 S A:SO4206 3.1 25.5 1.0 S A:SO4207 3.2 28.3 1.0 O2 A:SO4207 3.2 23.4 1.0 O3 B:SO4204 3.3 29.2 0.3 O A:HOH304 3.5 28.0 0.3 O A:HOH302 3.8 25.4 1.0 ZN B:ZN201 3.9 27.8 1.0 O4 B:SO4204 4.0 29.2 0.3 CB A:ASP5 4.1 27.1 1.0 O2 A:SO4206 4.1 29.8 1.0 S B:SO4204 4.2 28.2 0.3 O4 A:SO4206 4.2 22.6 1.0 O4 A:SO4207 4.3 23.8 1.0 O1 A:SO4207 4.3 27.6 1.0 O1 B:SO4204 4.5 25.4 0.3 OD1 A:ASP2 4.8 29.8 1.0 ZN A:ZN204 4.9 36.9 1.0

Zinc binding site 2 out of 7 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:31.4 occ:1.00 OE1 A:GLU8 1.8 28.4 1.0 O4 A:SO4206 2.1 22.6 1.0 CD A:GLU8 2.5 26.7 1.0 OE2 A:GLU8 2.6 28.4 1.0 O3 A:SO4206 3.0 26.1 1.0 S A:SO4206 3.1 25.5 1.0 OD1 A:ASP5 3.8 28.5 1.0 O A:HOH328 4.0 38.5 1.0 CG A:GLU8 4.0 26.9 1.0 O2 A:SO4206 4.0 29.8 1.0 O1 A:SO4206 4.2 25.1 1.0 CB A:GLU8 4.5 26.2 1.0 CG A:ASP5 4.7 28.2 1.0

Zinc binding site 3 out of 7 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:36.9 occ:1.00 O4 A:SO4207 1.9 23.8 1.0 OD2 A:ASP2 2.0 27.6 1.0 CG A:ASP2 2.8 29.3 1.0 OD1 A:ASP2 3.1 29.8 1.0 S A:SO4207 3.1 28.3 1.0 O3 A:SO4207 3.4 24.3 1.0 O2 A:SO4207 4.0 23.4 1.0 O1 A:SO4207 4.0 27.6 1.0 OD1 A:ASP5 4.1 28.5 1.0 O A:HOH318 4.1 29.5 1.0 CB A:ASP2 4.2 28.5 1.0 OE1 A:GLU4 4.3 37.5 1.0 CB A:GLU4 4.3 29.7 1.0 N B:ALA1 4.4 33.5 1.0 CG A:ASP5 4.5 28.2 1.0 OD2 A:ASP5 4.6 28.9 1.0 CD A:GLU4 4.6 34.9 1.0 O A:HOH302 4.7 25.4 1.0 ZN A:ZN202 4.9 29.5 1.0 CG A:GLU4 4.9 32.9 1.0 N A:ASP5 4.9 27.0 1.0

Zinc binding site 4 out of 7 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:38.2 occ:1.00 OD2 A:ASP39 2.2 29.8 1.0 O A:ALA1 2.5 27.1 1.0 N A:ALA1 2.6 30.3 1.0 CG A:ASP39 3.0 28.1 1.0 OD1 A:ASP39 3.0 29.2 1.0 C A:ALA1 3.3 29.8 1.0 CA A:ALA1 3.4 29.6 1.0 CB A:ALA1 3.9 29.6 1.0 NZ A:LYS42 4.1 44.6 1.0 CE A:LYS42 4.3 42.7 1.0 CB A:ASP39 4.4 27.4 1.0 O A:HOH324 4.4 26.7 1.0 N A:ASP2 4.6 29.5 1.0 OD1 A:ASN6 4.7 26.8 1.0

Zinc binding site 5 out of 7 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:27.8 occ:1.00 OD2 B:ASP5 1.9 27.3 1.0 O2 A:SO4207 2.0 23.4 1.0 O1 B:SO4204 2.0 25.4 0.3 CG B:ASP5 2.9 26.6 1.0 S A:SO4207 3.1 28.3 1.0 S B:SO4204 3.1 28.2 0.3 OD1 B:ASP5 3.2 25.5 1.0 O3 B:SO4204 3.4 29.2 0.3 ZN B:ZN202 3.4 30.6 1.0 O1 A:SO4207 3.4 27.6 1.0 O4 B:SO4204 3.7 29.2 0.3 O3 A:SO4207 3.7 24.3 1.0 ZN A:ZN202 3.9 29.5 1.0 OD1 B:ASP2 4.1 29.2 1.0 OD2 B:ASP2 4.2 30.0 1.0 CG B:ASP2 4.2 29.1 1.0 CB B:ASP5 4.2 26.6 1.0 O4 A:SO4207 4.3 23.8 1.0 O2 B:SO4204 4.3 29.2 0.3 N B:ASP2 4.4 29.5 1.0 CA B:ALA1 4.5 32.5 1.0 O A:HOH302 4.7 25.4 1.0 OE1 B:GLU4 4.8 33.6 1.0 C B:ALA1 5.0 31.5 1.0 O B:HOH301 5.0 21.0 1.0

Zinc binding site 6 out of 7 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:30.6 occ:1.00 O B:HOH301 1.9 21.0 1.0 OD1 B:ASP5 2.1 25.5 1.0 OE1 B:GLU4 2.6 33.6 1.0 OE2 B:GLU4 2.8 34.4 1.0 CD B:GLU4 3.0 33.7 1.0 CG B:ASP5 3.1 26.6 1.0 ZN B:ZN201 3.4 27.8 1.0 OD2 B:ASP5 3.5 27.3 1.0 OD1 B:ASP2 4.2 29.2 1.0 O1 B:SO4204 4.2 25.4 0.3 CB B:ASP5 4.4 26.6 1.0 OD2 B:ASP2 4.5 30.0 1.0 CG B:GLU4 4.5 33.3 1.0 N B:ASP5 4.6 26.6 1.0 OE1 B:GLU8 4.6 29.9 1.0 CA B:ASP5 4.6 26.5 1.0 CG B:ASP2 4.8 29.1 1.0

Zinc binding site 7 out of 7 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:78.9 occ:1.00 O B:HOH312 2.0 31.4 1.0 O B:ALA1 2.5 31.6 1.0 OD2 B:ASP39 2.8 38.0 1.0 O B:HOH308 3.2 32.6 1.0 OD1 B:ASP39 3.3 40.2 1.0 CG B:ASP39 3.4 36.0 1.0 C B:ALA1 3.6 31.5 1.0 N B:ALA1 3.8 33.5 1.0 CA B:ALA1 4.1 32.5 1.0 O A:HOH318 4.2 29.5 1.0 CB B:ALA1 4.5 33.0 1.0 N B:ASP2 4.7 29.5 1.0 CB B:ASP39 4.9 33.6 1.0

T.Miyamoto, M.Kuribayashi, S.Nagao, Y.Shomura, Y.Higuchi, S.Hirota. Domain-Swapped Cytochrome CB562 Dimer and Its Nanocage Encapsulating A Zn-SO4 Cluster in the Internal Cavity Chem Sci 2015.
ISSN: ESSN 2041-6539
DOI: 10.1039/C5SC02428E