Cobalt in PDB 7mk4: Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2

The structure of Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2, PDB code: 7mk4 was solved by T.S.Choi, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.42 / 1.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.529, 61.075, 64.572, 90, 90, 90
R / Rfree (%)	19.6 / 21.4

The structure of Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Cobalt atom in the Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 (pdb code 7mk4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2, PDB code: 7mk4:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co202 b:14.7 occ:1.00 NE2 A:HIS100 2.1 13.5 1.0 NE2 B:HIS67 2.2 13.1 1.0 O A:HOH402 2.2 14.2 1.0 NE2 A:HIS104 2.2 13.3 1.0 NE2 B:HIS71 2.2 13.8 1.0 NE2 A:HIS60 2.3 13.9 1.0 CE1 A:HIS100 3.1 12.8 1.0 CD2 A:HIS100 3.1 14.7 1.0 CE1 B:HIS67 3.1 14.6 1.0 CE1 A:HIS60 3.1 14.8 1.0 CE1 B:HIS71 3.1 14.6 1.0 CD2 A:HIS104 3.1 14.3 1.0 CD2 B:HIS67 3.2 13.4 1.0 CE1 A:HIS104 3.2 15.5 1.0 CD2 B:HIS71 3.2 12.5 1.0 CD2 A:HIS60 3.3 13.5 1.0 ND1 A:HIS100 4.2 12.9 1.0 CG A:HIS100 4.3 14.4 1.0 ND1 B:HIS67 4.3 14.6 1.0 ND1 A:HIS60 4.3 15.7 1.0 ND1 B:HIS71 4.3 14.9 1.0 ND1 A:HIS104 4.3 16.7 1.0 CG B:HIS67 4.3 12.5 1.0 CG A:HIS104 4.3 14.3 1.0 O B:HOH368 4.3 16.8 1.0 O A:HOH437 4.3 23.0 1.0 CG B:HIS71 4.3 12.6 1.0 CG A:HIS60 4.4 14.5 1.0 O A:HOH441 4.5 29.9 1.0 O A:HOH393 4.8 16.1 1.0

Cobalt binding site 2 out of 2 in the Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Co-Bound Crystal Structure of the Engineered Cyt CB562 Variant, DICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:14.5 occ:1.00 NE2 B:HIS100 2.1 11.7 1.0 O A:HOH406 2.1 15.1 1.0 NE2 A:HIS71 2.2 12.1 1.0 NE2 B:HIS104 2.2 13.2 1.0 NE2 A:HIS67 2.2 13.2 1.0 NE2 B:HIS60 2.3 13.1 1.0 CE1 B:HIS100 3.1 12.3 1.0 CE1 A:HIS71 3.1 14.5 1.0 CE1 A:HIS67 3.1 16.2 1.0 CD2 B:HIS100 3.1 13.5 1.0 CD2 B:HIS104 3.1 12.4 1.0 CE1 B:HIS104 3.2 15.0 1.0 CD2 A:HIS67 3.2 12.5 1.0 CE1 B:HIS60 3.2 12.2 1.0 CD2 A:HIS71 3.2 11.5 1.0 CD2 B:HIS60 3.3 13.0 1.0 ND1 B:HIS100 4.2 12.7 1.0 ND1 A:HIS71 4.2 13.2 1.0 ND1 A:HIS67 4.2 15.8 1.0 CG B:HIS100 4.3 13.5 1.0 ND1 B:HIS104 4.3 16.6 1.0 CG B:HIS104 4.3 15.3 1.0 O A:HOH372 4.3 18.1 1.0 ND1 B:HIS60 4.3 12.9 1.0 CG A:HIS71 4.3 11.7 1.0 CG A:HIS67 4.3 12.6 1.0 CG B:HIS60 4.4 13.6 1.0 O B:HOH454 4.4 27.5 1.0 O B:HOH453 4.4 25.0 1.0 O B:HOH376 4.9 29.9 1.0

T.S.Choi, F.A.Tezcan. Overcoming Universal Restrictions on Metal Selectivity By Protein Design. Nature V. 603 522 2022.
ISSN: ESSN 1476-4687
PubMed: 35236987
DOI: 10.1038/S41586-022-04469-8