Cobalt in PDB 7t7k: Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+

The structure of Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+, PDB code: 7t7k was solved by A.Jacewicz, A.M.Sanchez, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.42 / 1.90
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.654, 116.314, 151.862, 90, 90, 90
R / Rfree (%)	16.4 / 19.6

The structure of Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+ also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Cobalt atom in the Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+ (pdb code 7t7k). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+, PDB code: 7t7k:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co505 b:19.1 occ:0.77 OD1 B:ASP286 2.6 23.8 1.0 OD1 B:ASN249 2.6 21.8 1.0 OD2 B:ASP195 2.8 33.2 1.0 O B:HOH643 3.0 27.2 1.0 O B:PHE283 3.0 16.4 1.0 OD1 B:ASP248 3.3 23.4 0.7 OD1 B:ASP195 3.3 24.8 1.0 CG B:ASP195 3.3 25.2 1.0 CG B:ASN249 3.6 24.7 1.0 CG B:ASP286 3.8 26.0 1.0 CB B:PHE283 3.9 19.5 1.0 OG B:SER285 3.9 23.8 1.0 O B:HOH889 3.9 37.8 1.0 O B:HOH799 4.0 26.0 1.0 ND2 B:ASN249 4.0 20.9 1.0 C B:PHE283 4.1 18.4 1.0 N B:ASP286 4.2 18.6 1.0 CG B:ASP248 4.3 19.4 0.7 N B:SER285 4.4 17.7 1.0 OD2 B:ASP286 4.5 33.3 1.0 C B:SER285 4.6 23.5 1.0 OD2 B:ASP248 4.6 20.7 0.6 CB B:ASP195 4.6 17.4 1.0 CA B:PHE283 4.6 18.8 1.0 CA B:ASP286 4.7 18.7 1.0 OG B:SER197 4.7 23.4 1.0 CB B:ASP286 4.8 20.1 1.0 CA B:SER285 4.8 20.3 1.0 CB B:ASN249 4.8 18.7 1.0 O B:HOH621 4.9 30.6 1.0 CB B:SER285 4.9 22.9 1.0 CG B:PHE283 5.0 26.2 1.0 O B:TRP282 5.0 21.1 1.0

Cobalt binding site 2 out of 4 in the Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co506 b:19.7 occ:0.81 O B:HOH910 2.7 42.2 1.0 O B:HOH601 2.8 47.0 1.0 O B:GLY172 2.8 25.6 1.0 OG B:SER174 2.8 28.3 1.0 O B:HOH866 2.9 33.7 1.0 C B:GLY172 3.6 33.1 1.0 N B:SER174 4.0 24.0 1.0 CB B:SER174 4.0 24.7 1.0 O1 B:PO4503 4.0 41.5 0.7 CA B:GLY172 4.2 24.3 1.0 O2 B:PO4503 4.5 42.8 0.7 N B:ASP173 4.5 24.8 1.0 CA B:SER174 4.6 20.8 1.0 O B:HOH856 4.8 43.5 1.0 C B:ASP173 4.9 22.7 1.0 CA B:ASP173 4.9 27.2 1.0 P B:PO4503 4.9 59.2 0.7

Cobalt binding site 3 out of 4 in the Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Co509 b:21.2 occ:1.00 OD2 A:ASP286 2.6 26.6 1.0 OD1 A:ASN249 2.7 21.5 1.0 OD2 A:ASP195 2.8 30.8 1.0 OD1 A:ASP195 2.9 29.8 1.0 O A:PHE283 3.0 17.6 1.0 O A:HOH773 3.0 25.7 1.0 CG A:ASP195 3.1 33.0 1.0 OD1 A:ASP248 3.3 24.4 0.8 CG A:ASN249 3.6 20.7 1.0 O A:HOH883 3.7 35.6 1.0 CB A:PHE283 3.8 19.9 1.0 CG A:ASP286 3.8 33.5 1.0 OG A:SER285 3.9 19.9 1.0 O A:HOH827 4.0 28.9 1.0 C A:PHE283 4.0 19.0 1.0 ND2 A:ASN249 4.0 20.7 1.0 N A:ASP286 4.2 17.5 1.0 CG A:ASP248 4.3 19.4 0.6 N A:SER285 4.3 19.8 1.0 CB A:ASP195 4.4 22.6 1.0 CA A:PHE283 4.5 18.1 1.0 OD1 A:ASP286 4.6 29.4 1.0 C A:SER285 4.6 19.5 1.0 OG A:SER197 4.6 23.1 1.0 OD2 A:ASP248 4.7 23.2 0.7 CA A:ASP286 4.7 20.0 1.0 O A:HOH605 4.8 23.5 1.0 O A:TRP282 4.8 20.4 1.0 CB A:ASP286 4.8 23.2 1.0 CA A:SER285 4.8 17.5 1.0 CB A:ASN249 4.9 22.1 1.0 CA A:ASP195 4.9 22.1 1.0 CG A:PHE283 4.9 19.6 1.0 CB A:SER285 5.0 25.0 1.0 CB A:SER197 5.0 26.1 1.0

Cobalt binding site 4 out of 4 in the Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of SPAC806.04C Protein From Fission Yeast Bound to CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Co510 b:21.6 occ:0.58 O A:ASP100 2.7 39.3 1.0 O A:ASN106 2.8 23.3 1.0 OD1 A:ASN106 3.0 30.1 1.0 O A:HOH938 3.0 28.9 1.0 CG A:ASN106 3.1 35.6 1.0 ND2 A:ASN106 3.4 43.8 1.0 C A:ASN106 3.7 29.7 1.0 O A:ASN101 3.7 36.7 1.0 C A:ASP100 3.9 44.6 1.0 CB A:ASN106 3.9 24.4 1.0 C A:ASN101 4.0 32.6 1.0 CA A:ALA102 4.1 23.6 1.0 N A:ALA102 4.2 26.6 1.0 CA A:ASN106 4.4 23.8 1.0 CE A:MET12 4.5 26.9 1.0 N A:ALA107 4.5 20.6 1.0 OD2 A:ASP100 4.6 72.4 1.0 CA A:ALA107 4.7 22.1 1.0 CB A:ASP100 4.7 46.2 1.0 CA A:ASP100 4.8 32.9 1.0 N A:ASN101 4.8 39.3 1.0 O A:HOH913 4.8 50.0 1.0 CG A:ASP100 4.9 67.0 1.0 O A:HOH635 4.9 28.3 1.0 N A:SER103 4.9 23.8 1.0 CA A:ASN101 4.9 45.6 1.0 CB A:ALA102 5.0 29.6 1.0

A.M.Sanchez, A.Jacewicz, S.Shuman. Fission Yeast DUF89 and DUF8901 Are Cobalt/Nickel-Dependent Phosphatase-Pyrophosphatases That Act Via A Covalent Aspartyl-Phosphate Intermediate. J.Biol.Chem. V. 298 01851 2022.
ISSN: ESSN 1083-351X
PubMed: 35314193
DOI: 10.1016/J.JBC.2022.101851