Nickel in PDB 7u1v: Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3

The structure of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3, PDB code: 7u1v 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)	59.49 / 2.10
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.495, 115.864, 161.674, 90, 90, 90
R / Rfree (%)	17.9 / 20.9

The structure of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 also contains other interesting chemical elements:

Potassium	(K)	1 atom
Fluorine	(F)	6 atoms

The binding sites of Nickel atom in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 (pdb code 7u1v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3, PDB code: 7u1v:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:31.9 occ:0.54 O A:HOH667 2.0 31.3 1.0 OD1 A:ASP286 2.0 31.0 1.0 OD2 A:BFD248 2.0 31.3 1.0 F2 A:BFD248 2.1 34.5 1.0 O A:HOH650 2.2 28.9 1.0 OD1 A:ASN249 2.2 32.7 1.0 CG A:ASP286 3.0 32.5 1.0 CG A:BFD248 3.0 28.5 1.0 CG A:ASN249 3.0 32.2 1.0 BE A:BFD248 3.1 36.0 1.0 OD2 A:ASP286 3.4 32.2 1.0 ND2 A:ASN249 3.4 32.4 1.0 F3 A:BFD248 3.4 32.4 1.0 OD1 A:BFD248 3.4 32.7 1.0 O A:HOH739 4.0 36.7 1.0 OD1 A:ASP195 4.0 33.7 1.0 CG A:ASP195 4.2 34.6 1.0 OG A:SER285 4.3 30.6 1.0 O A:PHE283 4.3 32.3 1.0 N A:ASN249 4.3 31.2 1.0 CB A:ASN249 4.3 29.3 1.0 CB A:ASP286 4.3 29.4 1.0 CB A:BFD248 4.4 31.1 1.0 C A:BFD248 4.4 31.4 1.0 OD2 A:ASP195 4.4 39.6 1.0 F1 A:BFD248 4.4 30.1 1.0 CB A:PHE283 4.4 30.3 1.0 CA A:ASN249 4.5 32.3 1.0 CA A:ASP286 4.5 31.5 1.0 N A:ASP286 4.6 30.4 1.0 CA A:BFD248 4.7 34.3 1.0 O A:HOH689 4.8 29.5 1.0 O A:BFD248 4.8 30.1 1.0 O A:HOH694 5.0 32.2 1.0

Nickel binding site 2 out of 3 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:49.1 occ:1.00 OD1 B:ASP286 2.0 32.4 1.0 OD2 B:BFD248 2.1 34.8 1.0 F1 B:BFD248 2.1 32.0 1.0 O B:HOH654 2.2 30.7 1.0 O B:HOH661 2.2 31.4 1.0 OD1 B:ASN249 2.2 35.4 1.0 CG B:ASP286 3.0 31.0 1.0 CG B:ASN249 3.0 33.8 1.0 CG B:BFD248 3.1 31.1 1.0 BE B:BFD248 3.1 33.9 1.0 ND2 B:ASN249 3.3 30.8 1.0 OD2 B:ASP286 3.3 32.0 1.0 OD1 B:BFD248 3.5 28.2 1.0 F2 B:BFD248 3.5 29.0 1.0 OD1 B:ASP195 4.0 39.6 1.0 O B:HOH801 4.1 35.6 1.0 OG B:SER285 4.2 34.7 1.0 O B:PHE283 4.2 33.3 1.0 OD2 B:ASP195 4.3 42.5 1.0 CG B:ASP195 4.3 40.5 1.0 CB B:ASP286 4.3 30.7 1.0 CB B:ASN249 4.3 34.0 1.0 N B:ASN249 4.4 28.1 1.0 C B:BFD248 4.4 31.2 1.0 CB B:BFD248 4.4 29.8 1.0 CB B:PHE283 4.4 31.5 1.0 CA B:ASP286 4.5 33.7 1.0 F3 B:BFD248 4.5 30.7 1.0 CA B:ASN249 4.5 31.9 1.0 N B:ASP286 4.5 29.8 1.0 CA B:BFD248 4.7 30.9 1.0 O B:BFD248 4.8 31.1 1.0 O B:HOH735 4.8 30.4 1.0

Nickel binding site 3 out of 3 in the Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of SPAC806.04C Protein From Fission Yeast Covalently Bound to BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:77.0 occ:0.40 O B:HOH621 1.9 55.5 1.0 O B:HOH601 2.0 63.8 1.0 O B:HOH777 2.7 69.6 1.0 O B:HOH774 3.2 60.2 1.0 N B:MET1 3.9 58.9 1.0 O B:ASP343 4.3 50.9 1.0 CA B:MET1 4.8 58.6 1.0 O B:HOH773 4.9 56.6 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