Nickel in PDB 5trq: WELO5 Small Molecule Halogenase with Ni(II) and Succinate

The structure of WELO5 Small Molecule Halogenase with Ni(II) and Succinate, PDB code: 5trq was solved by M.A.Mcdonough, E.Gallimore, I.J.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.22 / 1.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.063, 46.066, 74.437, 91.77, 90.54, 108.71
R / Rfree (%)	18.8 / 20.7

The structure of WELO5 Small Molecule Halogenase with Ni(II) and Succinate also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Nickel atom in the WELO5 Small Molecule Halogenase with Ni(II) and Succinate (pdb code 5trq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the WELO5 Small Molecule Halogenase with Ni(II) and Succinate, PDB code: 5trq:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the WELO5 Small Molecule Halogenase with Ni(II) and Succinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of WELO5 Small Molecule Halogenase with Ni(II) and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:12.9 occ:1.00 O A:HOH552 2.1 15.3 1.0 NE2 A:HIS164 2.1 13.1 1.0 NE2 A:HIS259 2.1 11.6 1.0 O A:HOH406 2.2 17.8 1.0 O A:HOH599 2.2 12.7 1.0 O3 A:SIN303 2.2 13.9 1.0 CE1 A:HIS164 3.0 13.2 1.0 CE1 A:HIS259 3.1 11.4 1.0 CD2 A:HIS164 3.1 11.2 1.0 CD2 A:HIS259 3.1 10.8 1.0 C4 A:SIN303 3.2 20.5 1.0 O4 A:SIN303 3.6 22.5 1.0 O A:HOH412 3.9 28.7 1.0 ND1 A:HIS164 4.2 13.4 1.0 ND1 A:HIS259 4.2 11.6 1.0 CG A:HIS164 4.2 10.8 1.0 CG A:HIS259 4.3 11.1 1.0 OG A:SER189 4.3 14.6 1.0 O A:HOH644 4.3 21.3 1.0 O A:HOH602 4.4 39.4 1.0 O A:HOH485 4.4 15.7 1.0 O A:HOH648 4.4 16.1 1.0 C3 A:SIN303 4.5 23.1 1.0 CE1 A:PHE276 4.6 18.8 1.0 O A:HOH483 4.8 26.8 1.0

Nickel binding site 2 out of 4 in the WELO5 Small Molecule Halogenase with Ni(II) and Succinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of WELO5 Small Molecule Halogenase with Ni(II) and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:18.0 occ:1.00 O A:HOH427 2.0 20.2 1.0 OD2 A:ASP226 2.1 20.5 1.0 O A:HOH544 2.2 19.9 1.0 CG A:ASP226 3.0 28.8 1.0 OD1 A:ASP226 3.3 26.9 1.0 O A:HOH640 4.1 36.1 1.0 O A:ASP226 4.2 15.8 1.0 CB A:ASP226 4.4 19.9 1.0 C A:ASP226 4.7 14.5 1.0 CA A:ASP226 5.0 17.0 1.0

Nickel binding site 3 out of 4 in the WELO5 Small Molecule Halogenase with Ni(II) and Succinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of WELO5 Small Molecule Halogenase with Ni(II) and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:12.9 occ:1.00 NE2 B:HIS164 2.1 12.9 1.0 O4 B:SIN303 2.1 14.6 1.0 O B:HOH409 2.1 18.0 1.0 O B:HOH518 2.1 15.6 1.0 NE2 B:HIS259 2.2 12.1 1.0 O B:HOH581 2.2 13.1 1.0 CE1 B:HIS164 3.0 12.1 1.0 C4 B:SIN303 3.1 19.9 1.0 CD2 B:HIS164 3.1 12.7 1.0 CE1 B:HIS259 3.1 11.3 1.0 CD2 B:HIS259 3.2 10.3 1.0 O3 B:SIN303 3.4 21.6 1.0 O B:HOH406 3.9 29.1 1.0 ND1 B:HIS164 4.1 11.8 1.0 OG B:SER189 4.2 14.2 1.0 CG B:HIS164 4.2 11.4 1.0 ND1 B:HIS259 4.2 11.1 1.0 CG B:HIS259 4.3 9.4 1.0 O B:HOH622 4.3 22.7 1.0 O B:HOH617 4.4 32.7 1.0 O B:HOH459 4.4 15.8 1.0 O B:HOH635 4.4 18.3 1.0 C3 B:SIN303 4.5 21.3 1.0 CE1 B:PHE276 4.6 20.1 1.0 O B:HOH486 4.9 24.7 1.0

Nickel binding site 4 out of 4 in the WELO5 Small Molecule Halogenase with Ni(II) and Succinate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of WELO5 Small Molecule Halogenase with Ni(II) and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:17.8 occ:1.00 O B:HOH422 2.0 19.7 1.0 OD2 B:ASP226 2.0 18.3 1.0 O B:HOH536 2.1 20.9 1.0 O B:HOH527 2.2 20.0 1.0 CG B:ASP226 3.0 29.5 1.0 OD1 B:ASP226 3.3 23.1 1.0 O B:HOH621 4.2 33.8 1.0 O B:ASP226 4.2 16.4 1.0 O B:HOH639 4.2 49.6 1.0 CB B:ASP226 4.3 18.4 1.0 C B:ASP226 4.7 15.0 1.0 CA B:ASP226 5.0 16.9 1.0

E.O.Gallimore, M.A.Mcdonough, I.J.Clifton, C.J.Schofield. WELO5 Small Molecule Halogenase with Ni(II) and Succinate To Be Published.