Nickel in PDB 5flh: Free State of Ni-Quercetinase

The structure of Free State of Ni-Quercetinase, PDB code: 5flh was solved by J.-H.Jeoung, D.Nianios, S.Fetzner, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.70 / 1.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.692, 107.692, 144.067, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 23

The binding sites of Nickel atom in the Free State of Ni-Quercetinase (pdb code 5flh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Free State of Ni-Quercetinase, PDB code: 5flh:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Free State of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Free State of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni500 b:27.9 occ:1.00 NE2 A:HIS115 2.0 23.9 1.0 NE2 A:HIS71 2.0 29.2 1.0 OE1 A:GLU76 2.0 26.7 1.0 O A:HOH2063 2.1 27.6 1.0 NE2 A:HIS69 2.1 29.1 1.0 O A:HOH2064 2.1 31.8 1.0 CE1 A:HIS115 2.9 29.4 1.0 CE1 A:HIS71 3.0 32.5 1.0 CE1 A:HIS69 3.0 31.2 1.0 CD A:GLU76 3.0 34.0 1.0 CD2 A:HIS69 3.1 30.2 1.0 CD2 A:HIS71 3.1 30.9 1.0 CD2 A:HIS115 3.1 25.9 1.0 OE2 A:GLU76 3.4 36.3 1.0 ND1 A:HIS115 4.0 24.7 1.0 ND1 A:HIS71 4.1 29.9 1.0 ND1 A:HIS69 4.1 30.2 1.0 CG A:HIS69 4.2 32.3 1.0 CG A:HIS115 4.2 26.6 1.0 CG A:HIS71 4.2 33.1 1.0 O A:HOH2096 4.2 41.0 1.0 CG A:GLU76 4.4 32.3 1.0 CB A:GLU76 4.9 26.0 1.0

Nickel binding site 2 out of 2 in the Free State of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Free State of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni500 b:16.9 occ:1.00 NE2 B:HIS69 2.0 16.5 1.0 OE1 B:GLU76 2.0 20.2 1.0 O B:HOH2083 2.1 20.3 1.0 NE2 B:HIS115 2.1 16.6 1.0 NE2 B:HIS71 2.1 13.7 1.0 O B:HOH2082 2.1 16.8 1.0 CE1 B:HIS69 3.0 18.4 1.0 CE1 B:HIS115 3.0 16.1 1.0 CD B:GLU76 3.1 20.0 1.0 CD2 B:HIS69 3.1 14.8 1.0 CE1 B:HIS71 3.1 19.3 1.0 CD2 B:HIS71 3.1 16.2 1.0 CD2 B:HIS115 3.1 15.4 1.0 OE2 B:GLU76 3.4 22.6 1.0 O B:HOH2184 4.0 30.1 1.0 ND1 B:HIS69 4.1 17.2 1.0 ND1 B:HIS115 4.2 15.5 1.0 CG B:HIS69 4.2 16.8 1.0 ND1 B:HIS71 4.2 17.8 1.0 CG B:HIS115 4.3 14.7 1.0 CG B:HIS71 4.3 14.5 1.0 CG B:GLU76 4.5 17.3 1.0 O B:HOH2096 4.6 33.2 1.0 C2 B:DMS1187 4.7 25.6 0.8 CB B:GLU76 4.8 19.1 1.0 CZ B:PHE78 4.9 23.9 1.0

J.Jeoung, D.Nianios, S.Fetzner, H.Dobbek. Quercetin 2,4-Dioxygenase Activates Dioxygen in A Side-on O2 -Ni Complex. Angew.Chem.Int.Ed.Engl. V. 55 3281 2016.
ISSN: ISSN 1433-7851
PubMed: 26846734
DOI: 10.1002/ANIE.201510741