Nickel in PDB 8hfb: Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis

All present enzymatic activity of Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis:
1.13.11.24;

The structure of Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis, PDB code: 8hfb was solved by H.Eom, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.19 / 2.24
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	94.299, 125.211, 119.008, 90, 90, 90
R / Rfree (%)	21.3 / 25.1

The binding sites of Nickel atom in the Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis (pdb code 8hfb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis, PDB code: 8hfb:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1005 b:52.7 occ:1.00 O A:HOH1163 2.1 45.3 1.0 NE2 A:HIS275 2.2 53.3 1.0 OE2 A:GLU241 2.2 55.6 1.0 NE2 A:HIS234 2.2 61.2 1.0 O A:HOH1170 2.3 53.2 1.0 NE2 A:HIS236 2.3 58.8 1.0 CE1 A:HIS275 3.0 53.7 1.0 CE1 A:HIS234 3.1 61.6 1.0 CD A:GLU241 3.2 55.0 1.0 CE1 A:HIS236 3.2 59.2 1.0 CD2 A:HIS275 3.3 53.6 1.0 CD2 A:HIS234 3.3 61.1 1.0 CD2 A:HIS236 3.4 59.0 1.0 OE1 A:GLU241 3.4 56.3 1.0 ND1 A:HIS275 4.2 53.7 1.0 ND1 A:HIS234 4.2 61.6 1.0 CG A:HIS275 4.3 53.6 1.0 ND1 A:HIS236 4.4 59.6 1.0 CG A:HIS234 4.4 61.4 1.0 CG A:HIS236 4.5 59.8 1.0 CG A:GLU241 4.5 54.4 1.0 CZ A:PHE243 4.7 52.7 1.0 CB A:GLU241 4.9 53.4 1.0

Nickel binding site 2 out of 4 in the Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1006 b:50.2 occ:1.00 OE1 A:GLU69 2.2 51.8 1.0 NE2 A:HIS64 2.2 55.5 1.0 NE2 A:HIS103 2.2 48.5 1.0 O A:HOH1118 2.2 46.9 1.0 NE2 A:HIS62 2.3 54.0 1.0 O A:HOH1176 2.4 44.6 1.0 CD2 A:HIS64 3.1 55.5 1.0 CD A:GLU69 3.1 52.2 1.0 CE1 A:HIS103 3.2 49.1 1.0 CE1 A:HIS62 3.2 54.0 1.0 CD2 A:HIS103 3.2 48.7 1.0 CE1 A:HIS64 3.2 55.7 1.0 CD2 A:HIS62 3.3 54.1 1.0 OE2 A:GLU69 3.4 51.8 1.0 CG A:HIS64 4.3 56.0 1.0 ND1 A:HIS103 4.3 49.0 1.0 ND1 A:HIS64 4.3 55.9 1.0 ND1 A:HIS62 4.3 54.3 1.0 CG A:HIS103 4.4 48.8 1.0 CG A:HIS62 4.4 54.2 1.0 CG A:GLU69 4.5 52.2 1.0 CB A:GLU69 4.9 52.1 1.0

Nickel binding site 3 out of 4 in the Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:51.3 occ:1.00 OE2 B:GLU69 2.2 53.5 1.0 NE2 B:HIS103 2.2 51.6 1.0 NE2 B:HIS62 2.2 52.5 1.0 O B:HOH664 2.2 50.2 1.0 NE2 B:HIS64 2.3 54.6 1.0 O B:HOH610 2.4 54.1 1.0 CD B:GLU69 3.0 53.8 1.0 CE1 B:HIS62 3.2 52.8 1.0 CE1 B:HIS103 3.2 51.7 1.0 CD2 B:HIS64 3.2 54.8 1.0 OE1 B:GLU69 3.2 54.0 1.0 CE1 B:HIS64 3.3 54.6 1.0 CD2 B:HIS103 3.3 51.9 1.0 CD2 B:HIS62 3.3 52.5 1.0 ND1 B:HIS62 4.3 52.7 1.0 ND1 B:HIS103 4.3 51.5 1.0 ND1 B:HIS64 4.4 55.2 1.0 CG B:HIS64 4.4 55.4 1.0 CG B:HIS103 4.4 52.0 1.0 CG B:HIS62 4.4 52.8 1.0 CG B:GLU69 4.5 53.6 1.0 CB B:GLU69 4.9 53.5 1.0

Nickel binding site 4 out of 4 in the Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Evolved Variant of Quercetin 2,4-Dioxygenase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni503 b:58.7 occ:1.00 OE2 B:GLU241 2.0 61.7 1.0 NE2 B:HIS275 2.2 58.8 1.0 O B:HOH647 2.2 58.0 1.0 NE2 B:HIS236 2.2 75.2 1.0 O B:HOH632 2.3 55.6 1.0 NE2 B:HIS234 2.3 70.8 1.0 CD2 B:HIS236 3.0 74.9 1.0 CD B:GLU241 3.1 62.1 1.0 CE1 B:HIS234 3.1 71.5 1.0 CE1 B:HIS275 3.2 59.1 1.0 CD2 B:HIS275 3.2 58.8 1.0 CE1 B:HIS236 3.3 75.2 1.0 CD2 B:HIS234 3.4 71.3 1.0 OE1 B:GLU241 3.5 63.9 1.0 CG B:HIS236 4.2 75.0 1.0 ND1 B:HIS275 4.3 58.5 1.0 ND1 B:HIS234 4.3 71.6 1.0 ND1 B:HIS236 4.3 75.4 1.0 CG B:HIS275 4.3 58.6 1.0 CG B:GLU241 4.4 61.5 1.0 CG B:HIS234 4.5 71.4 1.0 CZ B:PHE243 4.6 55.3 1.0 CB B:GLU241 4.8 60.6 1.0

H.Eom, Y.Cao, H.Kim, S.P.De Visser, W.J.Song. Underlying Role of Hydrophobic Environments in Tuning Metal Elements For Efficient Enzyme Catalysis. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 36853654
DOI: 10.1021/JACS.2C13337