Nickel in PDB 5fli: Enzyme-Substrate Complex of Ni-Quercetinase

All present enzymatic activity of Enzyme-Substrate Complex of Ni-Quercetinase:
1.13.11.24;

The structure of Enzyme-Substrate Complex of Ni-Quercetinase, PDB code: 5fli 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)	47.51 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.396, 113.752, 105.003, 90.00, 96.45, 90.00
R / Rfree (%)	19.5 / 23.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Nickel atom in the Enzyme-Substrate Complex of Ni-Quercetinase (pdb code 5fli). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the Enzyme-Substrate Complex of Ni-Quercetinase, PDB code: 5fli:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 12 in the Enzyme-Substrate Complex 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 Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni300 b:22.6 occ:1.00 O27 A:QUE301 2.1 34.0 0.7 NE2 A:HIS71 2.1 27.2 1.0 NE2 A:HIS115 2.2 20.8 1.0 NE2 A:HIS69 2.3 32.5 1.0 OE2 A:GLU76 2.5 31.8 1.0 OE1 A:GLU76 2.5 10.3 1.0 O A:HOH2046 2.5 17.5 1.0 CD A:GLU76 2.8 24.9 1.0 C10 A:QUE301 2.9 34.0 0.7 CE1 A:HIS71 3.0 22.8 1.0 CD2 A:HIS71 3.2 20.5 1.0 CE1 A:HIS115 3.2 17.7 1.0 CD2 A:HIS115 3.2 17.6 1.0 CD2 A:HIS69 3.2 29.2 1.0 CE1 A:HIS69 3.3 33.1 1.0 O13 A:QUE301 3.4 34.0 0.7 C9 A:QUE301 3.5 34.0 0.7 C11 A:QUE301 3.9 34.0 0.7 C19 A:QUE301 4.0 34.0 0.7 ND1 A:HIS71 4.1 24.0 1.0 CG A:GLU76 4.2 26.3 1.0 CG A:HIS71 4.2 23.5 1.0 ND1 A:HIS115 4.3 18.9 1.0 CG A:HIS115 4.3 17.3 1.0 C14 A:QUE301 4.3 34.0 0.7 ND1 A:HIS69 4.4 30.2 1.0 CG A:HIS69 4.4 27.6 1.0 C3 A:QUE301 4.7 34.0 0.7 O12 A:QUE301 5.0 34.0 0.7

Nickel binding site 2 out of 12 in the Enzyme-Substrate Complex 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 Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni300 b:21.1 occ:1.00 NE2 B:HIS115 2.1 19.9 1.0 NE2 B:HIS69 2.2 23.2 1.0 NE2 B:HIS71 2.2 27.1 1.0 OE1 B:GLU76 2.2 6.7 1.0 O27 B:QUE301 2.3 37.5 0.8 O B:HOH2043 2.6 23.9 1.0 OE2 B:GLU76 2.8 32.3 1.0 CD B:GLU76 2.8 20.3 1.0 CE1 B:HIS115 2.9 20.7 1.0 C10 B:QUE301 3.1 37.5 0.8 CE1 B:HIS69 3.1 31.9 1.0 CE1 B:HIS71 3.1 20.7 1.0 CD2 B:HIS69 3.1 24.0 1.0 CD2 B:HIS115 3.2 16.5 1.0 CD2 B:HIS71 3.3 20.1 1.0 O13 B:QUE301 3.5 37.5 0.8 C9 B:QUE301 3.6 37.5 0.8 ND1 B:HIS115 4.1 14.6 1.0 C11 B:QUE301 4.2 37.5 0.8 ND1 B:HIS69 4.2 21.7 1.0 CG B:GLU76 4.2 19.3 1.0 CG B:HIS69 4.2 21.8 1.0 CG B:HIS115 4.2 12.2 1.0 ND1 B:HIS71 4.3 22.1 1.0 C19 B:QUE301 4.3 37.5 0.8 CG B:HIS71 4.4 24.2 1.0 C14 B:QUE301 4.6 37.5 0.8 CB B:GLU76 4.9 21.6 1.0 C3 B:QUE301 4.9 37.5 0.8

Nickel binding site 3 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni300 b:25.2 occ:1.00 O27 C:QUE301 2.0 50.1 0.9 NE2 C:HIS69 2.0 36.4 1.0 NE2 C:HIS115 2.1 18.1 1.0 NE2 C:HIS71 2.2 26.6 1.0 OE2 C:GLU76 2.3 43.2 1.0 O C:HOH2033 2.6 24.4 1.0 OE1 C:GLU76 2.6 14.0 1.0 CD C:GLU76 2.7 32.6 1.0 C10 C:QUE301 2.8 50.1 0.9 CE1 C:HIS115 2.9 18.6 1.0 CE1 C:HIS69 3.0 30.7 1.0 CD2 C:HIS69 3.1 36.3 1.0 CE1 C:HIS71 3.1 26.4 1.0 CD2 C:HIS115 3.2 20.2 1.0 CD2 C:HIS71 3.3 22.4 1.0 O13 C:QUE301 3.5 50.1 0.9 C9 C:QUE301 3.5 50.1 0.9 C11 C:QUE301 3.9 50.1 0.9 C19 C:QUE301 4.1 50.1 0.9 ND1 C:HIS69 4.1 36.7 1.0 ND1 C:HIS115 4.1 15.5 1.0 CG C:HIS69 4.2 33.1 1.0 CG C:GLU76 4.2 32.4 1.0 ND1 C:HIS71 4.2 24.0 1.0 CG C:HIS115 4.3 17.7 1.0 CG C:HIS71 4.4 26.9 1.0 C14 C:QUE301 4.4 50.1 0.9 C3 C:QUE301 4.8 50.1 0.9 O12 C:QUE301 5.0 50.1 0.9

Nickel binding site 4 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni300 b:17.8 occ:1.00 OE2 D:GLU76 1.8 15.9 1.0 NE2 D:HIS115 2.0 13.5 1.0 NE2 D:HIS71 2.1 22.4 1.0 NE2 D:HIS69 2.1 29.9 1.0 O27 D:QUE301 2.3 28.0 0.8 O D:HOH2033 2.6 21.3 1.0 CD D:GLU76 2.7 31.2 1.0 CE1 D:HIS115 2.8 18.7 1.0 C10 D:QUE301 3.0 28.0 0.8 CE1 D:HIS71 3.1 16.7 1.0 CE1 D:HIS69 3.1 26.5 1.0 OE1 D:GLU76 3.1 47.4 1.0 CD2 D:HIS69 3.1 27.1 1.0 CD2 D:HIS71 3.1 17.3 1.0 CD2 D:HIS115 3.2 15.1 1.0 O13 D:QUE301 3.4 28.0 0.8 C9 D:QUE301 3.5 28.0 0.8 ND1 D:HIS115 4.0 14.4 1.0 C11 D:QUE301 4.1 28.0 0.8 CG D:GLU76 4.1 29.4 1.0 ND1 D:HIS69 4.2 23.4 1.0 ND1 D:HIS71 4.2 20.4 1.0 CG D:HIS115 4.2 15.1 1.0 CG D:HIS69 4.2 25.1 1.0 CG D:HIS71 4.3 20.0 1.0 C19 D:QUE301 4.4 28.0 0.8 C14 D:QUE301 4.6 28.0 0.8 C3 D:QUE301 4.7 28.0 0.8

Nickel binding site 5 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni300 b:28.6 occ:1.00 NE2 E:HIS69 2.1 31.6 1.0 NE2 E:HIS115 2.1 30.9 1.0 OE1 E:GLU76 2.2 20.2 1.0 NE2 E:HIS71 2.2 49.8 1.0 O27 E:QUE301 2.2 37.2 0.8 OE2 E:GLU76 2.6 55.5 1.0 CD E:GLU76 2.7 42.0 1.0 O E:HOH2047 2.7 22.2 1.0 CE1 E:HIS115 3.0 36.8 1.0 CD2 E:HIS69 3.0 32.4 1.0 C10 E:QUE301 3.0 37.2 0.8 CE1 E:HIS69 3.1 36.2 1.0 CD2 E:HIS71 3.1 42.9 1.0 CE1 E:HIS71 3.2 42.2 1.0 CD2 E:HIS115 3.2 33.0 1.0 O13 E:QUE301 3.6 37.2 0.8 C9 E:QUE301 3.7 37.2 0.8 C19 E:QUE301 4.1 37.2 0.8 C11 E:QUE301 4.1 37.2 0.8 CG E:HIS69 4.1 36.0 1.0 ND1 E:HIS115 4.1 37.5 1.0 ND1 E:HIS69 4.1 35.8 1.0 CG E:GLU76 4.2 41.4 1.0 ND1 E:HIS71 4.3 47.0 1.0 CG E:HIS71 4.3 45.7 1.0 CG E:HIS115 4.3 35.1 1.0 C14 E:QUE301 4.5 37.2 0.8 CB E:GLU76 4.8 46.3 1.0 C3 E:QUE301 4.9 37.2 0.8

Nickel binding site 6 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni300 b:34.3 occ:1.00 OE2 F:GLU76 1.9 62.2 1.0 NE2 F:HIS115 2.1 37.4 1.0 NE2 F:HIS69 2.2 39.1 1.0 NE2 F:HIS71 2.3 50.4 1.0 O27 F:QUE301 2.4 37.1 0.8 O F:HOH2032 2.4 29.2 1.0 CD F:GLU76 2.6 48.3 1.0 OE1 F:GLU76 2.8 30.2 1.0 CD2 F:HIS69 3.0 44.2 1.0 CE1 F:HIS115 3.1 41.2 1.0 CD2 F:HIS115 3.1 38.9 1.0 C10 F:QUE301 3.1 37.1 0.8 CE1 F:HIS71 3.2 48.9 1.0 CE1 F:HIS69 3.2 43.0 1.0 CD2 F:HIS71 3.3 44.0 1.0 O13 F:QUE301 3.3 37.1 0.8 C9 F:QUE301 3.5 37.1 0.8 CG F:GLU76 3.9 46.0 1.0 ND1 F:HIS115 4.2 39.1 1.0 C11 F:QUE301 4.2 37.1 0.8 CG F:HIS69 4.2 44.1 1.0 CG F:HIS115 4.2 39.2 1.0 ND1 F:HIS69 4.3 42.0 1.0 C19 F:QUE301 4.3 37.1 0.8 ND1 F:HIS71 4.3 49.4 1.0 CG F:HIS71 4.4 46.4 1.0 C14 F:QUE301 4.7 37.1 0.8 C3 F:QUE301 4.8 37.1 0.8 CB F:GLU76 4.9 49.2 1.0

Nickel binding site 7 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni300 b:23.0 occ:1.00 OE2 G:GLU76 1.9 6.7 0.2 NE2 G:HIS115 2.0 8.9 1.0 NE2 G:HIS71 2.2 33.9 1.0 OE1 G:GLU76 2.2 6.7 0.8 NE2 G:HIS69 2.3 38.2 1.0 O27 G:QUE301 2.4 47.2 0.8 O G:HOH2033 2.5 20.2 1.0 CD G:GLU76 2.7 22.9 0.2 CE1 G:HIS115 2.9 12.6 1.0 CD G:GLU76 3.0 22.9 0.8 OE1 G:GLU76 3.0 36.3 0.2 CD2 G:HIS115 3.1 13.8 1.0 CE1 G:HIS69 3.1 39.2 1.0 CE1 G:HIS71 3.1 36.0 1.0 C10 G:QUE301 3.1 47.2 0.8 CD2 G:HIS71 3.2 26.9 1.0 OE2 G:GLU76 3.2 36.3 0.8 CD2 G:HIS69 3.2 41.5 1.0 O13 G:QUE301 3.6 47.2 0.8 C9 G:QUE301 3.7 47.2 0.8 ND1 G:HIS115 4.0 10.8 1.0 CG G:GLU76 4.1 22.4 0.2 C19 G:QUE301 4.1 47.2 0.8 C11 G:QUE301 4.1 47.2 0.8 ND1 G:HIS69 4.1 40.1 1.0 CG G:HIS115 4.2 13.1 1.0 ND1 G:HIS71 4.2 32.2 1.0 CG G:HIS69 4.3 38.6 1.0 CG G:GLU76 4.3 22.4 0.8 CG G:HIS71 4.3 34.2 1.0 C14 G:QUE301 4.6 47.2 0.8 C3 G:QUE301 4.9 47.2 0.8 CB G:GLU76 5.0 21.4 0.8

Nickel binding site 8 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni300 b:22.4 occ:1.00 NE2 H:HIS71 2.1 29.7 1.0 NE2 H:HIS69 2.1 31.6 1.0 OE1 H:GLU76 2.1 8.4 1.0 NE2 H:HIS115 2.2 28.2 1.0 O27 H:QUE301 2.2 22.5 0.8 O H:HOH2048 2.6 14.5 0.6 CD H:GLU76 2.8 24.9 1.0 C10 H:QUE301 3.0 22.5 0.8 OE2 H:GLU76 3.0 43.8 1.0 CE1 H:HIS115 3.0 26.6 1.0 CD2 H:HIS71 3.0 25.1 1.0 CD2 H:HIS69 3.0 27.1 1.0 CE1 H:HIS71 3.1 24.7 1.0 CE1 H:HIS69 3.1 24.1 1.0 CD2 H:HIS115 3.2 28.3 1.0 O13 H:QUE301 3.4 22.5 0.8 C9 H:QUE301 3.5 22.5 0.8 C11 H:QUE301 4.0 22.5 0.8 C19 H:QUE301 4.1 22.5 0.8 ND1 H:HIS71 4.2 26.6 1.0 CG H:GLU76 4.2 22.9 1.0 ND1 H:HIS115 4.2 22.5 1.0 ND1 H:HIS69 4.2 30.3 1.0 CG H:HIS71 4.2 28.5 1.0 CG H:HIS69 4.2 29.1 1.0 CG H:HIS115 4.3 26.2 1.0 C14 H:QUE301 4.5 22.5 0.8 C3 H:QUE301 4.8 22.5 0.8 CZ H:PHE78 4.8 27.1 1.0 CB H:GLU76 4.8 29.9 1.0

Nickel binding site 9 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni300 b:33.0 occ:1.00 O I:HOH2040 2.0 28.5 1.0 OE1 I:GLU76 2.1 24.3 1.0 CE1 I:HIS115 2.1 37.2 1.0 NE2 I:HIS71 2.2 48.4 1.0 NE2 I:HIS69 2.3 38.2 1.0 O I:HOH2041 2.4 33.0 1.0 NE2 I:HIS115 2.8 34.6 1.0 CD I:GLU76 2.8 45.4 1.0 OE2 I:GLU76 2.9 65.0 1.0 CE1 I:HIS69 3.1 41.7 1.0 CD2 I:HIS71 3.1 39.8 1.0 CD2 I:HIS69 3.2 42.1 1.0 CE1 I:HIS71 3.2 41.0 1.0 ND1 I:HIS115 3.3 34.8 1.0 CD2 I:HIS115 4.1 40.4 1.0 CG I:GLU76 4.2 44.4 1.0 ND1 I:HIS69 4.2 38.9 1.0 CG I:HIS69 4.3 37.6 1.0 CG I:HIS71 4.3 42.6 1.0 ND1 I:HIS71 4.3 42.5 1.0 CG I:HIS115 4.3 34.5 1.0 CB I:GLU76 4.9 49.7 1.0

Nickel binding site 10 out of 12 in the Enzyme-Substrate Complex of Ni-Quercetinase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Enzyme-Substrate Complex of Ni-Quercetinase within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni300 b:37.3 occ:1.00 OE2 J:GLU76 2.0 23.1 1.0 NE2 J:HIS115 2.0 31.8 1.0 NE2 J:HIS71 2.1 54.6 1.0 O27 J:QUE301 2.3 46.9 0.8 NE2 J:HIS69 2.3 42.7 1.0 CD J:GLU76 2.6 41.1 1.0 OE1 J:GLU76 2.6 56.1 1.0 O J:HOH2035 2.8 22.5 1.0 CE1 J:HIS115 3.0 36.4 1.0 CD2 J:HIS69 3.0 40.8 1.0 C10 J:QUE301 3.0 46.9 0.8 CD2 J:HIS115 3.0 32.4 1.0 CD2 J:HIS71 3.1 47.7 1.0 CE1 J:HIS71 3.1 52.3 1.0 CE1 J:HIS69 3.4 44.3 1.0 O13 J:QUE301 3.5 46.9 0.8 C9 J:QUE301 3.6 46.9 0.8 CG J:GLU76 4.0 41.8 1.0 C19 J:QUE301 4.0 46.9 0.8 C11 J:QUE301 4.0 46.9 0.8 ND1 J:HIS115 4.1 35.2 1.0 CG J:HIS115 4.1 33.6 1.0 CG J:HIS69 4.2 39.8 1.0 CG J:HIS71 4.2 48.7 1.0 ND1 J:HIS71 4.2 51.9 1.0 ND1 J:HIS69 4.4 39.3 1.0 C14 J:QUE301 4.5 46.9 0.8 C3 J:QUE301 4.8 46.9 0.8 CB J:GLU76 5.0 42.9 1.0

J.H.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: ESSN 1521-3773
PubMed: 26846734
DOI: 10.1002/ANIE.201510741