Nickel in PDB 5daq: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxycyclopeptin

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxycyclopeptin, PDB code: 5daq was solved by M.Groll, A.Braeuer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.730, 120.010, 67.020, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.7

The binding sites of Nickel atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxycyclopeptin (pdb code 5daq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxycyclopeptin, PDB code: 5daq:

Nickel binding site 1 out of 1 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxycyclopeptin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with 4-Methoxycyclopeptin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:21.7 occ:1.00 O1 A:AKG402 2.0 23.2 1.0 O5 A:AKG402 2.2 24.5 1.0 OD1 A:ASP136 2.2 18.3 1.0 NE2 A:HIS211 2.2 18.1 1.0 O A:HOH549 2.3 25.6 1.0 NE2 A:HIS134 2.3 18.7 1.0 C1 A:AKG402 2.8 22.3 1.0 C2 A:AKG402 2.8 23.7 1.0 CG A:ASP136 3.1 19.0 1.0 CD2 A:HIS211 3.2 18.5 1.0 CE1 A:HIS211 3.2 18.1 1.0 CD2 A:HIS134 3.2 19.3 1.0 CE1 A:HIS134 3.3 18.3 1.0 OD2 A:ASP136 3.3 21.1 1.0 O2 A:AKG402 4.0 23.5 1.0 ND1 A:HIS211 4.2 18.6 1.0 O A:HOH724 4.3 41.2 1.0 CG A:HIS211 4.3 19.2 1.0 C8 A:58D403 4.3 24.6 1.0 C3 A:AKG402 4.3 24.2 1.0 ND1 A:HIS134 4.4 16.6 1.0 CG A:HIS134 4.4 18.8 1.0 C7 A:58D403 4.4 22.3 1.0 CB A:ASP136 4.5 18.1 1.0 OE1 A:GLN131 4.7 20.9 1.0 C9 A:58D403 4.7 25.7 1.0 C15 A:58D403 4.8 21.6 1.0 C4 A:AKG402 4.9 22.8 1.0 C19 A:58D403 4.9 21.1 1.0 C14 A:58D403 4.9 25.6 1.0 CA A:ASP136 4.9 17.1 1.0 C18 A:58D403 5.0 21.0 1.0 N A:ASP136 5.0 17.4 1.0

A.Brauer, P.Beck, L.Hintermann, M.Groll. Structure of the Dioxygenase Asqj: Mechanistic Insights Into A One-Pot Multistep Quinolone Antibiotic Biosynthesis. Angew.Chem.Int.Ed.Engl. V. 55 422 2016.
ISSN: ESSN 1521-3773
PubMed: 26553478
DOI: 10.1002/ANIE.201507835