Nickel in PDB 5daw: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with Cyclopeptin

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with Cyclopeptin, PDB code: 5daw 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 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.270, 118.600, 67.220, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 19.8

The binding sites of Nickel atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Asqj in Complex with Cyclopeptin (pdb code 5daw). 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 Cyclopeptin, PDB code: 5daw:

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


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 Cyclopeptin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:19.7 occ:1.00 O1 A:AKG402 2.0 20.9 1.0 OD1 A:ASP136 2.1 18.3 1.0 O5 A:AKG402 2.2 22.6 1.0 O A:HOH521 2.2 25.4 1.0 NE2 A:HIS211 2.2 17.9 1.0 NE2 A:HIS134 2.2 18.9 1.0 C1 A:AKG402 2.8 22.2 1.0 C2 A:AKG402 2.8 22.0 1.0 CE1 A:HIS211 3.1 17.4 1.0 CG A:ASP136 3.1 18.7 1.0 CE1 A:HIS134 3.1 20.1 1.0 CD2 A:HIS211 3.1 18.7 1.0 CD2 A:HIS134 3.2 19.0 1.0 OD2 A:ASP136 3.3 18.9 1.0 O2 A:AKG402 4.0 22.4 1.0 ND1 A:HIS211 4.2 18.4 1.0 CG A:HIS211 4.2 18.2 1.0 ND1 A:HIS134 4.3 20.1 1.0 O A:HOH693 4.3 35.7 1.0 C3 A:AKG402 4.3 21.4 1.0 CG A:HIS134 4.3 19.2 1.0 C8 A:58K403 4.4 20.4 1.0 C7 A:58K403 4.5 19.3 1.0 CB A:ASP136 4.5 17.6 1.0 OE1 A:GLN131 4.7 20.1 1.0 C9 A:58K403 4.8 21.3 1.0 C4 A:AKG402 4.8 22.1 1.0 C14 A:58K403 4.8 22.9 1.0 C15 A:58K403 4.9 18.7 1.0 CA A:ASP136 4.9 17.4 1.0 N A:ASP136 5.0 17.1 1.0 C19 A:58K403 5.0 19.7 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