Nickel in PDB 5oa8: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with Demethylated Cyclopeptin (1D)

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with Demethylated Cyclopeptin (1D), PDB code: 5oa8 was solved by M.Groll, A.Braeuer, V.R.I.Kaila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	73.090, 120.060, 67.020, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.3

The binding sites of Nickel atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with Demethylated Cyclopeptin (1D) (pdb code 5oa8). 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_V72I Mutant in Complex with Demethylated Cyclopeptin (1D), PDB code: 5oa8:

Nickel binding site 1 out of 1 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with Demethylated Cyclopeptin (1D)


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_V72I Mutant in Complex with Demethylated Cyclopeptin (1D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:27.0 occ:1.00 OD1 A:ASP136 2.1 21.8 1.0 NE2 A:HIS211 2.1 22.6 1.0 O5 A:AKG402 2.1 29.8 1.0 NE2 A:HIS134 2.2 23.1 1.0 O1 A:AKG402 2.3 35.4 1.0 O A:HOH573 2.3 31.1 1.0 C2 A:AKG402 2.9 33.3 1.0 C1 A:AKG402 3.0 34.7 1.0 CE1 A:HIS211 3.1 23.6 1.0 CE1 A:HIS134 3.1 23.4 1.0 CG A:ASP136 3.1 24.5 1.0 CD2 A:HIS211 3.1 22.6 1.0 CD2 A:HIS134 3.2 23.1 1.0 OD2 A:ASP136 3.3 25.9 1.0 ND1 A:HIS211 4.2 23.4 1.0 ND1 A:HIS134 4.2 22.7 1.0 O2 A:AKG402 4.2 37.0 1.0 CG A:HIS211 4.2 23.6 1.0 CG A:HIS134 4.3 23.1 1.0 C3 A:AKG402 4.4 31.5 1.0 C7 A:58L403 4.5 33.8 1.0 CB A:ASP136 4.5 23.8 1.0 C8 A:58L403 4.6 33.2 1.0 OE1 A:GLN131 4.6 25.5 1.0 C14 A:58L403 4.7 34.1 1.0 C9 A:58L403 4.7 34.1 1.0 CA A:ASP136 4.9 22.5 1.0 C15 A:58L403 4.9 35.6 1.0 C4 A:AKG402 4.9 28.9 1.0 N A:ASP136 5.0 21.6 1.0

S.L.Mader, A.Brauer, M.Groll, V.R.I.Kaila. Catalytic Mechanism and Molecular Engineering of Quinolone Biosynthesis in Dioxygenase Asqj. Nat Commun V. 9 1168 2018.
ISSN: ESSN 2041-1723
PubMed: 29563492
DOI: 10.1038/S41467-018-03442-2