Nickel in PDB 5oa4: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with 4-Methoxycyclopeptin (1)

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with 4-Methoxycyclopeptin (1), PDB code: 5oa4 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 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.780, 120.910, 66.760, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 16.8

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with 4-Methoxycyclopeptin (1) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with 4-Methoxycyclopeptin (1) (pdb code 5oa4). 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 4-Methoxycyclopeptin (1), PDB code: 5oa4:

Nickel binding site 1 out of 1 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase ASQJ_V72I Mutant in Complex with 4-Methoxycyclopeptin (1)


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 4-Methoxycyclopeptin (1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:21.2 occ:1.00 O2 A:TRS403 1.8 24.6 0.8 OD1 A:ASP136 2.1 19.8 1.0 NE2 A:HIS134 2.1 18.1 1.0 NE2 A:HIS211 2.1 18.5 1.0 O1 A:TRS403 2.2 19.9 0.8 N A:TRS403 2.5 21.6 0.8 C2 A:TRS403 2.7 23.6 0.8 C A:TRS403 2.8 23.4 0.8 C1 A:TRS403 3.0 23.0 0.8 CE1 A:HIS211 3.1 19.1 1.0 CD2 A:HIS134 3.1 18.3 1.0 CE1 A:HIS134 3.1 18.7 1.0 CG A:ASP136 3.1 20.0 1.0 CD2 A:HIS211 3.1 18.5 1.0 OD2 A:ASP136 3.4 21.9 1.0 ND1 A:HIS211 4.2 18.7 1.0 ND1 A:HIS134 4.2 18.9 1.0 CG A:HIS211 4.2 18.7 1.0 CG A:HIS134 4.2 18.3 1.0 C3 A:TRS403 4.3 24.8 0.8 C8 A:58D402 4.4 23.4 1.0 CB A:ASP136 4.5 18.7 1.0 OE1 A:GLN131 4.6 20.2 1.0 C7 A:58D402 4.6 21.6 1.0 C9 A:58D402 4.7 24.7 1.0 CA A:ASP136 4.9 17.7 1.0 C14 A:58D402 4.9 24.7 1.0 N A:ASP136 4.9 17.7 1.0 C15 A:58D402 5.0 21.3 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