Nickel in PDB 6w1k: Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa

The structure of Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa, PDB code: 6w1k was solved by J.H.Pereira, M.G.Thompson, J.M.Blake-Hedges, J.D.Keasling, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.79 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.300, 98.200, 203.800, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.2

The binding sites of Nickel atom in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa (pdb code 6w1k). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa, PDB code: 6w1k:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:36.4 occ:0.75 OE1 A:GLU268 1.9 59.3 1.0 NE2 A:HIS60 2.1 28.8 1.0 O5 A:OOG402 2.1 78.8 1.0 NE2 A:HIS196 2.2 30.2 1.0 O3 A:OOG402 2.3 76.3 1.0 C5 A:OOG402 2.8 78.5 1.0 CE1 A:HIS196 2.9 30.9 1.0 HE1 A:HIS196 2.9 37.1 1.0 C6 A:OOG402 2.9 77.3 1.0 CD A:GLU268 3.0 63.9 1.0 CE1 A:HIS60 3.0 29.7 1.0 CD2 A:HIS60 3.1 28.0 1.0 HE1 A:HIS60 3.2 35.6 1.0 HD2 A:HIS60 3.3 33.6 1.0 CD2 A:HIS196 3.3 29.7 1.0 OE2 A:GLU268 3.4 60.9 1.0 HD2 A:HIS196 3.7 35.6 1.0 HG21 A:ILE303 3.9 42.7 1.0 OG1 A:THR198 3.9 33.7 1.0 HB2 A:ALA62 4.0 29.6 1.0 HE21 A:GLN242 4.0 42.5 1.0 HB3 A:GLU268 4.1 48.7 1.0 HE22 A:GLN242 4.1 42.5 1.0 ND1 A:HIS196 4.1 30.4 1.0 HE1 A:PHE295 4.1 43.6 1.0 H32C A:OOG402 4.1 95.0 1.0 HG1 A:THR198 4.1 40.4 1.0 ND1 A:HIS60 4.2 29.3 1.0 O4 A:OOG402 4.2 77.0 1.0 H22C A:OOG402 4.2 94.7 1.0 HB2 A:GLU268 4.2 48.7 1.0 CG A:GLU268 4.2 51.6 1.0 C4 A:OOG402 4.2 79.1 1.0 CG A:HIS60 4.2 27.9 1.0 CG A:HIS196 4.3 29.5 1.0 NE2 A:GLN242 4.4 35.5 1.0 CB A:GLU268 4.4 40.6 1.0 H4 A:OOG402 4.4 92.4 1.0 HD13 A:ILE303 4.5 52.9 1.0 C3 A:OOG402 4.6 79.2 1.0 HG3 A:GLU268 4.6 61.9 1.0 HG22 A:ILE303 4.6 42.7 1.0 CG2 A:ILE303 4.7 35.6 1.0 H41C A:OOG402 4.7 94.9 1.0 HB3 A:ALA62 4.7 29.6 1.0 CB A:ALA62 4.7 24.7 1.0 H42C A:OOG402 4.8 94.9 1.0 HG21 A:THR198 4.8 37.1 1.0 HD1 A:HIS196 4.8 36.4 1.0 C2 A:OOG402 4.9 78.9 1.0 HG2 A:GLU268 4.9 61.9 1.0 CE1 A:PHE295 4.9 36.3 1.0 HD1 A:HIS60 4.9 35.1 1.0 HE2 A:TYR266 4.9 40.2 1.0 HD12 A:ILE303 5.0 52.9 1.0 HD1 A:PHE295 5.0 42.2 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:33.8 occ:0.73 OE2 B:GLU268 1.8 38.6 1.0 NE2 B:HIS60 2.1 30.3 1.0 O5 B:OOG402 2.2 0.2 1.0 NE2 B:HIS196 2.2 26.0 1.0 O3 B:OOG402 2.3 99.2 1.0 C5 B:OOG402 2.8 0.5 1.0 CD B:GLU268 2.9 38.1 1.0 CE1 B:HIS196 2.9 26.2 1.0 C6 B:OOG402 2.9 0.4 1.0 HE1 B:HIS196 3.0 31.4 1.0 CE1 B:HIS60 3.0 31.1 1.0 HE1 B:HIS60 3.1 37.2 1.0 CD2 B:HIS60 3.2 29.5 1.0 CD2 B:HIS196 3.3 26.3 1.0 OE1 B:GLU268 3.3 39.8 1.0 HD2 B:HIS60 3.4 35.4 1.0 HD2 B:HIS196 3.6 31.5 1.0 OG1 B:THR198 3.9 31.5 1.0 HG21 B:ILE303 4.0 35.8 1.0 HE2 B:PHE295 4.0 44.7 1.0 HG1 B:THR198 4.0 37.8 1.0 H32C B:OOG402 4.0 0.3 1.0 HE21 B:GLN242 4.1 36.0 1.0 HB2 B:ALA62 4.1 29.9 1.0 HB3 B:GLU268 4.1 33.3 1.0 ND1 B:HIS196 4.1 25.7 1.0 CG B:GLU268 4.2 33.2 1.0 ND1 B:HIS60 4.2 30.1 1.0 HB2 B:GLU268 4.2 33.3 1.0 HE22 B:GLN242 4.2 36.0 1.0 O4 B:OOG402 4.2 0.3 1.0 C4 B:OOG402 4.2 0.7 1.0 H22C B:OOG402 4.2 0.6 1.0 CG B:HIS60 4.3 28.8 1.0 CG B:HIS196 4.3 25.5 1.0 CB B:GLU268 4.4 27.8 1.0 H4 B:OOG402 4.4 0.4 1.0 NE2 B:GLN242 4.5 30.0 1.0 HD13 B:ILE303 4.5 36.9 1.0 HG22 B:ILE303 4.6 35.8 1.0 C3 B:OOG402 4.6 0.1 1.0 HG3 B:GLU268 4.6 39.8 1.0 H41C B:OOG402 4.7 1.0 1.0 CG2 B:ILE303 4.7 29.9 1.0 H42C B:OOG402 4.8 1.0 1.0 HB3 B:ALA62 4.8 29.9 1.0 HG2 B:GLU268 4.8 39.8 1.0 CE2 B:PHE295 4.8 37.3 1.0 HG21 B:THR198 4.8 33.2 1.0 CB B:ALA62 4.8 25.0 1.0 HD1 B:HIS196 4.9 30.9 1.0 HD2 B:PHE295 4.9 40.5 1.0 C2 B:OOG402 4.9 99.7 1.0 HD1 B:HIS60 4.9 36.1 1.0 HD12 B:ILE303 4.9 36.9 1.0 OH B:TYR266 4.9 29.4 1.0 HE2 B:TYR266 5.0 34.8 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni403 b:36.6 occ:0.75 OE2 C:GLU268 2.0 56.8 1.0 NE2 C:HIS60 2.1 27.2 1.0 O5 C:OOG404 2.2 87.8 1.0 O3 C:OOG404 2.2 85.1 1.0 NE2 C:HIS196 2.2 29.5 1.0 C5 C:OOG404 2.8 87.3 1.0 C6 C:OOG404 2.8 85.9 1.0 CE1 C:HIS60 2.9 27.1 1.0 CE1 C:HIS196 3.0 28.2 1.0 HE1 C:HIS196 3.0 33.9 1.0 HE1 C:HIS60 3.0 32.5 1.0 CD C:GLU268 3.0 61.9 1.0 CD2 C:HIS60 3.3 26.8 1.0 CD2 C:HIS196 3.4 30.1 1.0 OE1 C:GLU268 3.4 60.1 1.0 HD2 C:HIS60 3.5 32.2 1.0 HD2 C:HIS196 3.7 36.0 1.0 OG1 C:THR198 3.9 32.7 1.0 HG21 C:ILE303 4.0 42.1 1.0 HE21 C:GLN242 4.0 37.0 1.0 HE22 C:GLN242 4.0 37.0 1.0 HB2 C:ALA62 4.0 27.0 1.0 O4 C:OOG404 4.1 86.0 1.0 HE2 C:PHE295 4.1 35.0 1.0 H32C C:OOG404 4.1 0.9 1.0 HG1 C:THR198 4.1 39.2 1.0 ND1 C:HIS60 4.1 27.6 1.0 HB3 C:GLU268 4.2 45.2 1.0 ND1 C:HIS196 4.2 27.6 1.0 C4 C:OOG404 4.2 87.8 1.0 HB2 C:GLU268 4.2 45.2 1.0 H22C C:OOG404 4.2 0.6 1.0 CG C:GLU268 4.3 48.8 1.0 CG C:HIS60 4.3 27.5 1.0 H4 C:OOG404 4.3 0.1 1.0 NE2 C:GLN242 4.3 30.8 1.0 CG C:HIS196 4.4 28.6 1.0 CB C:GLU268 4.5 37.7 1.0 HD13 C:ILE303 4.6 53.7 1.0 C3 C:OOG404 4.6 87.5 1.0 HG22 C:ILE303 4.6 42.1 1.0 H41C C:OOG404 4.7 0.3 1.0 HG3 C:GLU268 4.7 58.5 1.0 CG2 C:ILE303 4.7 35.1 1.0 H42C C:OOG404 4.8 0.3 1.0 CB C:ALA62 4.8 22.5 1.0 HB3 C:ALA62 4.8 27.0 1.0 HG21 C:THR198 4.8 37.1 1.0 HD1 C:HIS60 4.9 33.1 1.0 CE2 C:PHE295 4.9 29.2 1.0 HD1 C:HIS196 4.9 33.1 1.0 C2 C:OOG404 4.9 86.4 1.0 HD12 C:ILE303 4.9 53.7 1.0 HG2 C:GLU268 5.0 58.5 1.0 HD2 C:PHE295 5.0 35.0 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Oryza Sativa within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:32.6 occ:0.75 OE2 D:GLU268 1.9 35.0 1.0 NE2 D:HIS60 2.1 22.5 1.0 NE2 D:HIS196 2.2 24.0 1.0 O5 D:OOG402 2.2 54.0 1.0 O3 D:OOG402 2.3 50.8 1.0 C5 D:OOG402 2.9 52.3 1.0 CE1 D:HIS196 2.9 23.4 1.0 HE1 D:HIS196 2.9 28.1 1.0 CE1 D:HIS60 2.9 23.4 1.0 CD D:GLU268 2.9 34.1 1.0 C6 D:OOG402 3.0 51.8 1.0 HE1 D:HIS60 3.0 28.1 1.0 CD2 D:HIS60 3.2 21.8 1.0 CD2 D:HIS196 3.3 23.5 1.0 OE1 D:GLU268 3.4 35.9 1.0 HD2 D:HIS60 3.5 26.1 1.0 HD2 D:HIS196 3.7 28.2 1.0 OG1 D:THR198 3.9 31.5 1.0 HG21 D:ILE303 3.9 34.6 1.0 HB2 D:ALA62 4.0 24.1 1.0 HE21 D:GLN242 4.0 33.3 1.0 HE1 D:PHE295 4.1 37.9 1.0 HE22 D:GLN242 4.1 33.3 1.0 ND1 D:HIS196 4.1 23.6 1.0 H22C D:OOG402 4.1 58.4 1.0 ND1 D:HIS60 4.1 23.1 1.0 HB3 D:GLU268 4.1 30.8 1.0 HG1 D:THR198 4.1 37.8 1.0 O4 D:OOG402 4.2 51.7 1.0 CG D:GLU268 4.2 29.9 1.0 HB2 D:GLU268 4.2 30.8 1.0 CG D:HIS60 4.3 21.9 1.0 C4 D:OOG402 4.3 50.9 1.0 H32C D:OOG402 4.3 59.8 1.0 CG D:HIS196 4.3 22.6 1.0 HD13 D:ILE303 4.3 38.5 1.0 NE2 D:GLN242 4.4 27.8 1.0 H4 D:OOG402 4.4 62.0 1.0 CB D:GLU268 4.4 25.7 1.0 HG22 D:ILE303 4.5 34.6 1.0 HG3 D:GLU268 4.6 35.9 1.0 CG2 D:ILE303 4.7 28.9 1.0 C3 D:OOG402 4.7 49.8 1.0 H41C D:OOG402 4.8 61.0 1.0 HG21 D:THR198 4.8 35.3 1.0 HB3 D:ALA62 4.8 24.1 1.0 CB D:ALA62 4.8 20.2 1.0 HD1 D:HIS196 4.8 28.2 1.0 CE1 D:PHE295 4.8 31.6 1.0 C2 D:OOG402 4.8 48.7 1.0 HD1 D:HIS60 4.9 27.6 1.0 H42C D:OOG402 4.9 61.0 1.0 HD1 D:PHE295 4.9 35.4 1.0 HG2 D:GLU268 4.9 35.9 1.0

M.G.Thompson, J.M.Blake-Hedges, J.H.Pereira, J.A.Hangasky, M.S.Belcher, W.M.Moore, J.F.Barajas, P.Cruz-Morales, L.J.Washington, R.W.Haushalter, C.B.Eiben, Y.Liu, W.Skyrud, V.T.Benites, T.P.Barnum, E.E.K.Baidoo, H.V.Scheller, M.A.Marletta, P.M.Shih, P.D.Adams, J.D.Keasling. An Iron (II) Dependent Oxygenase Performs the Last Missing Step of Plant Lysine Catabolism. Nat Commun V. 11 2931 2020.
ISSN: ESSN 2041-1723
PubMed: 32523014
DOI: 10.1038/S41467-020-16815-3