Nickel in PDB 6w1h: Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Pseudomonas Putida

The structure of Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Pseudomonas Putida, PDB code: 6w1h 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)	72.05 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.442, 100.284, 103.577, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.4

The binding sites of Nickel atom in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Pseudomonas Putida (pdb code 6w1h). 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 Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Pseudomonas Putida, PDB code: 6w1h:

Nickel binding site 1 out of 1 in the Crystal Structure of the Hydroxyglutarate Synthase in Complex with 2- Oxoadipate From Pseudomonas Putida


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 Pseudomonas Putida within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni500 b:14.5 occ:0.94 OE1 A:GLU294 2.0 13.5 1.0 O3 A:OOG501 2.1 16.2 1.0 NE2 A:HIS226 2.1 14.3 1.0 O5 A:OOG501 2.1 17.6 1.0 NE2 A:HIS70 2.2 14.7 1.0 O A:HOH612 2.4 22.1 1.0 C6 A:OOG501 2.8 16.2 1.0 C5 A:OOG501 2.8 17.6 1.0 CE1 A:HIS226 2.9 14.9 1.0 CD A:GLU294 2.9 14.4 1.0 CE1 A:HIS70 3.0 15.9 1.0 HE1 A:HIS70 3.0 19.1 1.0 HE1 A:HIS226 3.1 17.9 1.0 CD2 A:HIS226 3.1 12.7 1.0 HG1 A:THR228 3.2 14.3 1.0 OE2 A:GLU294 3.2 18.3 1.0 CD2 A:HIS70 3.4 13.7 1.0 HD2 A:HIS226 3.4 15.3 1.0 HD2 A:HIS70 3.6 16.4 1.0 HB2 A:ALA72 3.9 16.4 1.0 OG1 A:THR228 3.9 11.9 1.0 O4 A:OOG501 4.0 15.2 1.0 ND1 A:HIS226 4.1 14.9 1.0 H21C A:OOG501 4.2 30.2 1.0 ND1 A:HIS70 4.2 14.3 1.0 CG A:HIS226 4.2 12.8 1.0 O A:HOH871 4.2 18.2 1.0 HE2 A:PHE399 4.3 17.6 1.0 H4 A:OOG501 4.3 18.2 1.0 C4 A:OOG501 4.3 18.5 1.0 CG A:GLU294 4.3 12.7 1.0 CG A:HIS70 4.4 14.2 1.0 H31C A:OOG501 4.5 26.7 1.0 HG2 A:GLU294 4.5 15.3 1.0 HD2 A:PHE399 4.5 15.0 1.0 HB3 A:GLU294 4.6 15.4 1.0 HG13 A:VAL402 4.6 27.3 1.0 O A:VAL402 4.6 19.6 1.0 HB2 A:ALA404 4.7 34.5 1.0 H41C A:OOG501 4.7 22.2 1.0 CB A:ALA72 4.7 13.7 1.0 H A:ALA404 4.7 29.1 1.0 HB3 A:ALA72 4.7 16.4 1.0 HB A:THR228 4.7 11.9 1.0 C3 A:OOG501 4.8 22.2 1.0 HG21 A:THR228 4.8 14.1 1.0 HB2 A:GLU294 4.8 15.4 1.0 H42C A:OOG501 4.8 22.2 1.0 HG12 A:VAL402 4.8 27.3 1.0 HD1 A:HIS226 4.8 17.9 1.0 CB A:GLU294 4.9 12.8 1.0 CB A:THR228 4.9 9.9 1.0 HD1 A:HIS70 4.9 17.2 1.0 C2 A:OOG501 4.9 25.1 1.0 CE2 A:PHE399 4.9 14.7 1.0 HG3 A:GLU294 5.0 15.3 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