Atomistry » Nickel » PDB 6vwz-6z8m » 6w1k
Atomistry »
  Nickel »
    PDB 6vwz-6z8m »
      6w1k »

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

Protein crystallography data

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

Nickel Binding Sites:

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 6w1k

Go back to Nickel Binding Sites List in 6w1k
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 6w1k

Go back to Nickel Binding Sites List in 6w1k
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 6w1k

Go back to Nickel Binding Sites List in 6w1k
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 6w1k

Go back to Nickel Binding Sites List in 6w1k
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

Reference:

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
Page generated: Thu Oct 10 08:57:00 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy