Nickel in PDB 1ynu: Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine

All present enzymatic activity of Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine:
4.4.1.14;

The structure of Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine, PDB code: 1ynu was solved by G.Capitani, M.Tschopp, A.C.Eliot, J.F.Kirsch, M.G.Grutter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.300, 59.360, 79.050, 90.00, 124.20, 90.00
R / Rfree (%)	23.4 / 28.9

The structure of Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine (pdb code 1ynu). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine, PDB code: 1ynu:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine


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 Apple Acc Synthase in Complex with L-Vinylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:66.6 occ:1.00 NE2 A:HIS113 2.0 32.8 1.0 O A:HOH928 2.1 49.1 1.0 O A:HOH1019 2.5 48.6 1.0 O A:HOH983 2.5 66.8 1.0 OD1 A:ASP290 2.9 45.1 1.0 CE1 A:HIS113 2.9 31.7 1.0 CD2 A:HIS113 3.1 31.8 1.0 O A:HOH948 3.5 53.8 1.0 CG A:ASP290 3.8 44.9 1.0 OD2 A:ASP290 4.0 46.2 1.0 ND1 A:HIS113 4.1 32.4 1.0 CG A:HIS113 4.2 31.6 1.0 O A:HOH959 4.8 45.7 1.0 O A:HOH972 4.8 61.4 1.0 OD2 A:ASP110 4.9 44.7 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Apple Acc Synthase in Complex with L-Vinylglycine


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 Apple Acc Synthase in Complex with L-Vinylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:46.9 occ:1.00 N A:TRS901 1.9 37.0 1.0 ND1 A:HIS86 2.1 36.1 1.0 OD1 A:ASP84 2.3 34.5 1.0 O A:HOH1012 2.5 30.3 1.0 O1 A:TRS901 2.5 37.2 1.0 CG A:ASP84 2.9 33.1 1.0 OD2 A:ASP84 2.9 33.3 1.0 CE1 A:HIS86 2.9 36.1 1.0 C A:TRS901 2.9 37.4 1.0 C1 A:TRS901 3.1 37.5 1.0 CG A:HIS86 3.1 35.8 1.0 C2 A:TRS901 3.5 38.0 1.0 CB A:HIS86 3.6 34.2 1.0 NE2 A:HIS86 4.1 37.3 1.0 CD2 A:HIS86 4.2 35.9 1.0 C3 A:TRS901 4.2 37.6 1.0 O2 A:TRS901 4.2 36.9 1.0 N A:HIS86 4.3 33.0 1.0 CB A:ASP84 4.3 32.8 1.0 CA A:HIS86 4.6 33.1 1.0 O3 A:TRS901 4.6 37.5 1.0 CE1 A:TYR85 4.7 36.8 1.0 O A:HOH925 4.7 48.1 1.0 CD1 A:TYR85 4.7 35.5 1.0 N A:TYR85 4.7 32.6 1.0 CA A:ASP84 4.8 32.5 1.0 C A:ASP84 5.0 32.7 1.0

G.Capitani, M.Tschopp, A.C.Eliot, J.F.Kirsch, M.G.Grutter. Structure of Acc Synthase Inactivated By the Mechanism-Based Inhibitor L-Vinylglycine. Febs Lett. V. 579 2458 2005.
ISSN: ISSN 0014-5793
PubMed: 15848188
DOI: 10.1016/J.FEBSLET.2005.03.048