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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 1ynu:

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

Potassium (K) 1 atom

Nickel Binding Sites:

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 1ynu

Go back to Nickel Binding Sites List in 1ynu
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 1ynu

Go back to Nickel Binding Sites List in 1ynu
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

Reference:

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
Page generated: Wed Dec 16 01:16:41 2020

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