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Vanadium in PDB 5bk9: Aad-1 Bound to the Vanadyl Ion and Succinate

Enzymatic activity of Aad-1 Bound to the Vanadyl Ion and Succinate

All present enzymatic activity of Aad-1 Bound to the Vanadyl Ion and Succinate:
1.14.11.44;

Protein crystallography data

The structure of Aad-1 Bound to the Vanadyl Ion and Succinate, PDB code: 5bk9 was solved by C.Ongpipattanakul, J.R.Chekan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.51
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.915, 97.868, 69.855, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 21.7

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Aad-1 Bound to the Vanadyl Ion and Succinate (pdb code 5bk9). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Aad-1 Bound to the Vanadyl Ion and Succinate, PDB code: 5bk9:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 5bk9

Go back to Vanadium Binding Sites List in 5bk9
Vanadium binding site 1 out of 2 in the Aad-1 Bound to the Vanadyl Ion and Succinate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Aad-1 Bound to the Vanadyl Ion and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V302

b:19.2
occ:1.00
V1 A:VVO302 0.0 19.2 1.0
O1 A:VVO302 1.9 21.6 1.0
NE2 A:HIS111 2.1 15.6 1.0
OD1 A:ASP113 2.2 19.6 1.0
NE2 A:HIS270 2.2 14.6 1.0
O4 A:SIN301 2.2 24.1 1.0
O3 A:SIN301 2.3 23.0 1.0
C4 A:SIN301 2.6 23.3 1.0
CE1 A:HIS111 3.0 15.5 1.0
CE1 A:HIS270 3.1 14.9 1.0
CG A:ASP113 3.2 19.3 1.0
CD2 A:HIS270 3.2 14.7 1.0
CD2 A:HIS111 3.2 15.5 1.0
OD2 A:ASP113 3.5 21.3 1.0
C3 A:SIN301 4.1 23.2 1.0
ND1 A:HIS111 4.2 15.4 1.0
ND1 A:HIS270 4.2 14.7 1.0
CG A:HIS111 4.3 15.1 1.0
CG A:HIS270 4.3 14.4 1.0
CZ2 A:TRP263 4.5 14.8 1.0
NH1 A:ARG285 4.5 22.7 1.0
CB A:ASP113 4.6 17.5 1.0
CH2 A:TRP263 4.8 15.4 1.0
CA A:GLY107 4.9 22.5 1.0
CA A:ASP113 4.9 16.0 1.0
C2 A:SIN301 4.9 22.6 1.0

Vanadium binding site 2 out of 2 in 5bk9

Go back to Vanadium Binding Sites List in 5bk9
Vanadium binding site 2 out of 2 in the Aad-1 Bound to the Vanadyl Ion and Succinate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Aad-1 Bound to the Vanadyl Ion and Succinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V301

b:30.1
occ:1.00
V1 B:VVO301 0.0 30.1 1.0
O1 B:VVO301 1.9 32.8 1.0
NE2 B:HIS270 2.1 17.9 1.0
NE2 B:HIS111 2.2 22.3 1.0
OD1 B:ASP113 2.3 23.8 1.0
CE1 B:HIS270 3.0 17.4 1.0
CE1 B:HIS111 3.0 22.6 1.0
CD2 B:HIS270 3.2 17.5 1.0
CD2 B:HIS111 3.3 22.1 1.0
CG B:ASP113 3.4 23.1 1.0
OD2 B:ASP113 3.7 25.0 1.0
ND1 B:HIS270 4.1 17.2 1.0
ND1 B:HIS111 4.2 21.8 1.0
CG B:HIS270 4.3 16.9 1.0
CG B:HIS111 4.3 21.3 1.0
CZ2 B:TRP263 4.5 16.0 1.0
CB B:ASP113 4.7 21.3 1.0
NH1 B:ARG285 4.7 22.2 1.0
CH2 B:TRP263 4.8 16.4 1.0
CA B:GLY107 4.9 45.6 1.0
O B:HOH411 4.9 29.6 1.0
CA B:ASP113 5.0 19.6 1.0

Reference:

J.R.Chekan, C.Ongpipattanakul, T.R.Wright, B.Zhang, J.M.Bollinger Jr., L.J.Rajakovich, C.Krebs, R.M.Cicchillo, S.K.Nair. Molecular Basis For Enantioselective Herbicide Degradation Imparted By Aryloxyalkanoate Dioxygenases in Transgenic Plants. Proc.Natl.Acad.Sci.Usa V. 116 13299 2019.
ISSN: ESSN 1091-6490
PubMed: 31209034
DOI: 10.1073/PNAS.1900711116
Page generated: Thu Oct 29 07:05:46 2020

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