Vanadium in PDB 5bk9: 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;

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

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 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 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

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