Sodium in PDB 8cay: Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like

The structure of Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like, PDB code: 8cay was solved by S.Morera, A.Vigouroux, S.Siragu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.20 / 1.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.1, 40.209, 103.425, 90, 114.43, 90
R / Rfree (%)	19.6 / 22.6

The binding sites of Sodium atom in the Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like (pdb code 8cay). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like, PDB code: 8cay:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:19.0 occ:1.00 H A:VAL507 2.1 15.5 1.0 O A:THR511 2.6 17.8 1.0 HA A:PRO506 2.6 17.8 1.0 HG22 A:VAL507 2.8 16.1 1.0 HZ2 A:TRP504 2.9 17.3 1.0 HA A:MET512 2.9 15.9 1.0 N A:VAL507 3.1 15.5 1.0 OH A:TYR496 3.1 20.7 1.0 O A:HOH811 3.1 15.7 1.0 HB3 A:PRO506 3.2 19.3 1.0 CA A:PRO506 3.4 17.8 1.0 HE1 A:TYR496 3.4 18.1 1.0 HG2 A:MET512 3.5 18.4 1.0 HH A:TYR496 3.5 20.7 1.0 CZ A:TYR496 3.6 19.2 1.0 CB A:PRO506 3.7 19.3 1.0 CZ2 A:TRP504 3.7 17.3 1.0 CE1 A:TYR496 3.7 18.1 1.0 C A:THR511 3.7 16.8 1.0 C A:PRO506 3.7 16.8 1.0 O A:VAL507 3.7 15.1 1.0 HH2 A:TRP504 3.8 17.4 1.0 CG2 A:VAL507 3.8 16.1 1.0 HB2 A:PRO506 3.9 19.3 1.0 CA A:MET512 3.9 15.9 1.0 CA A:VAL507 4.1 15.2 1.0 CH2 A:TRP504 4.1 17.4 1.0 H A:GLU513 4.2 16.7 1.0 H A:THR511 4.2 18.5 1.0 HG23 A:VAL507 4.2 16.1 1.0 N A:MET512 4.2 15.5 1.0 O A:PHE509 4.3 17.1 1.0 CG A:MET512 4.3 18.4 1.0 HG13 A:VAL507 4.3 16.4 1.0 HG3 A:MET512 4.3 18.4 1.0 C A:VAL507 4.4 15.2 1.0 CB A:VAL507 4.5 15.6 1.0 HG21 A:VAL507 4.5 16.0 1.0 CE2 A:TYR496 4.5 17.1 1.0 CB A:MET512 4.6 15.6 1.0 CD1 A:TYR496 4.7 16.1 1.0 N A:PRO506 4.7 18.1 1.0 H A:PHE509 4.7 15.8 1.0 CE2 A:TRP504 4.8 16.4 1.0 O A:SER505 4.9 16.5 1.0 HB3 A:MET512 4.9 15.6 1.0 N A:GLU513 4.9 16.7 1.0 O A:HOH749 4.9 15.6 1.0 HE1 A:TRP504 4.9 16.4 1.0 HE2 A:TYR496 4.9 17.1 1.0 C A:MET512 4.9 16.5 1.0 N A:THR511 5.0 18.5 1.0 O A:PRO506 5.0 16.5 1.0 CG1 A:VAL507 5.0 16.4 1.0 CA A:THR511 5.0 18.0 1.0

Sodium binding site 2 out of 2 in the Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pbp Acca From A. Tumefaciens BO542 in Complex with Agrocinopine D-Like within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:55.1 occ:1.00 HD12 A:ILE296 2.4 34.5 1.0 OD1 A:ASP363 3.1 27.2 1.0 H A:ASP363 3.2 23.9 1.0 HB A:THR365 3.4 27.5 1.0 HD1 A:TYR362 3.4 22.6 1.0 HG1 A:THR365 3.5 31.7 1.0 CD1 A:ILE296 3.5 34.5 1.0 HA A:TYR362 3.6 25.6 1.0 CG A:ASP363 3.7 28.5 1.0 OD2 A:ASP363 3.8 29.0 1.0 HB A:ILE296 3.9 28.0 1.0 HD11 A:ILE296 4.0 34.5 1.0 HD13 A:ILE296 4.0 34.5 1.0 HG13 A:ILE296 4.1 30.9 1.0 H A:THR365 4.2 23.0 1.0 OG1 A:THR365 4.2 31.7 1.0 CD1 A:TYR362 4.2 22.7 1.0 N A:ASP363 4.2 23.9 1.0 CB A:THR365 4.2 27.5 1.0 CG1 A:ILE296 4.3 30.9 1.0 HE1 A:TYR362 4.4 22.7 1.0 CA A:TYR362 4.6 25.6 1.0 CE1 A:TYR362 4.7 22.7 1.0 CB A:ILE296 4.7 28.0 1.0 CB A:ASP363 4.8 25.9 1.0 HG21 A:THR365 4.9 28.2 1.0 HB3 A:ASP363 5.0 25.9 1.0 C A:TYR362 5.0 25.2 1.0

S.Morera, A.Vigouroux, M.Aumont-Nicaise, M.Ahmar, T.Meyer, A.El Sahili, G.Deicsics, A.Gonzalez-Mula, S.Li, J.Dore, S.Siragu, P.Legrand, C.Penot, F.Andre, D.Faure, L.Soulere, Y.Queneau, L.Vial. A Highly Conserved Ligand-Binding Site For Acca Transporters of Antibiotic and Quorum-Sensing Regulator in Agrobacterium Leads to A Different Specificity. Biochem.J. 2023.
ISSN: ESSN 1470-8728
PubMed: 38058289
DOI: 10.1042/BCJ20230273