Sodium in PDB 8c75: Pbp Acca From A. Tumefaciens BO542 in Apoform 3

The structure of Pbp Acca From A. Tumefaciens BO542 in Apoform 3, PDB code: 8c75 was solved by S.Morera, A.Vigouroux, P.Legrand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.19 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.99, 182.075, 58.606, 90, 94.09, 90
R / Rfree (%)	21.9 / 25.6

The binding sites of Sodium atom in the Pbp Acca From A. Tumefaciens BO542 in Apoform 3 (pdb code 8c75). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Pbp Acca From A. Tumefaciens BO542 in Apoform 3, PDB code: 8c75:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Pbp Acca From A. Tumefaciens BO542 in Apoform 3


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 Apoform 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:33.4 occ:1.00 H A:THR260 1.9 21.5 1.0 OD1 A:ASP494 2.2 40.4 1.0 HB A:THR259 2.8 23.3 1.0 N A:THR260 2.9 21.6 1.0 HA A:THR259 3.1 20.6 1.0 CZ A:TYR496 3.2 21.3 1.0 CE1 A:TYR496 3.3 20.8 1.0 CG A:ASP494 3.3 38.1 1.0 HA A:THR260 3.3 22.9 1.0 CD1 A:TYR496 3.5 19.7 1.0 CE2 A:TYR496 3.5 19.7 1.0 HE1 A:TYR496 3.6 20.8 1.0 CA A:THR259 3.7 20.6 1.0 O A:VAL495 3.7 22.6 1.0 CB A:THR259 3.7 23.3 1.0 CA A:THR260 3.7 22.9 1.0 HG1 A:THR260 3.7 25.5 1.0 OD2 A:ASP494 3.7 42.5 1.0 C A:THR259 3.8 21.2 1.0 OH A:TYR496 3.8 23.9 1.0 CG A:TYR496 3.8 19.0 1.0 CD2 A:TYR496 3.8 19.5 1.0 HH A:TYR496 4.0 23.9 1.0 H A:LEU261 4.0 24.4 1.0 HH21 A:ARG58 4.0 23.8 1.0 O A:HOH720 4.1 25.1 1.0 HE2 A:TYR496 4.1 19.7 1.0 HD1 A:TYR496 4.1 19.7 1.0 H A:VAL495 4.1 23.9 1.0 C A:VAL495 4.2 22.9 1.0 HA A:TYR496 4.2 20.9 1.0 HG22 A:THR259 4.3 25.4 1.0 OG1 A:THR260 4.3 25.5 1.0 O A:HOH754 4.4 30.5 1.0 HG1 A:THR259 4.5 23.4 1.0 HD2 A:TYR496 4.5 19.5 1.0 CB A:ASP494 4.5 28.4 1.0 N A:VAL495 4.5 23.8 1.0 CG2 A:THR259 4.5 25.3 1.0 NH2 A:ARG58 4.6 23.8 1.0 N A:TYR496 4.6 21.7 1.0 HB3 A:ASP494 4.6 28.4 1.0 OG1 A:THR259 4.6 23.4 1.0 HH22 A:ARG58 4.7 23.8 1.0 CB A:THR260 4.7 24.8 1.0 N A:LEU261 4.7 24.4 1.0 CA A:TYR496 4.7 20.9 1.0 C A:THR260 4.8 23.8 1.0 HG21 A:THR259 4.8 25.4 1.0 CB A:TYR496 4.9 19.4 1.0 O A:THR259 5.0 21.4 1.0

Sodium binding site 2 out of 3 in the Pbp Acca From A. Tumefaciens BO542 in Apoform 3


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 Apoform 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:25.8 occ:1.00 O B:HOH991 2.2 32.0 1.0 O B:HOH802 2.3 23.7 1.0 OD1 B:ASN328 2.5 26.9 1.0 OH B:TYR339 2.6 28.2 1.0 HE1 B:TYR339 3.0 24.9 1.0 H B:ASN328 3.2 19.7 1.0 HD3 B:PRO333 3.4 19.7 1.0 CZ B:TYR339 3.5 25.9 1.0 CG B:ASN328 3.5 26.8 1.0 CE1 B:TYR339 3.6 24.9 1.0 HA B:PRO327 3.8 21.5 1.0 HD21 B:ASN328 4.1 28.7 1.0 N B:ASN328 4.1 19.7 1.0 HG3 B:PRO333 4.2 21.6 1.0 ND2 B:ASN328 4.2 28.7 1.0 O B:HOH780 4.4 32.0 1.0 O B:HOH753 4.4 40.4 1.0 HB3 B:ASN328 4.4 22.0 1.0 CD B:PRO333 4.4 19.7 1.0 HA B:PHE332 4.5 19.6 1.0 CB B:ASN328 4.5 22.1 1.0 O B:ASN331 4.6 20.3 1.0 O B:HOH754 4.6 34.1 1.0 CE2 B:TYR339 4.7 25.0 1.0 CG B:PRO333 4.8 21.6 1.0 CA B:PRO327 4.8 21.5 1.0 CD1 B:TYR339 4.9 24.4 1.0 CA B:ASN328 4.9 20.6 1.0 HG B:SER325 4.9 25.6 1.0 C B:PRO327 5.0 21.0 1.0 HD2 B:PRO333 5.0 19.7 1.0

Sodium binding site 3 out of 3 in the Pbp Acca From A. Tumefaciens BO542 in Apoform 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pbp Acca From A. Tumefaciens BO542 in Apoform 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:32.5 occ:1.00 H B:THR260 2.0 24.7 1.0 OD1 B:ASP494 2.2 36.2 1.0 HB B:THR259 2.9 24.3 1.0 N B:THR260 2.9 24.7 1.0 CG B:ASP494 3.1 35.2 1.0 HA B:THR260 3.1 26.8 1.0 HA B:THR259 3.3 22.7 1.0 OD2 B:ASP494 3.3 38.5 1.0 CZ B:TYR496 3.4 21.9 1.0 CE1 B:TYR496 3.5 21.1 1.0 HG1 B:THR260 3.5 31.1 1.0 CA B:THR260 3.6 26.8 1.0 O B:HOH774 3.7 39.6 1.0 CE2 B:TYR496 3.7 21.7 1.0 O B:VAL495 3.8 20.3 1.0 CB B:THR259 3.8 24.2 1.0 O B:HOH722 3.8 28.9 1.0 CA B:THR259 3.8 22.7 1.0 HE1 B:TYR496 3.9 21.1 1.0 CD1 B:TYR496 3.9 20.4 1.0 OH B:TYR496 3.9 22.2 1.0 C B:THR259 3.9 23.4 1.0 HH21 B:ARG58 4.0 24.4 1.0 HH B:TYR496 4.0 22.2 1.0 H B:LEU261 4.0 26.7 1.0 O B:HOH730 4.1 41.6 1.0 H B:VAL495 4.1 21.2 1.0 CD2 B:TYR496 4.1 20.9 1.0 CG B:TYR496 4.1 20.6 1.0 OG1 B:THR260 4.2 31.1 1.0 HE2 B:TYR496 4.2 21.7 1.0 C B:VAL495 4.4 20.7 1.0 HD1 B:TYR496 4.4 20.4 1.0 CB B:ASP494 4.4 26.6 1.0 HG1 B:THR259 4.4 24.4 1.0 N B:VAL495 4.5 21.2 1.0 HH22 B:ARG58 4.5 24.4 1.0 NH2 B:ARG58 4.5 24.4 1.0 HA B:TYR496 4.5 20.8 1.0 CB B:THR260 4.5 29.7 1.0 HG22 B:THR259 4.6 25.1 1.0 N B:LEU261 4.7 26.7 1.0 OG1 B:THR259 4.7 24.4 1.0 CG2 B:THR259 4.7 25.1 1.0 O B:HOH752 4.7 29.6 1.0 HD2 B:TYR496 4.7 20.9 1.0 C B:THR260 4.7 27.5 1.0 HA B:ASP494 4.7 23.2 1.0 HB3 B:ASP494 4.8 26.6 1.0 N B:TYR496 4.8 20.4 1.0 HG23 B:THR260 4.9 30.8 1.0 HG21 B:THR259 5.0 25.1 1.0 C B:ASP494 5.0 22.4 1.0 CA B:ASP494 5.0 23.2 1.0 O B:HOH815 5.0 26.4 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