Sodium in PDB 6hm2: Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10

The structure of Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10, PDB code: 6hm2 was solved by S.Morera, L.Marty, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.73 / 1.74
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.570, 86.310, 106.520, 71.14, 81.00, 76.32
R / Rfree (%)	17.4 / 20.1

The binding sites of Sodium atom in the Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10 (pdb code 6hm2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10, PDB code: 6hm2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:25.9 occ:1.00 OAT A:G9Z401 2.7 20.2 1.0 OAS A:G9Z401 2.8 19.4 1.0 O A:THR166 2.8 16.1 1.0 OG1 A:THR166 3.0 14.9 1.0 N A:ASP164 3.1 15.9 1.0 CB A:ASP164 3.1 16.4 1.0 CAL A:G9Z401 3.1 18.4 1.0 O A:ASP164 3.2 19.6 1.0 CA A:ASP164 3.3 16.1 1.0 C A:ASP164 3.4 20.0 1.0 CB A:PRO162 3.5 17.7 1.0 CAK A:G9Z401 3.5 16.7 1.0 CD2 A:TYR167 3.6 20.2 1.0 C A:THR166 3.8 16.1 1.0 N A:THR166 4.1 15.6 1.0 N A:SER163 4.1 17.8 1.0 CB A:THR166 4.1 19.1 1.0 CA A:THR166 4.2 14.0 1.0 CE2 A:TYR167 4.3 21.0 1.0 C A:SER163 4.3 22.1 1.0 C A:PRO162 4.4 20.9 1.0 N A:ALA165 4.4 17.1 1.0 CAJ A:G9Z401 4.5 16.2 1.0 CA A:PRO162 4.5 16.8 1.0 CG A:ASP164 4.5 26.9 1.0 O A:HOH504 4.6 26.7 1.0 CG A:PRO162 4.6 21.5 1.0 OG A:SER163 4.6 21.9 1.0 CG A:TYR167 4.7 18.1 1.0 CA A:SER163 4.7 16.5 1.0 C A:ALA165 4.8 17.6 1.0 OG A:SER168 4.8 16.1 1.0 CB A:TYR167 4.8 16.1 1.0 O A:HOH547 4.9 25.5 1.0 N A:TYR167 4.9 13.9 1.0 O A:PRO162 5.0 19.1 1.0

Sodium binding site 2 out of 4 in the Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:24.4 occ:1.00 O B:THR166 2.7 14.9 1.0 OAT B:G9Z401 2.7 17.6 1.0 OAS B:G9Z401 2.9 21.8 1.0 OG1 B:THR166 3.0 17.0 1.0 N B:ASP164 3.1 16.0 1.0 CB B:ASP164 3.2 17.5 1.0 O B:ASP164 3.2 18.1 1.0 CAL B:G9Z401 3.2 17.3 1.0 CA B:ASP164 3.3 15.3 1.0 CB B:PRO162 3.4 15.4 1.0 C B:ASP164 3.4 18.2 1.0 CAK B:G9Z401 3.5 16.1 1.0 CD2 B:TYR167 3.6 17.3 1.0 C B:THR166 3.7 15.6 1.0 N B:THR166 4.1 16.5 1.0 N B:SER163 4.1 16.1 1.0 CB B:THR166 4.1 18.3 1.0 CA B:THR166 4.2 14.4 1.0 CE2 B:TYR167 4.3 18.7 1.0 C B:SER163 4.3 20.4 1.0 C B:PRO162 4.3 19.0 1.0 N B:ALA165 4.4 15.1 1.0 CA B:PRO162 4.4 14.7 1.0 CAJ B:G9Z401 4.4 18.2 1.0 CG B:PRO162 4.5 17.4 1.0 CG B:ASP164 4.6 25.7 1.0 CG B:TYR167 4.6 17.1 1.0 OG B:SER163 4.6 24.7 1.0 CB B:TYR167 4.7 14.9 1.0 C B:ALA165 4.7 18.2 1.0 CA B:SER163 4.7 15.4 1.0 O B:HOH532 4.8 30.4 1.0 OG B:SER168 4.8 18.9 1.0 N B:TYR167 4.8 13.3 1.0 O B:HOH578 4.9 18.9 1.0 O B:PRO162 5.0 19.2 1.0

Sodium binding site 3 out of 4 in the Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:24.3 occ:1.00 OAS C:G9Z401 2.7 21.3 1.0 OAT C:G9Z401 2.7 19.7 1.0 O C:THR166 2.7 18.1 1.0 OG1 C:THR166 3.0 18.3 1.0 N C:ASP164 3.1 18.4 1.0 CB C:ASP164 3.1 16.6 1.0 O C:ASP164 3.1 18.7 1.0 CAL C:G9Z401 3.3 19.5 1.0 CA C:ASP164 3.3 17.3 1.0 C C:ASP164 3.4 19.0 1.0 CB C:PRO162 3.5 15.6 1.0 CAK C:G9Z401 3.6 17.3 1.0 CD2 C:TYR167 3.6 15.7 1.0 C C:THR166 3.7 17.9 1.0 N C:THR166 4.0 14.4 1.0 CB C:THR166 4.1 14.5 1.0 N C:SER163 4.1 19.4 1.0 CA C:THR166 4.1 14.1 1.0 CE2 C:TYR167 4.2 16.8 1.0 C C:SER163 4.3 21.9 1.0 C C:PRO162 4.4 21.4 1.0 N C:ALA165 4.4 16.8 1.0 CAJ C:G9Z401 4.5 17.9 1.0 CA C:PRO162 4.5 15.4 1.0 CG C:ASP164 4.5 26.0 1.0 CG C:PRO162 4.6 20.6 1.0 CG C:TYR167 4.6 16.0 1.0 OG C:SER163 4.6 24.7 1.0 C C:ALA165 4.7 17.9 1.0 CB C:TYR167 4.7 13.3 1.0 CA C:SER163 4.7 19.5 1.0 O C:HOH546 4.8 35.9 1.0 O C:HOH524 4.8 26.3 1.0 OG C:SER168 4.8 21.8 1.0 N C:TYR167 4.8 14.6 1.0 O C:PRO162 5.0 20.9 1.0

Sodium binding site 4 out of 4 in the Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure in P1 Form of the Pbp Agtb in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:23.2 occ:1.00 O D:THR166 2.7 15.8 1.0 OAS D:G9Z401 2.8 19.2 1.0 OAT D:G9Z401 2.8 19.0 1.0 OG1 D:THR166 2.9 19.1 1.0 N D:ASP164 3.1 16.7 1.0 CB D:ASP164 3.1 18.1 1.0 O D:ASP164 3.1 18.2 1.0 CAL D:G9Z401 3.2 18.2 1.0 CA D:ASP164 3.3 17.5 1.0 C D:ASP164 3.3 20.1 1.0 CB D:PRO162 3.5 14.0 1.0 CAK D:G9Z401 3.6 16.2 1.0 CD2 D:TYR167 3.6 16.8 1.0 C D:THR166 3.7 18.1 1.0 N D:THR166 4.0 16.6 1.0 CB D:THR166 4.0 19.6 1.0 CA D:THR166 4.1 15.4 1.0 N D:SER163 4.1 16.9 1.0 CE2 D:TYR167 4.2 17.2 1.0 C D:SER163 4.3 20.1 1.0 N D:ALA165 4.3 17.9 1.0 C D:PRO162 4.4 19.6 1.0 CG D:ASP164 4.5 25.9 1.0 CA D:PRO162 4.5 13.9 1.0 CAJ D:G9Z401 4.5 16.0 1.0 CG D:PRO162 4.6 18.6 1.0 OG D:SER163 4.6 19.6 1.0 O D:HOH521 4.6 30.7 1.0 CG D:TYR167 4.6 16.6 1.0 C D:ALA165 4.7 19.9 1.0 O D:HOH532 4.7 23.0 1.0 CB D:TYR167 4.8 15.4 1.0 CA D:SER163 4.8 16.2 1.0 N D:TYR167 4.8 15.1 1.0 OG D:SER168 4.8 23.4 1.0

L.Marty, A.Vigouroux, M.Aumont-Nicaise, F.Pelissier, T.Meyer, C.Lavire, Y.Dessaux, S.Morera. Structural Basis For Two Efficient Modes of Agropinic Acid Opine Import Into the Bacterial Pathogenagrobacterium Tumefaciens. Biochem. J. V. 476 165 2019.
ISSN: ESSN 1470-8728
PubMed: 30552142
DOI: 10.1042/BCJ20180861