Zinc in PDB 6hlx: Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10

The structure of Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10, PDB code: 6hlx 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)	52.48 / 1.65
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.260, 89.260, 285.850, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 17.4

The binding sites of Zinc atom in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10 (pdb code 6hlx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10, PDB code: 6hlx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn613 b:26.4 occ:1.00 ND1 A:HIS215 2.0 26.2 1.0 OE2 A:GLU194 2.2 35.0 1.0 OE1 A:GLU194 2.3 24.0 1.0 CD A:GLU194 2.5 27.7 1.0 CE1 A:HIS215 3.0 24.2 1.0 CG A:HIS215 3.1 23.5 1.0 CB A:HIS215 3.5 20.5 1.0 CG A:GLU194 4.1 25.8 1.0 CG2 A:THR196 4.1 24.3 0.5 NE2 A:HIS215 4.1 24.6 1.0 OG1 A:THR196 4.2 25.4 0.5 CD2 A:HIS215 4.2 24.8 1.0 CE1 A:TYR28 4.6 23.0 1.0 CA A:HIS215 4.9 19.1 1.0 CZ A:TYR28 4.9 28.9 1.0 CB A:GLU194 4.9 21.0 1.0

Zinc binding site 2 out of 6 in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn614 b:39.8 occ:1.00 OD1 A:ASP289 1.9 34.4 1.0 O A:HOH1026 2.0 35.4 1.0 CG A:ASP289 2.6 34.3 1.0 OD2 A:ASP289 2.7 31.6 1.0 O A:HOH1073 2.8 32.0 1.0 CB A:ASP289 4.1 28.9 1.0 OG A:SER291 4.1 41.0 1.0 CB A:SER291 4.3 30.4 1.0 CD2 A:HIS327 4.5 42.1 1.0 O A:HOH1052 4.6 39.8 1.0 N A:SER291 4.6 26.4 1.0 CB A:HIS327 4.6 35.4 1.0 CA A:ASP289 4.7 27.2 1.0 CG A:HIS327 4.8 39.3 1.0 N A:ARG290 4.9 26.2 1.0

Zinc binding site 3 out of 6 in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn615 b:45.2 occ:1.00 O A:HOH726 1.9 34.6 1.0 NE2 A:HIS327 2.0 41.7 1.0 CE1 A:HIS327 2.8 40.6 1.0 CD2 A:HIS327 3.2 42.1 1.0 CG2 A:VAL329 3.4 39.1 1.0 OE2 A:GLU368 3.8 36.5 1.0 ND1 A:HIS327 4.0 40.8 1.0 O A:HOH721 4.2 32.7 1.0 NZ A:LYS371 4.2 53.1 1.0 CG A:HIS327 4.2 39.3 1.0 O A:HOH713 4.3 43.6 1.0 CB A:ASP289 4.6 28.9 1.0 CD A:LYS371 4.6 46.5 1.0 CD A:GLU368 4.7 47.6 1.0 OE1 A:GLU368 4.7 45.8 1.0 O A:ALA287 4.8 34.4 1.0 CB A:VAL329 4.8 39.3 1.0 OD1 A:ASP289 4.9 34.4 1.0 O A:HOH1098 4.9 45.0 1.0

Zinc binding site 4 out of 6 in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn616 b:24.7 occ:1.00 O A:HOH1032 1.9 26.6 1.0 NE2 A:HIS513 1.9 32.1 1.0 NE2 A:HIS511 2.1 26.6 1.0 OD2 A:ASP235 2.1 20.6 1.0 OD1 A:ASP235 2.7 23.7 1.0 CG A:ASP235 2.7 22.9 1.0 CD2 A:HIS513 2.9 33.2 1.0 CD2 A:HIS511 3.0 27.9 1.0 CE1 A:HIS513 3.0 31.9 1.0 CE1 A:HIS511 3.1 26.5 1.0 O A:THR26 3.9 26.9 1.0 CG A:HIS513 4.1 32.4 1.0 ND1 A:HIS513 4.1 33.1 1.0 CG A:HIS511 4.1 27.2 1.0 O A:HOH1059 4.1 43.6 1.0 CD2 A:TYR28 4.2 23.6 1.0 N A:TYR28 4.2 19.8 1.0 CB A:ASP235 4.2 20.7 1.0 ND1 A:HIS511 4.2 27.7 1.0 CG A:TYR28 4.3 21.2 1.0 CD1 A:ILE508 4.3 32.1 1.0 CB A:TYR28 4.6 19.2 1.0 CA A:LEU27 4.6 19.1 1.0 CE2 A:TYR28 4.6 25.0 1.0 CD1 A:TYR28 4.8 22.1 1.0 C A:THR26 4.8 26.6 1.0 C A:LEU27 4.8 22.3 1.0 O A:HOH1001 4.9 38.5 1.0 N A:ASP235 5.0 20.8 1.0

Zinc binding site 5 out of 6 in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn617 b:27.3 occ:1.00 NE2 A:HIS88 2.0 24.0 1.0 OE2 A:GLU77 2.1 26.8 1.0 OE1 A:GLU77 2.2 26.9 1.0 CD A:GLU77 2.5 32.5 1.0 CE1 A:HIS88 3.0 23.5 1.0 CD2 A:HIS88 3.1 23.8 1.0 CG2 A:THR86 3.8 25.2 1.0 CG A:GLU77 4.0 24.3 1.0 ND1 A:HIS88 4.2 23.8 1.0 CG A:HIS88 4.2 22.0 1.0 CB A:THR86 4.4 25.1 1.0 CB A:GLU77 4.8 23.3 1.0 O A:HOH981 5.0 24.6 1.0

Zinc binding site 6 out of 6 in the Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Pbp Agaa in Complex with Agropinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn618 b:35.3 occ:1.00 O A:HOH930 1.8 36.2 1.0 OE1 A:GLU213 2.1 25.3 1.0 OE2 A:GLU213 2.6 24.7 1.0 CD A:GLU213 2.6 27.4 1.0 NZ A:LYS198 3.7 80.1 1.0 CG A:GLU213 4.1 25.4 1.0 O A:HOH727 4.2 46.8 1.0 CE A:LYS198 4.7 65.2 1.0 NE2 A:HIS215 4.7 24.6 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