Calcium in PDB 5l9l: Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine

The structure of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine, PDB code: 5l9l was solved by L.Marty, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.14 / 1.80
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	70.820, 70.820, 133.220, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.1

The binding sites of Calcium atom in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine (pdb code 5l9l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine, PDB code: 5l9l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:33.8 occ:1.00 O A:HOH612 3.1 28.2 1.0 N A:GLY40 3.3 24.4 1.0 NH1 A:ARG238 3.3 24.8 1.0 O A:HOH697 3.6 33.6 1.0 CD A:ARG238 3.7 21.6 1.0 CA A:ALA218 3.7 25.0 1.0 CB A:ALA221 3.9 23.5 1.0 CA A:GLY40 3.9 24.9 1.0 CB A:ALA218 4.1 26.2 1.0 CA A:GLY39 4.1 26.7 1.0 N A:ALA218 4.2 25.0 1.0 C A:GLY39 4.2 29.0 1.0 CZ A:ARG238 4.4 26.2 1.0 O A:GLY217 4.4 25.6 1.0 C A:GLY217 4.5 26.7 1.0 NE A:ARG238 4.5 22.5 1.0 O A:HOH558 4.6 27.9 1.0 CA A:ARG238 4.9 19.7 1.0 CG A:ARG238 4.9 24.2 1.0 O A:HOH631 4.9 29.5 1.0 C A:ALA218 4.9 25.4 1.0 CB A:ARG238 4.9 18.6 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:54.4 occ:1.00 OG1 A:THR260 2.6 30.6 1.0 O A:HOH597 2.8 34.1 1.0 O A:LEU258 3.0 29.5 1.0 C A:GLY259 3.5 28.8 1.0 N A:THR260 3.6 28.6 1.0 CB A:THR260 3.6 35.8 1.0 CA A:GLY259 3.8 23.4 1.0 C A:LEU258 3.8 28.5 1.0 O A:HOH695 3.9 43.4 1.0 O A:GLY259 3.9 27.5 1.0 CG1 A:VAL331 4.0 31.6 1.0 CA A:THR260 4.2 28.3 1.0 N A:GLY259 4.2 23.5 1.0 OD1 A:ASN129 4.3 34.8 1.0 CG2 A:ILE90 4.3 30.2 1.0 CB A:SER330 4.5 33.0 1.0 N A:VAL331 4.5 29.8 1.0 OG A:SER330 4.5 39.4 1.0 CG A:LEU258 4.6 33.3 1.0 O A:VAL331 4.8 33.3 1.0 CG2 A:THR260 4.9 31.2 1.0 CA A:SER330 4.9 28.3 1.0 CD1 A:ILE90 5.0 39.2 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:54.9 occ:1.00 N A:TYR251 2.8 28.3 1.0 O A:TYR251 3.3 27.9 1.0 CA A:ALA250 3.4 28.0 1.0 CD1 A:TYR251 3.5 32.1 1.0 C A:ALA250 3.5 29.9 1.0 CB A:ALA250 3.7 29.7 1.0 CA A:TYR251 3.8 28.1 1.0 CE1 A:TYR251 3.9 35.7 1.0 C A:TYR251 3.9 30.1 1.0 CG A:TYR251 4.0 29.5 1.0 CB A:TYR251 4.4 28.9 1.0 CZ A:TYR251 4.7 40.1 1.0 CD2 A:TYR251 4.7 30.1 1.0 N A:ALA250 4.7 27.4 1.0 O A:ALA250 4.7 26.5 1.0 CD1 A:ILE243 4.8 36.6 1.0 O A:PHE249 4.9 30.7 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:71.5 occ:1.00 O A:HOH511 2.3 24.6 1.0 O A:HOH608 2.5 31.1 1.0 N A:ASN248 3.0 27.7 1.0 O A:HOH624 3.1 27.2 1.0 O A:HOH672 3.2 30.9 1.0 CB A:ASN248 3.2 33.0 1.0 CA A:ASN248 3.7 28.7 1.0 O A:GLY246 3.8 27.5 1.0 C A:ALA247 3.9 29.8 1.0 CA A:ALA247 3.9 24.1 1.0 O A:HOH702 4.1 57.5 1.0 O A:HOH618 4.4 50.9 1.0 O A:LYS225 4.4 28.5 1.0 CG A:ASN248 4.6 49.8 1.0 O B:HOH689 4.6 42.2 1.0 C A:GLY246 4.7 28.7 1.0 C A:ASN248 4.7 31.3 1.0 N A:ALA247 4.8 25.6 1.0 CB A:ALA247 5.0 24.2 1.0 ND2 A:ASN248 5.0 44.2 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:35.2 occ:1.00 N B:GLY40 3.2 27.1 1.0 NH1 B:ARG238 3.3 24.9 1.0 O B:HOH562 3.3 29.6 1.0 CD B:ARG238 3.7 23.9 1.0 CA B:ALA218 3.8 23.5 1.0 CA B:GLY40 3.9 26.6 1.0 O B:HOH698 4.0 39.2 1.0 CB B:ALA221 4.0 23.4 1.0 CA B:GLY39 4.1 24.1 1.0 CB B:ALA218 4.1 25.1 1.0 O B:HOH567 4.1 32.5 1.0 C B:GLY39 4.2 30.6 1.0 N B:ALA218 4.2 24.1 1.0 CZ B:ARG238 4.3 29.2 1.0 O B:GLY217 4.5 26.7 1.0 NE B:ARG238 4.5 27.4 1.0 C B:GLY217 4.5 27.6 1.0 O B:HOH575 4.7 26.3 1.0 O B:HOH654 4.8 31.2 1.0 CA B:ARG238 4.9 21.9 1.0 CG B:ARG238 4.9 26.4 1.0 N B:TRP41 5.0 26.6 1.0 CB B:ARG238 5.0 21.5 1.0 C B:ALA218 5.0 25.2 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:88.5 occ:1.00 OD1 B:ASP230 3.0 26.4 1.0 O B:GLY227 3.1 30.7 1.0 CG B:ASP230 3.7 26.5 1.0 OD2 B:ASP230 3.9 30.3 1.0 O B:GLU228 4.0 30.7 1.0 O B:HOH606 4.1 31.4 1.0 O B:VAL229 4.1 26.9 1.0 O B:HOH611 4.1 41.2 1.0 C B:GLU228 4.1 29.5 1.0 C B:VAL229 4.2 27.8 1.0 CD B:LYS161 4.2 55.8 1.0 C B:GLY227 4.3 29.1 1.0 N B:VAL229 4.4 25.7 1.0 ND2 B:ASN137 4.4 24.9 1.0 N B:ASP230 4.5 24.8 1.0 CA B:VAL229 4.6 26.3 1.0 OG1 B:THR140 4.6 25.4 1.0 CA B:GLU228 4.6 26.1 1.0 CA B:ASP230 4.9 23.9 1.0 N B:GLU228 4.9 25.5 1.0 CB B:ASP230 4.9 25.1 1.0 CE B:LYS161 5.0 70.5 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Pbp Mota From A. Tumefaciens B6 in Complex with Glucopine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:54.1 occ:1.00 O B:HOH700 2.6 25.9 1.0 O B:HOH617 2.6 25.6 1.0 O A:HOH708 2.8 31.6 1.0 CB B:GLN222 3.7 24.9 1.0 CB A:GLN222 3.8 22.9 1.0 CA B:GLN219 3.9 22.0 1.0 O B:ALA218 3.9 25.2 1.0 CG A:GLN222 3.9 26.1 1.0 CG B:GLN222 4.0 29.9 1.0 N B:GLN219 4.1 22.4 1.0 C B:ALA218 4.2 25.2 1.0 CA A:GLN219 4.2 22.3 1.0 O A:ALA218 4.3 21.1 1.0 O B:HOH628 4.4 32.9 1.0 CB B:GLN219 4.5 22.9 1.0 N A:GLN219 4.5 22.8 1.0 C A:ALA218 4.6 25.4 1.0 O A:HOH607 4.6 30.1 1.0 OE1 A:GLN222 4.7 30.5 1.0 CB A:GLN219 4.7 22.7 1.0 OE1 B:GLN222 4.8 32.3 1.0 CD A:GLN222 4.8 37.7 1.0 CB B:ALA218 4.9 25.1 1.0 O B:HOH567 4.9 32.5 1.0 CD B:GLN222 4.9 35.6 1.0 C B:GLN219 5.0 25.4 1.0 O B:HOH536 5.0 34.1 1.0 CG B:GLN219 5.0 31.7 1.0

L.Marty, A.Vigouroux, M.Aumont-Nicaise, Y.Dessaux, D.Faure, S.Morera. Structural Basis For High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens. J.Biol.Chem. V. 291 22638 2016.
ISSN: ESSN 1083-351X
PubMed: 27609514
DOI: 10.1074/JBC.M116.745562