Chlorine in PDB 5otc: Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.

The structure of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid., PDB code: 5otc was solved by A.Vigouroux, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.31 / 2.20
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	113.990, 113.990, 37.800, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 20.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. (pdb code 5otc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid., PDB code: 5otc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl308 b:85.5 occ:1.00 O A:SER125 3.5 44.7 1.0 CE A:LYS129 3.7 89.9 1.0 O A:ALA123 3.9 45.9 1.0 C A:ASP124 4.2 48.6 1.0 C A:SER125 4.2 46.9 1.0 NZ A:LYS129 4.2 98.3 1.0 O A:ASP124 4.3 49.2 1.0 N A:SER125 4.4 43.2 1.0 CB A:LEU128 4.4 39.5 1.0 CA A:ASP124 4.5 45.4 1.0 CG A:LYS129 4.5 63.1 1.0 CD A:LYS129 4.5 76.0 1.0 CD1 A:LEU128 4.6 42.8 1.0 C A:ALA123 4.9 45.9 1.0 N A:PRO126 4.9 44.7 1.0 CA A:SER125 4.9 42.9 1.0 CA A:PRO126 5.0 44.0 1.0

Chlorine binding site 2 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl309 b:68.3 occ:1.00 ND1 A:HIS170 2.9 36.6 1.0 N A:GLN165 3.0 35.0 1.0 O A:LEU205 3.2 38.1 1.0 CD1 A:ILE189 3.4 36.9 1.0 CA A:VAL164 3.6 35.7 1.0 CG A:HIS170 3.7 35.3 1.0 CB A:HIS170 3.7 32.4 1.0 CB A:VAL164 3.8 38.9 1.0 C A:VAL164 3.8 38.5 1.0 CE1 A:HIS170 3.9 36.1 1.0 CB A:GLN165 3.9 35.5 1.0 CA A:GLN165 4.0 35.0 1.0 CG1 A:VAL164 4.1 38.4 1.0 OG1 A:THR168 4.3 36.8 1.0 OG A:SER204 4.3 37.5 1.0 C A:LEU205 4.4 38.2 1.0 O A:GLN165 4.6 36.0 1.0 CG1 A:ILE189 4.8 37.6 1.0 CB A:ALA206 4.8 33.5 1.0 C A:GLN165 4.8 37.1 1.0 CG2 A:VAL192 4.9 37.4 1.0 CD2 A:HIS170 4.9 36.5 1.0 O A:GLY163 4.9 37.7 1.0 N A:VAL164 4.9 35.6 1.0 NE2 A:HIS170 4.9 36.8 1.0 O A:VAL164 5.0 37.1 1.0

Chlorine binding site 3 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl310 b:73.7 occ:1.00 OG1 A:THR118 2.9 38.1 1.0 O A:GLY227 3.1 33.5 1.0 NE A:ARG229 3.6 68.0 1.0 CB A:THR118 3.7 36.5 1.0 C A:PHE226 3.7 35.9 1.0 CG2 A:THR118 3.8 31.9 1.0 CG A:ARG229 3.9 46.8 1.0 O A:PHE226 3.9 34.7 1.0 N A:PHE226 3.9 33.5 1.0 CA A:PHE226 3.9 32.4 1.0 N A:GLY227 4.1 33.4 1.0 C A:GLY227 4.2 34.6 1.0 CD A:ARG229 4.3 59.4 1.0 CB A:MET225 4.4 35.8 1.0 C A:MET225 4.4 37.8 1.0 NH2 A:ARG229 4.4 64.3 1.0 CZ A:ARG229 4.4 76.7 1.0 CA A:GLY227 4.7 31.7 1.0 O A:PRO228 4.7 32.3 1.0 O A:MET225 4.8 40.1 1.0 C A:PRO228 4.9 36.4 1.0 O A:HOH439 4.9 36.3 1.0

Chlorine binding site 4 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl311 b:93.9 occ:1.00 O A:ALA86 3.8 42.6 1.0 C1 A:PGE319 4.0 71.6 1.0 O A:GLY87 4.2 47.0 1.0 C6 A:PGE319 4.2 71.3 1.0 O2 A:PGE319 4.2 70.6 1.0 C3 A:PGE319 4.3 68.5 1.0 O3 A:PGE319 4.4 69.6 1.0 CA A:GLY87 4.5 40.9 1.0 C2 A:PGE319 4.6 71.9 1.0 C5 A:PGE319 4.6 69.5 1.0 C A:GLY87 4.6 46.3 1.0 O1 A:PGE319 4.7 72.1 1.0 C A:ALA86 4.8 42.1 1.0 O4 A:PGE319 4.9 72.5 1.0 C4 A:PGE319 4.9 68.7 1.0

Chlorine binding site 5 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl312 b:78.8 occ:1.00 N A:ASP187 3.1 41.1 1.0 ND2 A:ASN191 3.1 57.7 1.0 OD2 A:ASP187 3.6 75.1 1.0 O A:HOH463 3.6 79.1 1.0 CA A:TYR186 3.6 38.0 1.0 CG A:ASP187 3.7 63.1 1.0 CB A:TYR186 3.8 37.9 1.0 CD2 A:TYR186 3.8 39.8 1.0 C A:TYR186 3.9 41.7 1.0 CB A:ASP187 3.9 45.6 1.0 CG A:ASN191 3.9 66.4 1.0 CB A:ASN191 4.0 42.6 1.0 CA A:ASP187 4.1 42.3 1.0 CG A:TYR186 4.2 38.4 1.0 OD1 A:ASP187 4.3 62.5 1.0 N A:THR188 4.6 42.3 1.0 CE2 A:TYR186 4.8 40.9 1.0 C A:ASP187 5.0 46.0 1.0 O A:THR185 5.0 43.7 1.0 N A:TYR186 5.0 38.5 1.0 OD1 A:ASN191 5.0 59.3 1.0

Chlorine binding site 6 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl313 b:55.5 occ:1.00 O A:GLY240 2.8 39.3 1.0 OH A:TYR112 2.8 38.2 1.0 N A:ALA94 3.0 31.0 1.0 N A:MET96 3.0 30.8 1.0 N A:ALA95 3.5 31.3 1.0 CA A:MET93 3.6 34.7 1.0 CB A:MET96 3.6 32.3 1.0 C A:MET93 3.7 35.6 1.0 CZ A:TYR112 3.7 41.1 1.0 C A:GLY240 3.8 41.1 1.0 CA A:MET96 3.8 29.8 1.0 CG1 A:VAL239 3.8 40.0 1.0 O A:ILE92 3.8 35.2 1.0 C A:ALA94 3.8 34.5 1.0 CE2 A:TYR112 4.0 36.7 1.0 CA A:ALA94 4.0 30.6 1.0 O A:MET96 4.0 32.9 1.0 C A:ALA95 4.0 33.6 1.0 CA A:ALA95 4.1 29.5 1.0 N A:MET93 4.3 35.4 1.0 C A:ILE92 4.4 37.1 1.0 C A:MET96 4.4 33.1 1.0 N A:GLY240 4.5 37.7 1.0 N A:VAL241 4.5 36.8 1.0 O A:ALA94 4.6 33.9 1.0 CA A:VAL241 4.6 34.9 1.0 CB A:MET93 4.6 37.9 1.0 CA A:GLY240 4.7 38.4 1.0 OD1 A:ASP55 4.7 39.7 1.0 CG A:MET93 4.8 41.4 1.0 O A:MET93 4.9 36.2 1.0 CE1 A:TYR112 4.9 37.3 1.0 CG2 A:ILE92 4.9 35.0 1.0 OD2 A:ASP55 5.0 39.5 1.0

Chlorine binding site 7 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl314 b:78.1 occ:1.00 O A:THR130 3.7 41.7 1.0 O A:HOH413 3.8 47.8 1.0 O A:LEU128 3.9 44.8 1.0 NE2 A:GLN131 4.1 80.1 1.0 O A:HOH439 4.6 36.3 1.0 C A:THR130 4.6 42.7 1.0 O A:HOH471 4.7 52.4 1.0 O A:LYS129 4.9 47.6 1.0 CA A:GLN131 4.9 40.0 1.0 C A:LYS129 4.9 47.5 1.0

Chlorine binding site 8 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl315 b:88.0 occ:1.00 OG1 A:THR122 3.0 40.5 1.0 O A:ASP202 3.5 42.4 1.0 CA A:ASP202 3.9 37.6 1.0 OG1 A:THR121 3.9 40.9 1.0 OD1 A:ASP202 4.0 50.3 1.0 OG A:SER125 4.1 43.0 1.0 CB A:ASP202 4.1 39.8 1.0 CB A:THR122 4.1 40.3 1.0 C A:ASP202 4.1 41.7 1.0 CG2 A:THR122 4.2 34.5 1.0 CB A:SER125 4.2 43.5 1.0 N A:THR122 4.5 36.7 1.0 CG A:ASP202 4.6 46.8 1.0 O A:HOH470 4.7 64.1 1.0 O A:ILE201 4.8 39.6 1.0 CA A:SER125 4.9 42.9 1.0 CA A:THR122 5.0 36.9 1.0

Chlorine binding site 9 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl316 b:97.7 occ:1.00 O A:SER180 3.5 41.0 1.0 CB A:GLN182 4.0 40.3 1.0 N A:GLN182 4.1 36.7 1.0 CA A:GLN182 4.3 37.8 1.0 C A:SER180 4.5 39.4 1.0 C A:VAL181 4.7 38.1 1.0 CG A:GLN182 4.7 52.2 1.0 O A:HOH422 4.9 39.8 1.0

Chlorine binding site 10 out of 11 in the Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of the Periplasmic Binding Protein (Pbp) Noct From Agrobacterium Tumefaciens C58 in Complex with Noroctopinic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl317 b:73.7 occ:1.00 N A:ALA40 3.0 37.5 1.0 O A:HOH443 3.1 46.1 1.0 OD2 A:ASP190 3.2 69.9 1.0 CB A:ALA40 3.5 37.6 1.0 O2 A:EDO307 3.6 62.7 1.0 C2 A:EDO307 3.7 63.0 1.0 O A:SER38 3.8 39.1 1.0 CG A:ASP190 3.8 62.1 1.0 CA A:ALA40 3.8 36.9 1.0 CA A:TYR39 3.9 35.3 1.0 C A:TYR39 3.9 40.4 1.0 OD1 A:ASP190 3.9 61.7 1.0 C A:SER38 4.0 39.9 1.0 N A:TYR39 4.0 36.8 1.0 CG2 A:ILE189 4.1 41.3 1.0 CE1 A:PHE210 4.2 38.0 1.0 O A:ALA40 4.3 41.4 1.0 C A:ALA40 4.6 40.6 1.0 CZ A:PHE210 4.7 36.0 1.0 CA A:SER38 4.9 39.0 1.0

A.Vigouroux, A.El Sahili, J.Lang, M.Aumont-Nicaise, Y.Dessaux, D.Faure, S.Morera. Structural Basis For High Specificity of Octopine Binding in the Plant Pathogen Agrobacterium Tumefaciens. Sci Rep V. 7 18033 2017.
ISSN: ESSN 2045-2322
PubMed: 29269740
DOI: 10.1038/S41598-017-18243-8