Chlorine in PDB 5ldp: Crystal Structure of E.Coli Ligt Complexed with Atp

The structure of Crystal Structure of E.Coli Ligt Complexed with Atp, PDB code: 5ldp was solved by M.Myllykoski, P.Kursula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.150, 73.470, 77.610, 90.00, 128.34, 90.00
R / Rfree (%)	16.9 / 20.9

The structure of Crystal Structure of E.Coli Ligt Complexed with Atp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of E.Coli Ligt Complexed with Atp (pdb code 5ldp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of E.Coli Ligt Complexed with Atp, PDB code: 5ldp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of E.Coli Ligt Complexed with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of E.Coli Ligt Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:62.4 occ:1.00 O A:HOH414 2.6 58.4 1.0 ND2 A:ASN41 3.0 52.2 1.0 N A:ALA38 3.2 45.1 1.0 O A:HOH411 3.3 49.5 1.0 CB A:ALA38 3.7 53.4 1.0 CG1 A:VAL37 3.9 38.8 1.0 CA A:VAL37 3.9 40.5 1.0 CB A:ASN41 3.9 40.1 1.0 CG A:ASN41 3.9 43.3 1.0 C A:VAL37 4.0 43.2 1.0 CA A:ALA38 4.1 44.1 1.0 OG1 A:THR164 4.1 77.4 1.0 NH1 A:ARG35 4.4 84.1 1.0 CB A:VAL37 4.5 33.9 1.0 O A:PRO36 4.7 43.3 1.0 O A:ALA38 4.8 44.6 1.0 O A:THR164 4.9 56.9 1.0 C A:ALA38 5.0 45.6 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of E.Coli Ligt Complexed with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of E.Coli Ligt Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:70.3 occ:1.00 O A:HOH324 2.9 49.8 1.0 N A:GLN81 3.1 32.1 1.0 CA A:GLY80 3.3 30.2 1.0 C A:GLY80 3.7 36.0 1.0 O A:GLN81 3.7 41.6 1.0 CA A:GLN81 4.2 39.0 1.0 C A:GLN81 4.4 39.7 1.0 N A:GLY80 4.6 26.6 1.0 O A:ALA79 4.6 32.2 1.0 CB A:GLN81 4.7 41.7 1.0 CZ2 A:TRP89 4.7 37.0 1.0 O A:GLY80 4.9 32.7 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of E.Coli Ligt Complexed with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of E.Coli Ligt Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:80.1 occ:1.00 N A:ILE138 2.6 50.2 1.0 CA A:THR137 3.3 46.9 1.0 C A:THR137 3.4 48.5 1.0 CG2 A:THR137 3.6 45.4 1.0 CA A:ILE138 3.6 39.1 1.0 O A:ILE138 3.8 40.2 1.0 CB A:ILE138 3.9 39.8 1.0 O A:VAL136 3.9 56.5 1.0 CG1 A:ILE138 4.0 44.7 1.0 CB A:THR137 4.0 50.1 1.0 C A:ILE138 4.1 36.7 1.0 N A:THR137 4.3 51.6 1.0 O A:HOH431 4.5 59.2 1.0 C A:VAL136 4.5 53.3 1.0 O A:THR137 4.6 46.2 1.0 OG1 A:THR137 4.6 59.9 1.0 O A:HOH375 4.8 52.3 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of E.Coli Ligt Complexed with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of E.Coli Ligt Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:58.8 occ:1.00 O A:HOH304 2.3 52.0 1.0 NE2 A:HIS125 2.9 28.4 1.0 OG1 A:THR127 2.9 36.8 1.0 O A:HOH396 3.5 30.5 1.0 O2' A:ATP201 3.6 30.4 1.0 O A:HOH337 3.8 31.0 1.0 CE1 A:HIS125 3.8 39.8 1.0 CD2 A:HIS125 3.8 28.5 1.0 CB A:THR127 4.2 29.9 1.0 NH1 A:ARG130 4.5 74.7 1.0 CG1 A:VAL87 4.6 36.4 1.0 CG2 A:VAL87 4.6 35.9 1.0 CG2 A:THR127 4.7 35.0 1.0 O A:HOH389 4.9 24.4 1.0 ND1 A:HIS125 5.0 30.7 1.0 CG A:HIS125 5.0 28.2 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of E.Coli Ligt Complexed with Atp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of E.Coli Ligt Complexed with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl204 b:56.8 occ:1.00 O B:HOH302 2.2 53.9 1.0 OG1 B:THR127 2.9 28.0 1.0 NE2 B:HIS125 3.0 28.7 1.0 O2' B:ATP201 3.5 40.4 1.0 O B:HOH368 3.6 34.5 1.0 O B:HOH320 3.8 31.6 1.0 CE1 B:HIS125 3.9 32.5 1.0 O B:HOH326 3.9 47.0 1.0 CD2 B:HIS125 3.9 29.0 1.0 NH1 B:ARG130 4.1 45.9 0.5 CB B:THR127 4.1 30.9 1.0 CG1 B:VAL87 4.5 36.0 1.0 CG2 B:THR127 4.7 29.9 1.0 CG2 B:VAL87 4.8 39.4 1.0 O B:HOH377 4.8 23.4 1.0 NH2 B:ARG130 4.8 45.1 0.5 CZ B:ARG130 4.9 49.9 0.5 C2' B:ATP201 4.9 43.7 1.0

M.Myllykoski, P.Kursula. Structural Aspects of Nucleotide Ligand Binding By A Bacterial 2H Phosphoesterase. Plos One V. 12 70355 2017.
ISSN: ESSN 1932-6203
PubMed: 28141848
DOI: 10.1371/JOURNAL.PONE.0170355