Chlorine in PDB 5byl: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium, PDB code: 5byl was solved by S.J.Caldwell, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.92 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.290, 99.900, 93.620, 90.00, 105.09, 90.00
R / Rfree (%)	15.6 / 19.8

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Chlorine atom in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium (pdb code 5byl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium, PDB code: 5byl:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:70.6 occ:1.00 O A:HOH1107 2.9 50.0 1.0 NE2 A:GLN462 3.3 75.8 1.0 NH1 A:ARG469 3.3 48.5 1.0 CG2 A:ILE465 3.8 45.2 1.0 CD A:ARG469 3.8 41.2 1.0 N A:GLU466 3.9 43.6 1.0 CA A:GLU466 3.9 47.4 1.0 CB A:GLU466 4.1 53.0 1.0 CZ A:ARG469 4.2 42.9 1.0 C A:ILE465 4.3 42.3 1.0 CB A:ILE465 4.3 44.4 1.0 CG A:GLU466 4.4 66.2 1.0 NE A:ARG469 4.4 40.5 1.0 CD A:GLN462 4.5 71.0 1.0 O A:HOH1049 4.5 54.2 1.0 O A:ILE465 4.7 40.8 1.0 CG A:GLN462 4.8 68.4 1.0 O A:GLN462 4.8 55.8 1.0 CA A:ILE465 5.0 42.7 1.0

Chlorine binding site 2 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl802 b:72.3 occ:1.00 O B:HOH1107 3.0 53.6 1.0 NE2 B:GLN462 3.2 69.2 1.0 NH1 B:ARG469 3.3 40.7 1.0 CG B:GLU466 3.4 60.3 1.0 CG2 B:ILE465 3.5 44.1 1.0 CD B:ARG469 3.8 35.8 1.0 N B:GLU466 3.9 44.8 1.0 CA B:GLU466 4.0 48.7 1.0 O B:HOH1049 4.1 58.2 1.0 CB B:ILE465 4.2 42.6 1.0 C B:ILE465 4.3 42.6 1.0 CZ B:ARG469 4.3 38.0 1.0 CB B:GLU466 4.3 54.6 1.0 CD B:GLN462 4.4 64.4 1.0 NE B:ARG469 4.5 35.1 1.0 CD B:GLU466 4.6 74.5 1.0 O B:ILE465 4.7 36.6 1.0 CG B:GLN462 4.8 64.0 1.0 O B:GLN462 4.9 45.8 1.0 CA B:ILE465 4.9 41.4 1.0 O B:HOH1215 5.0 63.3 1.0

Chlorine binding site 3 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppcp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:59.1 occ:1.00 O C:HOH1107 2.6 56.7 1.0 NE2 C:GLN462 3.2 57.0 1.0 NH1 C:ARG469 3.4 30.6 1.0 CG2 C:ILE465 3.7 35.1 1.0 N C:GLU466 3.8 33.5 1.0 CA C:GLU466 3.8 36.2 1.0 CD C:ARG469 3.8 30.5 1.0 CB C:GLU466 4.1 41.9 1.0 C C:ILE465 4.2 33.0 1.0 CB C:ILE465 4.3 35.1 1.0 CZ C:ARG469 4.3 31.7 1.0 CD C:GLN462 4.4 55.5 1.0 O C:HOH1049 4.4 62.6 1.0 CG C:GLU466 4.5 52.7 1.0 NE C:ARG469 4.5 29.8 1.0 O C:ILE465 4.6 29.9 1.0 CG C:GLN462 4.6 52.4 1.0 O C:GLN462 4.7 42.0 1.0 CA C:ILE465 4.9 32.3 1.0

S.J.Caldwell, Y.Huang, A.M.Berghuis. Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase Aph(2)-Ia. Structure V. 24 935 2016.
ISSN: ISSN 0969-2126
PubMed: 27161980
DOI: 10.1016/J.STR.2016.04.002