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

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin, PDB code: 5iqd 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)	90.26 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.220, 99.670, 93.400, 90.00, 104.90, 90.00
R / Rfree (%)	16.2 / 20.2

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

Magnesium

(Mg)

8 atoms

The binding sites of Chlorine atom in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Ribostamycin (pdb code 5iqd). 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 Gmppnp, Magnesium, and Ribostamycin, PDB code: 5iqd:
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 Gmppnp, Magnesium, and Ribostamycin


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 Gmppnp, Magnesium, and Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:62.8 occ:1.00 O A:HOH1107 3.0 55.5 1.0 NE2 A:GLN462 3.1 64.2 1.0 NH1 A:ARG469 3.4 41.5 1.0 CG2 A:ILE465 3.6 42.0 1.0 CA A:GLU466 3.8 46.8 1.0 N A:GLU466 3.8 43.9 1.0 CD A:ARG469 4.0 39.4 1.0 CB A:GLU466 4.0 52.5 1.0 C A:ILE465 4.2 42.8 1.0 CB A:ILE465 4.3 43.6 1.0 CD A:GLN462 4.3 63.4 1.0 CZ A:ARG469 4.3 40.4 1.0 CG A:GLU466 4.4 60.4 1.0 O A:HOH1049 4.5 57.6 1.0 NE A:ARG469 4.6 39.3 1.0 O A:ILE465 4.6 40.4 1.0 O A:GLN462 4.6 52.0 1.0 CG A:GLN462 4.7 60.9 1.0 CA A:ILE465 4.9 41.8 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 Gmppnp, Magnesium, and Ribostamycin


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 Gmppnp, Magnesium, and Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl802 b:72.2 occ:1.00 O B:HOH1107 3.0 54.6 1.0 NE2 B:GLN462 3.1 65.4 1.0 CG B:GLU466 3.3 59.1 1.0 NH1 B:ARG469 3.4 38.8 1.0 CG2 B:ILE465 3.6 42.0 1.0 CD B:ARG469 4.0 34.5 1.0 CA B:GLU466 4.0 45.2 1.0 N B:GLU466 4.0 39.9 1.0 O B:HOH1049 4.0 50.1 1.0 CB B:GLU466 4.2 51.8 1.0 CD B:GLN462 4.3 63.2 1.0 CZ B:ARG469 4.4 38.0 1.0 CB B:ILE465 4.4 40.0 1.0 C B:ILE465 4.4 40.2 1.0 CD B:GLU466 4.6 71.9 1.0 NE B:ARG469 4.6 36.5 1.0 O B:ILE465 4.8 40.4 1.0 CG B:GLN462 4.8 61.7 1.0 O B:GLN462 4.9 52.0 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 Gmppnp, Magnesium, and Ribostamycin


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 Gmppnp, Magnesium, and Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:64.0 occ:1.00 O C:HOH1107 2.3 56.1 1.0 NE2 C:GLN462 3.2 59.5 1.0 NH1 C:ARG469 3.5 30.9 1.0 CA C:GLU466 3.7 35.4 1.0 CG2 C:ILE465 3.8 33.8 1.0 N C:GLU466 3.8 36.2 1.0 CB C:GLU466 3.9 41.2 1.0 CD C:ARG469 3.9 27.9 1.0 C C:ILE465 4.2 33.0 1.0 CB C:ILE465 4.4 35.7 1.0 CD C:GLN462 4.4 55.5 1.0 CG C:GLU466 4.4 50.8 1.0 CZ C:ARG469 4.4 29.1 1.0 O C:HOH1049 4.5 61.6 1.0 NE C:ARG469 4.5 27.0 1.0 O C:ILE465 4.6 30.9 1.0 O C:GLN462 4.6 39.2 1.0 CG C:GLN462 4.7 51.9 1.0 CA C:ILE465 5.0 34.4 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