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

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Kanamycin A, PDB code: 5iqb 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)	90.13 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.430, 99.220, 93.510, 90.00, 105.46, 90.00
R / Rfree (%)	16.7 / 21.1

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

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


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 Kanamycin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:84.6 occ:1.00 NE2 A:GLN462 3.0 87.5 1.0 NH1 A:ARG469 3.5 57.6 1.0 CG2 A:ILE465 3.7 57.7 1.0 N A:GLU466 3.8 60.6 1.0 CA A:GLU466 3.9 64.9 1.0 CD A:ARG469 3.9 54.5 1.0 CB A:GLU466 4.0 75.9 1.0 CG A:GLU466 4.1 92.7 1.0 CD A:GLN462 4.2 91.4 1.0 C A:ILE465 4.3 57.0 1.0 CB A:ILE465 4.3 59.1 1.0 CZ A:ARG469 4.4 54.7 1.0 NE A:ARG469 4.6 52.7 1.0 CG A:GLN462 4.6 90.6 1.0 O A:GLN462 4.6 71.0 1.0 O A:ILE465 4.7 52.8 1.0 CA A:ILE465 5.0 56.4 1.0

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


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 Kanamycin A within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:69.6 occ:1.00 O C:HOH1107 2.6 62.4 1.0 NE2 C:GLN462 3.0 69.9 1.0 NH1 C:ARG469 3.4 40.0 1.0 CG2 C:ILE465 3.7 42.8 1.0 CD C:ARG469 3.8 35.4 1.0 N C:GLU466 3.9 41.1 1.0 CA C:GLU466 3.9 43.0 1.0 O C:HOH1049 4.0 65.2 1.0 CB C:GLU466 4.2 50.7 1.0 CD C:GLN462 4.2 64.6 1.0 CB C:ILE465 4.3 44.3 1.0 C C:ILE465 4.3 41.1 1.0 CZ C:ARG469 4.3 38.1 1.0 CG C:GLU466 4.3 58.0 1.0 NE C:ARG469 4.5 36.0 1.0 O C:ILE465 4.6 40.2 1.0 CG C:GLN462 4.7 62.1 1.0 O C:GLN462 4.7 45.6 1.0 CA C:ILE465 5.0 42.6 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