Chlorine in PDB 5iqc: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1, PDB code: 5iqc 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)	90.44 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.780, 98.890, 93.860, 90.00, 105.51, 90.00
R / Rfree (%)	17.9 / 22.9

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp, Magnesium, and Gentamicin C1 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 Gentamicin C1 (pdb code 5iqc). 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 Gentamicin C1, PDB code: 5iqc:
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 Gentamicin C1


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 Gentamicin C1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:75.0 occ:1.00 NE2 A:GLN462 3.0 85.0 1.0 NH1 A:ARG469 3.6 47.1 1.0 CG2 A:ILE465 3.6 51.9 1.0 CD A:ARG469 4.0 47.5 1.0 CA A:GLU466 4.1 60.0 1.0 N A:GLU466 4.1 55.1 1.0 CD A:GLN462 4.2 83.5 1.0 CB A:GLU466 4.2 71.6 1.0 CB A:ILE465 4.3 51.4 1.0 C A:ILE465 4.4 53.3 1.0 CG A:GLU466 4.5 88.0 1.0 CZ A:ARG469 4.5 45.9 1.0 CG A:GLN462 4.6 80.8 1.0 NE A:ARG469 4.7 46.3 1.0 O A:ILE465 4.8 45.7 1.0 O A:GLN462 4.8 62.2 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 Gentamicin C1


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 Gentamicin C1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:84.8 occ:1.00 CZ A:ARG336 3.6 82.4 1.0 NH1 A:ARG336 3.6 81.9 1.0 NH2 A:ARG336 3.7 86.6 1.0 CB A:ARG336 4.1 57.8 1.0 CG A:ARG336 4.1 62.0 1.0 NE A:ARG336 4.2 73.9 1.0 CD1 A:ILE333 4.3 58.3 1.0 CD A:ARG336 4.8 63.8 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 Gentamicin C1


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 Gentamicin C1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:50.2 occ:1.00 O C:HOH1107 2.9 41.5 1.0 NE2 C:GLN462 3.3 67.0 1.0 NH1 C:ARG469 3.4 39.9 1.0 CG2 C:ILE465 3.8 35.8 1.0 CD C:ARG469 3.8 35.5 1.0 CA C:GLU466 3.9 44.0 1.0 N C:GLU466 4.0 40.4 1.0 CB C:GLU466 4.1 50.8 1.0 CZ C:ARG469 4.3 39.7 1.0 CG C:GLU466 4.4 59.6 1.0 C C:ILE465 4.4 38.2 1.0 NE C:ARG469 4.4 38.7 1.0 CD C:GLN462 4.4 64.1 1.0 CB C:ILE465 4.5 37.7 1.0 O C:HOH1049 4.5 47.1 1.0 O C:ILE465 4.6 36.5 1.0 CG C:GLN462 4.8 61.2 1.0 O C:GLN462 4.8 52.4 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