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

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1, PDB code: 5iqg 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)	89.74 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.260, 98.480, 93.020, 90.00, 105.26, 90.00
R / Rfree (%)	18.9 / 23

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gdp, Magnesium, and Gentamicin C1 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 Gdp, Magnesium, and Gentamicin C1 (pdb code 5iqg). 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 Gdp, Magnesium, and Gentamicin C1, PDB code: 5iqg:
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 Gdp, 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 Gdp, Magnesium, and Gentamicin C1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:87.4 occ:1.00 NE2 A:GLN462 3.2 74.2 1.0 NH1 A:ARG469 3.4 61.7 1.0 CA A:GLU466 3.7 62.6 1.0 CG2 A:ILE465 3.7 56.8 1.0 N A:GLU466 3.8 61.0 1.0 CB A:GLU466 3.9 71.7 1.0 CD A:ARG469 3.9 53.4 1.0 CG A:GLU466 4.0 82.1 1.0 C A:ILE465 4.2 57.5 1.0 CB A:ILE465 4.3 58.7 1.0 CD A:GLN462 4.4 75.2 1.0 CZ A:ARG469 4.4 58.5 1.0 NE A:ARG469 4.6 56.2 1.0 O A:ILE465 4.6 54.1 1.0 CG A:GLN462 4.7 73.2 1.0 O A:GLN462 4.7 67.2 1.0 CA A:ILE465 5.0 56.6 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 Gdp, 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 Gdp, Magnesium, and Gentamicin C1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl802 b:90.3 occ:1.00 NE2 B:GLN462 2.9 75.7 1.0 CG B:GLU466 3.3 78.2 1.0 NH1 B:ARG469 3.4 54.1 1.0 CG2 B:ILE465 3.6 55.2 1.0 O B:HOH1049 3.6 68.7 1.0 CD B:ARG469 4.1 49.8 1.0 N B:GLU466 4.1 62.8 1.0 CD B:GLN462 4.1 77.6 1.0 CA B:GLU466 4.2 65.6 1.0 CD B:GLU466 4.3 90.6 1.0 CB B:ILE465 4.3 55.7 1.0 CB B:GLU466 4.3 72.6 1.0 CZ B:ARG469 4.5 51.0 1.0 C B:ILE465 4.5 59.9 1.0 CG B:GLN462 4.6 78.3 1.0 NE B:ARG469 4.7 48.7 1.0 OE1 B:GLU466 4.9 87.0 1.0 OE2 B:GLU466 4.9 96.2 1.0 O B:ILE465 4.9 64.5 1.0 O B:GLN462 4.9 71.3 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 Gdp, 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 Gdp, Magnesium, and Gentamicin C1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:83.4 occ:1.00 NH1 C:ARG469 3.6 45.4 1.0 NE2 C:GLN462 3.6 71.2 1.0 CA C:GLU466 3.6 51.6 1.0 CG C:GLU466 3.7 66.4 1.0 CB C:GLU466 3.7 57.5 1.0 N C:GLU466 3.9 50.1 1.0 CD C:ARG469 4.1 41.5 1.0 CG2 C:ILE465 4.2 46.9 1.0 C C:ILE465 4.4 48.4 1.0 CZ C:ARG469 4.5 43.4 1.0 NE C:ARG469 4.7 41.5 1.0 CD C:GLN462 4.7 71.5 1.0 CB C:ILE465 4.8 46.3 1.0 O C:ILE465 4.8 49.1 1.0 CG C:GLN462 4.9 66.4 1.0 CD C:GLU466 4.9 76.0 1.0 O C:GLN462 4.9 55.1 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