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

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium, PDB code: 5iqf 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)	89.13 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.454, 99.075, 92.350, 90.00, 105.18, 90.00
R / Rfree (%)	18 / 22.8

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

Magnesium

(Mg)

8 atoms

The binding sites of Chlorine atom in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium (pdb code 5iqf). 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium, PDB code: 5iqf:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:66.0 occ:1.00 NE2 A:GLN462 3.1 66.7 1.0 NH1 A:ARG469 3.3 44.3 1.0 CG2 A:ILE465 3.6 45.9 1.0 CD A:ARG469 3.8 39.8 1.0 CA A:GLU466 3.9 53.4 1.0 CG A:GLU466 4.0 68.7 1.0 N A:GLU466 4.0 50.5 1.0 CB A:GLU466 4.2 60.5 1.0 CZ A:ARG469 4.2 42.6 1.0 C A:ILE465 4.2 45.3 1.0 CB A:ILE465 4.3 46.4 1.0 CD A:GLN462 4.3 68.9 1.0 NE A:ARG469 4.4 41.7 1.0 O A:ILE465 4.5 44.1 1.0 O A:HOH1049 4.8 47.6 1.0 O A:GLN462 4.8 49.9 1.0 CG A:GLN462 4.9 65.0 1.0 CA A:ILE465 5.0 45.4 1.0 CG A:ARG469 5.0 38.2 1.0

Chlorine binding site 2 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl802 b:85.2 occ:1.00 NE2 B:GLN462 3.0 69.7 1.0 CG B:GLU466 3.8 75.8 1.0 NH1 B:ARG469 3.8 46.1 1.0 CG2 B:ILE465 3.9 43.3 1.0 CA B:GLU466 3.9 54.4 1.0 N B:GLU466 4.0 48.7 1.0 CB B:GLU466 4.1 65.3 1.0 CD B:ARG469 4.1 41.5 1.0 CD B:GLN462 4.2 71.3 1.0 O B:HOH1049 4.3 60.6 1.0 C B:ILE465 4.4 43.6 1.0 CB B:ILE465 4.5 44.0 1.0 CZ B:ARG469 4.7 43.2 1.0 CG B:GLN462 4.7 71.9 1.0 O B:ILE465 4.7 43.2 1.0 NE B:ARG469 4.8 40.5 1.0 O B:GLN462 4.8 53.0 1.0 CD B:GLU466 4.9 91.8 1.0

Chlorine binding site 3 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp 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 Aph(6')- Ie/Aph(2'')-Ia) in Complex with Gdp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:71.8 occ:1.00 O C:HOH1107 2.7 53.2 1.0 NE2 C:GLN462 3.2 60.2 1.0 NH1 C:ARG469 3.5 39.0 1.0 CA C:GLU466 3.8 45.1 1.0 CD C:ARG469 3.9 35.2 1.0 CG2 C:ILE465 3.9 38.9 1.0 N C:GLU466 3.9 43.0 1.0 CB C:GLU466 4.0 53.1 1.0 CG C:GLU466 4.2 59.1 1.0 C C:ILE465 4.3 39.0 1.0 CZ C:ARG469 4.4 37.9 1.0 CD C:GLN462 4.4 62.5 1.0 NE C:ARG469 4.5 35.2 1.0 CB C:ILE465 4.5 40.0 1.0 O C:ILE465 4.5 38.4 1.0 O C:GLN462 4.8 47.4 1.0 CG C:GLN462 4.8 62.1 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