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

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp and Magnesium, PDB code: 5iqa 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)	56.04 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.170, 100.320, 94.060, 90.00, 105.00, 90.00
R / Rfree (%)	16.7 / 20.6

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp 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 Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp and Magnesium (pdb code 5iqa). 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 and Magnesium, PDB code: 5iqa:
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 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 Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:65.4 occ:1.00 O A:HOH1107 3.0 54.9 1.0 NE2 A:GLN462 3.3 72.4 1.0 NH1 A:ARG469 3.4 49.7 1.0 CG2 A:ILE465 3.8 42.7 1.0 CA A:GLU466 3.8 50.7 1.0 N A:GLU466 3.8 45.8 1.0 CD A:ARG469 3.8 41.5 1.0 CB A:GLU466 4.0 62.4 1.0 C A:ILE465 4.2 42.6 1.0 CZ A:ARG469 4.3 47.2 1.0 CG A:GLU466 4.4 78.6 1.0 CB A:ILE465 4.4 41.9 1.0 NE A:ARG469 4.5 42.3 1.0 CD A:GLN462 4.5 71.6 1.0 O A:ILE465 4.6 39.6 1.0 O A:GLN462 4.7 52.6 1.0 CG A:GLN462 4.8 66.7 1.0 O A:HOH1049 4.8 59.5 1.0 CA A:ILE465 5.0 40.1 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 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 Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl802 b:71.6 occ:1.00 O B:HOH1107 3.2 55.3 1.0 NE2 B:GLN462 3.2 71.4 1.0 NH1 B:ARG469 3.2 37.0 1.0 CG B:GLU466 3.5 67.6 1.0 CG2 B:ILE465 3.7 36.8 1.0 O B:HOH1049 3.7 61.4 1.0 CD B:ARG469 3.9 37.1 1.0 N B:GLU466 4.2 44.1 1.0 CZ B:ARG469 4.2 36.8 1.0 CA B:GLU466 4.2 48.6 1.0 CD B:GLN462 4.4 66.3 1.0 CB B:ILE465 4.4 36.7 1.0 CB B:GLU466 4.4 58.3 1.0 NE B:ARG469 4.5 37.8 1.0 C B:ILE465 4.5 38.9 1.0 CD B:GLU466 4.6 83.1 1.0 O B:HOH1075 4.8 51.7 1.0 O B:ILE465 4.8 39.1 1.0 CG B:GLN462 4.9 65.1 1.0 OE2 B:GLU466 5.0 96.0 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 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 Aac(6')- Ie/Aph(2'')-Ia) in Complex with Gmppnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:60.6 occ:1.00 NE2 C:GLN462 3.2 56.8 1.0 NH1 C:ARG469 3.4 32.7 1.0 CG2 C:ILE465 3.8 38.2 1.0 N C:GLU466 3.9 35.1 1.0 CD C:ARG469 3.9 29.3 1.0 CA C:GLU466 3.9 36.8 1.0 CB C:GLU466 4.1 44.4 1.0 C C:ILE465 4.3 33.3 1.0 CD C:GLN462 4.3 55.4 1.0 CB C:ILE465 4.3 35.9 1.0 CZ C:ARG469 4.4 32.6 1.0 NE C:ARG469 4.5 28.1 1.0 CG C:GLU466 4.6 52.0 1.0 CG C:GLN462 4.6 51.9 1.0 O C:ILE465 4.6 30.5 1.0 O C:HOH1049 4.7 56.8 1.0 O C:GLN462 4.7 47.9 1.0 CA C:ILE465 5.0 33.8 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