Chlorine in PDB 5iqi: Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant in Complex with Gmppnp and Magnesium

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant in Complex with Gmppnp and Magnesium, PDB code: 5iqi 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)	89.76 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.169, 99.740, 92.970, 90.00, 105.10, 90.00
R / Rfree (%)	16.7 / 21.1

The structure of Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant 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) Y237F Mutant in Complex with Gmppnp and Magnesium (pdb code 5iqi). 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) Y237F Mutant in Complex with Gmppnp and Magnesium, PDB code: 5iqi:
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) Y237F Mutant 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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:69.4 occ:1.00 O A:HOH1107 3.1 57.6 1.0 NE2 A:GLN462 3.2 65.8 1.0 NH1 A:ARG469 3.5 45.0 1.0 CG2 A:ILE465 3.7 41.8 1.0 N A:GLU466 3.7 44.7 1.0 CA A:GLU466 3.7 48.3 1.0 CD A:ARG469 3.9 40.0 1.0 CB A:GLU466 4.0 56.7 1.0 CG A:GLU466 4.2 65.3 1.0 C A:ILE465 4.2 42.3 1.0 CB A:ILE465 4.3 41.7 1.0 CD A:GLN462 4.4 66.3 1.0 CZ A:ARG469 4.4 42.6 1.0 NE A:ARG469 4.5 39.5 1.0 O A:ILE465 4.6 39.5 1.0 O A:GLN462 4.6 53.1 1.0 CG A:GLN462 4.7 65.7 1.0 O A:HOH1049 4.9 58.0 1.0 CA A:ILE465 5.0 41.0 1.0

Chlorine binding site 2 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant 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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl802 b:76.0 occ:1.00 NE2 B:GLN462 3.1 69.3 1.0 CG B:GLU466 3.4 63.9 1.0 NH1 B:ARG469 3.4 45.0 1.0 CG2 B:ILE465 3.6 44.7 1.0 O B:HOH1049 3.8 61.5 1.0 CD B:ARG469 3.9 38.4 1.0 N B:GLU466 4.0 45.9 1.0 CA B:GLU466 4.0 51.0 1.0 CD B:GLN462 4.3 68.3 1.0 CB B:GLU466 4.3 58.3 1.0 CB B:ILE465 4.3 44.2 1.0 C B:ILE465 4.4 44.6 1.0 CZ B:ARG469 4.4 40.9 1.0 CD B:GLU466 4.6 75.7 1.0 NE B:ARG469 4.6 39.0 1.0 O B:HOH1215 4.6 57.6 1.0 CG B:GLN462 4.7 68.8 1.0 O B:ILE465 4.8 42.3 1.0 O B:GLN462 4.8 54.5 1.0

Chlorine binding site 3 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia (Ctd of Aac(6')- Ie/Aph(2'')-Ia) Y237F Mutant 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) Y237F Mutant in Complex with Gmppnp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl802 b:58.9 occ:1.00 O B:HOH1282 2.5 62.0 1.0 O C:HOH1107 2.6 47.1 1.0 NE2 C:GLN462 3.2 56.6 1.0 NH1 C:ARG469 3.4 31.9 1.0 CG2 C:ILE465 3.6 34.9 1.0 N C:GLU466 3.8 33.3 1.0 CD C:ARG469 3.8 26.9 1.0 CA C:GLU466 3.8 36.4 1.0 CB C:GLU466 4.1 42.0 1.0 C C:ILE465 4.2 32.1 1.0 CB C:ILE465 4.3 34.3 1.0 CZ C:ARG469 4.3 31.0 1.0 CD C:GLN462 4.4 54.4 1.0 O C:HOH1049 4.4 53.9 1.0 NE C:ARG469 4.4 27.9 1.0 CG C:GLU466 4.4 49.0 1.0 O C:ILE465 4.5 28.8 1.0 O C:GLN462 4.6 40.1 1.0 CG C:GLN462 4.7 52.5 1.0 CA C:ILE465 4.9 32.2 1.0 CG C:ARG469 5.0 26.7 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