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Chlorine in PDB 6cgg: Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin

Enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin

All present enzymatic activity of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin:
2.7.1.190;

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin, PDB code: 6cgg 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) 90.14 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.330, 99.780, 93.510, 90.00, 105.43, 90.00
R / Rfree (%) 17.8 / 22.3

Other elements in 6cgg:

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin (pdb code 6cgg). 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 in Complex with Gmppnp, Magnesium, and Arbekacin, PDB code: 6cgg:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6cgg

Go back to Chlorine Binding Sites List in 6cgg
Chlorine binding site 1 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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 in Complex with Gmppnp, Magnesium, and Arbekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:83.0
occ:1.00
NE2 A:GLN462 3.2 81.8 1.0
CB A:GLU466 3.5 72.8 1.0
CA A:GLU466 3.6 66.8 1.0
NH1 A:ARG469 3.7 59.8 1.0
N A:GLU466 3.7 65.2 1.0
CG A:GLU466 3.9 77.4 1.0
CG2 A:ILE465 3.9 62.9 1.0
CD A:ARG469 4.2 52.5 1.0
C A:ILE465 4.2 63.3 1.0
CD A:GLN462 4.3 85.2 1.0
CB A:ILE465 4.4 63.0 1.0
O A:GLN462 4.4 74.8 1.0
CG A:GLN462 4.5 84.2 1.0
CZ A:ARG469 4.5 55.8 1.0
O A:ILE465 4.7 59.6 1.0
NE A:ARG469 4.7 53.3 1.0
OE1 A:GLU466 4.9 93.9 1.0
CD A:GLU466 5.0 85.3 1.0
CA A:ILE465 5.0 62.0 1.0

Chlorine binding site 2 out of 3 in 6cgg

Go back to Chlorine Binding Sites List in 6cgg
Chlorine binding site 2 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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 in Complex with Gmppnp, Magnesium, and Arbekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:98.3
occ:1.00
O A:HOH1282 2.6 49.4 1.0
NE2 B:GLN462 2.9 82.9 1.0
NH1 B:ARG469 3.4 59.0 1.0
CG2 B:ILE465 4.0 59.8 1.0
CD B:GLN462 4.1 83.9 1.0
CZ B:ARG469 4.6 56.9 1.0
OE1 B:GLN462 4.8 82.2 1.0

Chlorine binding site 3 out of 3 in 6cgg

Go back to Chlorine Binding Sites List in 6cgg
Chlorine binding site 3 out of 3 in the Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Arbekacin


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 in Complex with Gmppnp, Magnesium, and Arbekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl802

b:67.8
occ:1.00
NE2 C:GLN462 3.4 58.2 1.0
NH1 C:ARG469 3.4 39.7 1.0
CA C:GLU466 3.7 48.5 1.0
CB C:GLU466 3.7 54.8 1.0
N C:GLU466 3.8 47.0 1.0
CG2 C:ILE465 3.8 42.3 1.0
CD C:ARG469 3.9 36.7 1.0
CG C:GLU466 4.2 59.7 1.0
C C:ILE465 4.2 44.8 1.0
CZ C:ARG469 4.3 38.8 1.0
CB C:ILE465 4.4 43.8 1.0
CD C:GLN462 4.5 60.6 1.0
NE C:ARG469 4.5 37.6 1.0
O C:ILE465 4.6 42.2 1.0
O C:GLN462 4.6 54.0 1.0
CG C:GLN462 4.7 59.4 1.0
CA C:ILE465 4.9 44.4 1.0

Reference:

S.J.Caldwell, A.M.Berghuis. Plasticity of Aminoglycoside Binding to Antibiotic Kinase Aph(2′′)-Ia. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 29661878
DOI: 10.1128/AAC.00202-18
Page generated: Sat Jul 12 12:23:18 2025

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