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

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

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

Protein crystallography data

The structure of Aminoglycoside Phosphotransferase (2'')-Ia in Complex with Gmppnp, Magnesium, and Dibekacin, PDB code: 6cav 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) 89.94 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.990, 98.340, 93.220, 90.00, 105.24, 90.00
R / Rfree (%) 19.2 / 24.4

Other elements in 6cav:

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

Chlorine binding site 1 out of 3 in 6cav

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


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:72.8
occ:1.00
 NE2 A:GLN462 2.8 77.6 1.0
NH1 A:ARG469 3.6 59.9 1.0
CG A:GLU466 4.0 74.2 1.0
CD A:GLN462 4.0 81.7 1.0
CG2 A:ILE465 4.0 55.1 1.0
CB A:GLU466 4.1 68.3 1.0
N A:GLU466 4.1 61.1 1.0
CA A:GLU466 4.1 62.2 1.0
CG A:GLN462 4.4 83.3 1.0
CD A:ARG469 4.4 56.3 1.0
CB A:ILE465 4.5 56.1 1.0
C A:ILE465 4.6 57.6 1.0
CZ A:ARG469 4.6 57.1 1.0
O A:GLN462 4.7 67.7 1.0
NE A:ARG469 4.9 57.1 1.0

Chlorine binding site 2 out of 3 in 6cav

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


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:85.2
occ:1.00
 NE2 B:GLN462 2.9 90.1 1.0
NH1 B:ARG469 3.2 61.3 1.0
CG B:GLU466 3.6 86.0 1.0
CG2 B:ILE465 3.8 65.9 1.0
CD B:ARG469 4.0 56.8 1.0
CD B:GLN462 4.2 92.6 1.0
CZ B:ARG469 4.2 58.0 1.0
N B:GLU466 4.3 72.1 1.0
CA B:GLU466 4.4 74.9 1.0
CB B:ILE465 4.4 66.4 1.0
NE B:ARG469 4.5 57.0 1.0
CB B:GLU466 4.5 82.4 1.0
C B:ILE465 4.6 68.6 1.0
CD B:GLU466 4.6 94.9 1.0
CG B:GLN462 4.8 92.3 1.0
O B:ILE465 4.9 68.9 1.0

Chlorine binding site 3 out of 3 in 6cav

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


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 Dibekacin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl802

b:69.3
occ:1.00
 NE2 C:GLN462 3.2 67.8 1.0
NH1 C:ARG469 3.3 48.3 1.0
CA C:GLU466 3.7 54.6 1.0
CG C:GLU466 3.8 67.6 1.0
CB C:GLU466 3.8 61.2 1.0
N C:GLU466 3.8 51.2 1.0
CD C:ARG469 4.0 44.0 1.0
CG2 C:ILE465 4.1 46.7 1.0
CZ C:ARG469 4.3 45.1 1.0
C C:ILE465 4.3 48.2 1.0
CD C:GLN462 4.4 69.6 1.0
NE C:ARG469 4.5 43.6 1.0
CB C:ILE465 4.5 47.9 1.0
O C:ILE465 4.6 48.1 1.0
O C:GLN462 4.8 57.6 1.0
CG C:GLN462 4.8 70.6 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 Dec 12 12:49:04 2020

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