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Chlorine in PDB 4fex: Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478

Enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478

All present enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478:
2.7.1.95;

Protein crystallography data

The structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478, PDB code: 4fex was solved by P.J.Stogios, E.Evdokimova, Z.Wawrzak, G.Minasov, O.Egorova, R.Di Leo, T.Shakya, P.Spanogiannopoulos, G.D.Wright, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.669, 93.694, 96.318, 118.84, 103.56, 93.44
R / Rfree (%) 18.4 / 24

Other elements in 4fex:

The structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478 (pdb code 4fex). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478, PDB code: 4fex:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4fex

Go back to Chlorine Binding Sites List in 4fex
Chlorine binding site 1 out of 4 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:82.1
occ:0.74
 CL A:0TO302 0.0 82.1 0.7
C20 A:0TO302 1.7 74.2 0.7
C18 A:0TO302 2.7 67.7 0.7
C21 A:0TO302 2.7 62.8 0.7
OG1 A:THR98 3.0 42.4 1.0
CG2 A:THR98 3.5 43.8 1.0
CB A:THR98 3.7 43.8 1.0
CD1 A:LEU72 3.7 42.0 1.0
CG A:PRO82 3.9 48.4 1.0
OE2 A:GLU68 3.9 59.1 1.0
C19 A:0TO302 4.0 75.3 0.7
C7 A:0TO302 4.0 62.8 0.7
CB A:PRO82 4.1 45.6 1.0
C17 A:0TO302 4.5 76.1 0.7
CG A:LEU72 4.8 50.8 1.0
CD A:GLU68 4.8 58.9 1.0
N5 A:0TO302 4.8 60.2 0.7
CD A:PRO82 4.9 46.4 1.0
CD2 A:LEU72 4.9 46.4 1.0

Chlorine binding site 2 out of 4 in 4fex

Go back to Chlorine Binding Sites List in 4fex
Chlorine binding site 2 out of 4 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:86.9
occ:0.79
 CL C:0TO302 0.0 86.9 0.8
C20 C:0TO302 1.7 81.7 0.8
C18 C:0TO302 2.7 76.1 0.8
C21 C:0TO302 2.7 76.3 0.8
OE2 C:GLU68 3.2 59.8 1.0
CD1 C:LEU72 3.8 46.0 1.0
CG C:PRO82 3.9 45.4 1.0
C7 C:0TO302 4.0 76.8 0.8
C19 C:0TO302 4.0 76.9 0.8
CD C:GLU68 4.4 69.0 1.0
CB C:PRO82 4.4 42.8 1.0
OG1 C:THR98 4.4 51.4 1.0
C17 C:0TO302 4.6 73.4 0.8
N C:ASP216 4.6 47.9 1.0
CG2 C:THR98 4.6 49.5 1.0
NZ C:LYS55 4.7 55.8 1.0
N5 C:0TO302 4.8 65.3 0.8
CG C:LEU72 4.8 38.7 1.0
CB C:THR98 4.9 47.5 1.0
CE C:LYS55 4.9 57.9 1.0
CB C:ILE215 5.0 40.7 1.0

Chlorine binding site 3 out of 4 in 4fex

Go back to Chlorine Binding Sites List in 4fex
Chlorine binding site 3 out of 4 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:89.3
occ:0.83
 CL D:0TO302 0.0 89.3 0.8
C20 D:0TO302 1.7 88.7 0.8
C18 D:0TO302 2.7 77.9 0.8
C21 D:0TO302 2.7 72.5 0.8
OE2 D:GLU68 3.1 61.8 1.0
CD D:GLU68 3.9 66.4 1.0
OE1 D:GLU68 4.0 58.1 1.0
C7 D:0TO302 4.0 66.8 0.8
C19 D:0TO302 4.0 82.6 0.8
CD1 D:LEU72 4.1 57.6 1.0
CG2 D:THR98 4.3 46.4 1.0
CG D:PRO82 4.3 50.5 1.0
N D:ASP216 4.3 47.2 1.0
OG1 D:THR98 4.4 50.2 1.0
CG D:LEU72 4.4 50.4 1.0
C17 D:0TO302 4.5 77.8 0.8
CD2 D:LEU72 4.7 47.8 1.0
CB D:THR98 4.7 41.5 1.0
N5 D:0TO302 4.7 65.0 0.8
CB D:PRO82 4.8 52.9 1.0
CD2 D:LEU96 4.9 46.1 1.0
CD D:PRO82 4.9 54.5 1.0

Chlorine binding site 4 out of 4 in 4fex

Go back to Chlorine Binding Sites List in 4fex
Chlorine binding site 4 out of 4 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Tyrphostin AG1478 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:80.8
occ:0.87
 CL E:0TO302 0.0 80.8 0.9
C20 E:0TO302 1.7 85.5 0.9
C18 E:0TO302 2.7 66.0 0.9
C21 E:0TO302 2.8 78.6 0.9
O E:HOH428 2.8 49.8 1.0
CD2 E:LEU72 3.5 48.8 1.0
OG1 E:THR98 3.6 55.2 1.0
OE2 E:GLU68 3.9 58.5 1.0
CG2 E:THR98 3.9 48.2 1.0
CG E:PRO82 4.0 46.5 1.0
C7 E:0TO302 4.0 63.7 0.9
C19 E:0TO302 4.0 74.3 0.9
CB E:THR98 4.1 52.1 1.0
CB E:PRO82 4.3 52.0 1.0
C17 E:0TO302 4.5 72.9 0.9
N E:ASP216 4.6 43.6 1.0
N5 E:0TO302 4.7 52.9 0.9
CD E:PRO82 4.7 50.7 1.0
CG E:LEU72 4.7 40.0 1.0
CD1 E:LEU72 4.8 49.8 1.0
CD E:GLU68 5.0 56.5 1.0

Reference:

P.J.Stogios, P.Spanogiannopoulos, E.Evdokimova, O.Egorova, T.Shakya, N.Todorovic, A.Capretta, G.D.Wright, A.Savchenko. Structure-Guided Optimization of Protein Kinase Inhibitors Reverses Aminoglycoside Antibiotic Resistance. Biochem.J. V. 454 191 2013.
ISSN: ISSN 0264-6021
PubMed: 23758273
DOI: 10.1042/BJ20130317
Page generated: Sun Jul 21 13:42:31 2024

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