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Sodium 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:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4fex

Go back to Sodium Binding Sites List in 4fex
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na303

b:57.4
occ:1.00
 O A:MET79 2.3 55.5 1.0
O A:THR76 2.4 47.8 1.0
O A:HOH433 2.4 48.9 1.0
O A:HOH434 2.6 59.4 1.0
O A:HOH417 2.6 54.0 1.0
OG1 A:THR76 2.7 53.2 1.0
C A:THR76 3.3 45.0 1.0
C A:MET79 3.5 53.9 1.0
CA A:THR76 3.5 46.0 1.0
CB A:THR76 3.7 40.3 1.0
CA A:PRO80 3.9 49.7 1.0
N A:LEU81 4.1 51.7 1.0
N A:PRO80 4.1 62.4 1.0
N A:MET79 4.5 56.1 1.0
C A:PRO80 4.5 53.9 1.0
CG2 A:THR76 4.5 36.0 1.0
N A:ALA77 4.5 39.2 1.0
CA A:MET79 4.6 51.3 1.0
N A:PHE78 4.8 42.6 1.0
C A:PHE78 4.9 48.2 1.0
N A:THR76 5.0 44.9 1.0

Sodium binding site 2 out of 2 in 4fex

Go back to Sodium Binding Sites List in 4fex
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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
B:Na302

b:76.3
occ:1.00
 O B:MET79 2.5 66.9 1.0
OG1 B:THR76 2.5 59.2 1.0
O B:THR76 2.6 63.5 1.0
C B:THR76 3.5 58.0 1.0
C B:MET79 3.6 64.4 1.0
CB B:THR76 3.6 51.2 1.0
CA B:THR76 3.7 53.0 1.0
N B:LEU81 3.7 58.9 1.0
CA B:PRO80 3.9 60.5 1.0
N B:PRO80 4.2 66.0 1.0
C B:PRO80 4.3 63.5 1.0
O B:LEU81 4.4 58.1 1.0
CG2 B:THR76 4.5 40.5 1.0
CB B:LEU81 4.7 52.4 1.0
CA B:LEU81 4.7 50.4 1.0
N B:ALA77 4.8 45.8 1.0
CA B:MET79 4.9 56.5 1.0
N B:MET79 4.9 65.8 1.0
CG2 B:THR83 4.9 59.2 1.0
C B:LEU81 5.0 48.8 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: Mon Oct 7 15:22:09 2024

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