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Sodium in PDB 4fev: Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1

Enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1

All present enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1:
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 Pyrazolopyrimidine PP1, PDB code: 4fev 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) 19.97 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.571, 94.217, 96.878, 61.12, 73.09, 87.44
R / Rfree (%) 15.4 / 20.4

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 Pyrazolopyrimidine PP1 (pdb code 4fev). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1, PDB code: 4fev:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4fev

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Sodium binding site 1 out of 7 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1


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 Pyrazolopyrimidine PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:30.4
occ:0.82
 O A:HOH671 2.4 34.6 1.0
O A:THR76 2.4 12.6 1.0
O A:HOH538 2.4 35.0 1.0
O A:HOH673 2.4 51.8 1.0
O A:MET79 2.4 16.5 1.0
OG1 A:THR76 2.6 22.6 1.0
C A:THR76 3.2 15.1 1.0
CA A:THR76 3.5 7.4 1.0
C A:MET79 3.5 20.3 1.0
CB A:THR76 3.6 16.4 1.0
N A:LEU81 4.0 19.1 1.0
CA A:PRO80 4.0 22.6 1.0
O A:HOH674 4.0 35.2 1.0
N A:PRO80 4.2 17.1 1.0
C A:PRO80 4.5 12.1 1.0
N A:MET79 4.5 20.5 1.0
N A:ALA77 4.5 11.7 1.0
CG2 A:THR76 4.6 15.8 1.0
CA A:MET79 4.7 16.4 1.0
CB A:LEU81 4.8 20.2 1.0
N A:THR76 4.9 5.0 1.0
O A:LEU81 4.9 19.9 1.0
CA A:LEU81 4.9 30.7 1.0

Sodium binding site 2 out of 7 in 4fev

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Sodium binding site 2 out of 7 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1


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 Pyrazolopyrimidine PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:37.0
occ:0.92
 O B:HOH577 2.2 46.3 1.0
O B:THR76 2.3 17.1 1.0
O B:HOH578 2.4 55.6 1.0
O B:MET79 2.4 26.3 1.0
OG1 B:THR76 3.2 32.8 1.0
C B:THR76 3.3 15.8 1.0
C B:MET79 3.4 27.0 1.0
CA B:THR76 3.7 18.5 1.0
CA B:PRO80 3.9 34.6 1.0
N B:PRO80 4.1 20.6 1.0
CB B:THR76 4.1 26.9 1.0
N B:MET79 4.3 30.3 1.0
N B:LEU81 4.4 20.6 1.0
CA B:MET79 4.5 19.5 1.0
N B:ALA77 4.5 19.4 1.0
C B:PRO80 4.7 33.8 1.0
N B:PHE78 4.8 20.4 1.0
C B:ALA77 4.9 50.9 1.0
O B:LEU75 4.9 14.8 1.0
CA B:ALA77 4.9 16.2 1.0

Sodium binding site 3 out of 7 in 4fev

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Sodium binding site 3 out of 7 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:19.8
occ:0.87
 OD1 D:ASN234 2.2 13.7 1.0
O D:HOH455 2.4 17.2 1.0
O D:HOH638 2.5 17.0 1.0
O D:HOH488 2.5 21.3 1.0
O D:HOH641 2.5 10.9 1.0
CG D:ASN234 3.4 15.4 1.0
CZ3 D:TRP233 4.1 15.8 1.0
O D:HOH439 4.1 14.8 1.0
CA D:ASN234 4.2 6.2 1.0
N4 D:KAN301 4.3 9.5 1.0
ND2 D:ASN234 4.3 7.0 1.0
O D:ASN234 4.3 7.0 1.0
CB D:ASN234 4.4 5.9 1.0
OE2 D:GLU169 4.5 35.0 1.0
OE1 D:GLU169 4.6 22.0 1.0
CG D:ASP167 4.6 14.2 1.0
NE2 D:GLN244 4.7 8.2 1.0
CE3 D:TRP233 4.7 13.1 1.0
OD1 D:ASP167 4.7 11.3 1.0
C D:ASN234 4.8 8.4 1.0
OD2 D:ASP167 4.8 14.4 1.0
CH2 D:TRP233 4.8 16.1 1.0
CB D:ASP167 4.9 8.4 1.0
CD D:GLU169 5.0 41.3 1.0

Sodium binding site 4 out of 7 in 4fev

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Sodium binding site 4 out of 7 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:32.8
occ:0.85
 O D:HOH571 2.3 32.2 1.0
O D:HOH644 2.4 46.6 1.0
O D:MET79 2.5 18.2 1.0
OG1 D:THR76 2.5 31.3 1.0
O D:THR76 2.6 18.2 1.0
C D:THR76 3.4 27.6 1.0
CA D:THR76 3.5 13.1 1.0
C D:MET79 3.5 19.6 1.0
CB D:THR76 3.6 16.3 1.0
N D:LEU81 3.7 18.4 1.0
CA D:PRO80 3.8 33.3 1.0
O D:HOH643 3.9 53.7 1.0
N D:PRO80 4.1 24.1 1.0
C D:PRO80 4.3 17.6 1.0
CG2 D:THR76 4.6 15.4 1.0
N D:MET79 4.6 21.6 1.0
CB D:LEU81 4.6 18.5 1.0
N D:ALA77 4.7 17.8 1.0
O D:LEU81 4.7 17.1 1.0
CA D:MET79 4.7 16.7 1.0
CA D:LEU81 4.7 17.9 1.0
N D:THR76 4.9 12.3 1.0
CG D:LEU81 5.0 30.2 1.0

Sodium binding site 5 out of 7 in 4fev

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Sodium binding site 5 out of 7 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:25.7
occ:0.80
 O E:MET79 2.3 16.2 1.0
O E:HOH450 2.4 28.8 1.0
O E:HOH476 2.4 41.7 1.0
O E:THR76 2.4 15.3 1.0
O E:HOH574 2.5 36.7 1.0
OG1 E:THR76 2.6 28.6 1.0
C E:THR76 3.3 20.3 1.0
C E:MET79 3.4 20.4 1.0
CA E:THR76 3.4 15.0 1.0
CB E:THR76 3.6 23.6 1.0
N E:LEU81 3.8 17.5 1.0
CA E:PRO80 3.9 25.7 1.0
N E:PRO80 4.0 15.6 1.0
N E:MET79 4.3 14.7 1.0
C E:PRO80 4.3 19.3 1.0
CA E:MET79 4.5 11.6 1.0
N E:ALA77 4.5 15.7 1.0
CG2 E:THR76 4.6 19.4 1.0
CB E:LEU81 4.6 20.1 1.0
CA E:LEU81 4.8 20.1 1.0
N E:THR76 4.8 9.2 1.0
O E:HOH632 4.8 45.1 1.0
O E:LEU75 4.9 10.1 1.0
CG E:LEU81 4.9 26.6 1.0
O E:LEU81 4.9 16.4 1.0
N E:PHE78 5.0 9.8 1.0

Sodium binding site 6 out of 7 in 4fev

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Sodium binding site 6 out of 7 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:13.7
occ:0.72
 O F:HOH480 2.3 24.2 1.0
O F:HOH438 2.3 18.2 1.0
OD1 F:ASN234 2.4 13.6 1.0
O F:HOH408 2.5 13.5 1.0
O F:HOH446 2.5 14.9 1.0
CG F:ASN234 3.6 10.8 1.0
CZ3 F:TRP233 4.0 9.6 1.0
O F:HOH459 4.0 14.8 1.0
CA F:ASN234 4.3 7.0 1.0
N4 F:KAN301 4.3 10.0 1.0
O F:ASN234 4.4 5.2 1.0
ND2 F:ASN234 4.5 6.7 1.0
OE2 F:GLU169 4.5 23.8 1.0
OE1 F:GLU169 4.5 16.4 1.0
CB F:ASN234 4.5 4.8 1.0
CG F:ASP167 4.6 10.1 1.0
CE3 F:TRP233 4.7 10.0 1.0
OD2 F:ASP167 4.7 14.4 1.0
NE2 F:GLN244 4.7 6.7 1.0
CH2 F:TRP233 4.7 14.3 1.0
OD1 F:ASP167 4.8 8.9 1.0
CB F:ASP167 4.8 6.9 1.0
C F:ASN234 4.9 4.9 1.0
CD F:GLU169 4.9 49.7 1.0

Sodium binding site 7 out of 7 in 4fev

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Sodium binding site 7 out of 7 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na304

b:32.5
occ:0.95
 O F:HOH577 2.4 43.6 1.0
O F:MET79 2.4 27.2 1.0
O F:THR76 2.4 31.8 1.0
O F:HOH617 2.4 41.8 1.0
OG1 F:THR76 2.5 28.7 1.0
O F:HOH585 2.6 42.6 1.0
C F:THR76 3.3 37.6 1.0
C F:MET79 3.4 23.0 1.0
CA F:THR76 3.5 20.9 1.0
CB F:THR76 3.6 28.6 1.0
CA F:PRO80 3.7 22.8 1.0
N F:LEU81 3.9 33.0 1.0
N F:PRO80 4.0 28.5 1.0
C F:PRO80 4.3 39.2 1.0
N F:MET79 4.4 33.0 1.0
CG2 F:THR76 4.5 22.7 1.0
CA F:MET79 4.5 19.4 1.0
N F:ALA77 4.5 20.4 1.0
CB F:LEU81 4.9 23.1 1.0
O F:LEU81 4.9 22.8 1.0
N F:THR76 4.9 14.8 1.0
CA F:LEU81 4.9 22.0 1.0
CB F:PRO80 5.0 25.1 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 15:21:26 2024

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