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Sodium in PDB 4few: Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2

Enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2

All present enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2:
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 PP2, PDB code: 4few 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) 23.90 / 1.98
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.280, 93.579, 96.399, 61.22, 73.18, 87.35
R / Rfree (%) 15.7 / 21.6

Other elements in 4few:

The structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 also contains other interesting chemical elements:

Chlorine (Cl) 8 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 Pyrazolopyrimidine PP2 (pdb code 4few). 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 PP2, PDB code: 4few:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4few

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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 PP2


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 PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:32.4
occ:0.92
 O A:HOH510 2.3 31.9 1.0
O A:ACT305 2.4 47.6 1.0
O A:THR76 2.4 23.8 1.0
OG1 A:THR76 2.4 26.0 1.0
O A:MSE79 2.5 20.5 1.0
O A:HOH486 2.5 36.9 1.0
C A:ACT305 3.2 40.5 1.0
C A:THR76 3.3 19.0 1.0
CA A:THR76 3.5 18.3 1.0
CB A:THR76 3.5 27.9 1.0
C A:MSE79 3.6 20.2 1.0
CH3 A:ACT305 3.6 27.1 1.0
CA A:PRO80 3.9 27.6 1.0
N A:LEU81 4.0 22.7 1.0
OXT A:ACT305 4.2 49.7 1.0
N A:PRO80 4.2 21.8 1.0
O A:HOH630 4.2 49.0 1.0
CG2 A:THR76 4.4 25.6 1.0
N A:MSE79 4.5 30.5 1.0
C A:PRO80 4.5 25.1 1.0
N A:ALA77 4.5 19.0 1.0
CA A:MSE79 4.6 27.8 1.0
O A:LEU81 4.9 24.9 1.0
CB A:LEU81 4.9 20.3 1.0
N A:THR76 4.9 20.6 1.0

Sodium binding site 2 out of 7 in 4few

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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 PP2


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 PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:44.0
occ:1.00
 O B:THR76 2.5 33.5 1.0
OG1 B:THR76 2.6 36.2 1.0
O B:ACT304 2.6 59.1 1.0
O B:MSE79 2.6 35.2 1.0
C B:ACT304 3.2 91.9 1.0
C B:THR76 3.3 29.9 1.0
OXT B:ACT304 3.4 67.1 1.0
CA B:THR76 3.5 33.2 1.0
C B:MSE79 3.6 35.1 1.0
CB B:THR76 3.6 32.0 1.0
CA B:PRO80 3.7 40.3 1.0
N B:LEU81 3.8 32.4 1.0
N B:PRO80 4.1 36.1 1.0
C B:PRO80 4.3 38.2 1.0
CH3 B:ACT304 4.3 31.7 1.0
N B:ALA77 4.6 27.5 1.0
CG2 B:THR76 4.7 37.9 1.0
N B:MSE79 4.7 43.6 1.0
CA B:MSE79 4.8 30.3 1.0
O B:LEU81 4.8 37.3 1.0
CB B:LEU81 4.8 30.9 1.0
CA B:LEU81 4.8 30.6 1.0
N B:THR76 4.9 35.7 1.0
CB B:PRO80 4.9 43.2 1.0

Sodium binding site 3 out of 7 in 4few

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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 PP2


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 PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:22.8
occ:0.86
 OD1 D:ASN234 2.3 20.2 1.0
O D:HOH469 2.4 27.8 1.0
O D:HOH583 2.5 21.8 1.0
O D:HOH522 2.5 20.5 1.0
O D:HOH612 2.5 21.2 1.0
CG D:ASN234 3.5 25.4 1.0
CZ3 D:TRP233 3.9 21.4 1.0
CA D:ASN234 4.2 17.8 1.0
O D:HOH418 4.3 19.8 1.0
O D:ASN234 4.3 16.5 1.0
N4 D:KAN301 4.3 19.4 1.0
O D:HOH584 4.3 22.6 1.0
ND2 D:ASN234 4.4 19.7 1.0
CB D:ASN234 4.4 13.2 1.0
OE1 D:GLU169 4.4 26.7 1.0
OE2 D:GLU169 4.5 35.5 1.0
CG D:ASP167 4.5 19.3 1.0
NE2 D:GLN244 4.6 19.1 1.0
CE3 D:TRP233 4.6 24.7 1.0
OD2 D:ASP167 4.7 23.1 1.0
CH2 D:TRP233 4.7 29.4 1.0
OD1 D:ASP167 4.7 24.8 1.0
C D:ASN234 4.7 21.2 1.0
CB D:ASP167 4.8 21.4 1.0
CD D:GLU169 4.9 39.3 1.0

Sodium binding site 4 out of 7 in 4few

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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 PP2


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 PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:41.0
occ:1.00
 O D:HOH524 2.4 33.6 1.0
OG1 D:THR76 2.4 37.7 1.0
O D:THR76 2.5 23.0 1.0
O D:MSE79 2.6 27.9 1.0
O D:ACT306 2.6 60.5 1.0
C D:THR76 3.3 36.8 1.0
CA D:THR76 3.4 28.3 1.0
CB D:THR76 3.5 30.4 1.0
C D:ACT306 3.6 66.2 1.0
C D:MSE79 3.6 34.7 1.0
N D:LEU81 3.8 28.8 1.0
CA D:PRO80 3.9 31.9 1.0
CH3 D:ACT306 4.2 45.0 1.0
N D:PRO80 4.2 31.1 1.0
CG2 D:THR76 4.3 26.4 1.0
C D:PRO80 4.4 30.2 1.0
OXT D:ACT306 4.4 61.0 1.0
N D:MSE79 4.5 30.0 1.0
N D:ALA77 4.6 28.0 1.0
CA D:MSE79 4.7 25.9 1.0
O D:LEU81 4.7 25.4 1.0
CB D:LEU81 4.7 22.6 1.0
CA D:LEU81 4.8 24.1 1.0
N D:THR76 4.9 21.8 1.0
CG D:LEU81 5.0 26.8 1.0

Sodium binding site 5 out of 7 in 4few

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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 PP2


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 PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:35.4
occ:1.00
 O E:THR76 2.4 23.4 1.0
O E:HOH521 2.4 33.5 1.0
O E:ACT304 2.4 47.0 1.0
O E:HOH581 2.5 21.2 0.5
OG1 E:THR76 2.5 38.5 1.0
O E:MSE79 2.5 24.4 1.0
C E:THR76 3.3 24.7 1.0
C E:ACT304 3.4 99.6 1.0
CA E:THR76 3.5 21.5 1.0
C E:MSE79 3.5 19.7 1.0
CB E:THR76 3.6 24.3 1.0
OXT E:ACT304 3.6 52.0 1.0
O E:HOH581 3.8 22.1 0.5
CA E:PRO80 3.9 21.0 1.0
N E:LEU81 3.9 25.3 1.0
N E:PRO80 4.1 18.8 1.0
C E:PRO80 4.4 27.0 1.0
N E:MSE79 4.4 24.1 1.0
N E:ALA77 4.5 21.9 1.0
CG2 E:THR76 4.5 21.3 1.0
CA E:MSE79 4.6 25.1 1.0
CH3 E:ACT304 4.7 37.6 1.0
N E:THR76 4.9 18.7 1.0
O E:LEU81 4.9 25.4 1.0
CB E:LEU81 5.0 29.5 1.0
CG E:LEU81 5.0 43.9 1.0

Sodium binding site 6 out of 7 in 4few

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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 PP2


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 PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:23.3
occ:0.87
 OD1 F:ASN234 2.3 30.3 1.0
O F:HOH515 2.4 22.0 1.0
O F:HOH600 2.4 19.9 1.0
O F:HOH513 2.5 19.6 1.0
O F:HOH525 2.5 24.4 1.0
CG F:ASN234 3.6 21.4 1.0
CZ3 F:TRP233 3.9 20.2 1.0
O F:HOH478 4.1 23.4 1.0
CA F:ASN234 4.3 18.4 1.0
OE2 F:GLU169 4.4 25.6 1.0
N4 F:KAN301 4.4 17.1 1.0
O F:ASN234 4.4 16.6 1.0
ND2 F:ASN234 4.4 14.5 1.0
CB F:ASN234 4.5 18.1 1.0
CH2 F:TRP233 4.6 27.8 1.0
OE1 F:GLU169 4.6 24.2 1.0
CG F:ASP167 4.6 18.7 1.0
NE2 F:GLN244 4.6 16.8 1.0
CE3 F:TRP233 4.6 19.4 1.0
OD2 F:ASP167 4.7 18.4 1.0
CB F:ASP167 4.8 14.8 1.0
OD1 F:ASP167 4.8 20.5 1.0
C F:ASN234 4.8 14.4 1.0
CD F:GLU169 4.9 47.6 1.0

Sodium binding site 7 out of 7 in 4few

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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 PP2


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 PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na304

b:37.7
occ:1.00
 OXT F:ACT305 2.1 0.4 1.0
O F:HOH602 2.3 42.9 1.0
O F:THR76 2.3 36.5 1.0
OG1 F:THR76 2.4 34.4 1.0
O F:HOH595 2.4 29.4 0.7
O F:MSE79 2.5 28.5 1.0
C F:THR76 3.2 50.2 1.0
C F:ACT305 3.4 0.3 1.0
CA F:THR76 3.4 24.1 1.0
CB F:THR76 3.5 26.5 1.0
C F:MSE79 3.5 29.8 1.0
CA F:PRO80 3.9 29.7 1.0
O F:ACT305 4.0 75.4 1.0
N F:LEU81 4.0 28.1 1.0
N F:PRO80 4.1 38.6 1.0
CG2 F:THR76 4.4 26.1 1.0
CH3 F:ACT305 4.4 61.4 1.0
C F:PRO80 4.5 41.0 1.0
N F:ALA77 4.5 25.0 1.0
N F:MSE79 4.5 42.0 1.0
CA F:MSE79 4.6 32.3 1.0
N F:THR76 4.9 21.6 1.0
O F:LEU81 4.9 28.3 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 15:21:36 2024

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