Atomistry » Sodium » PDB 4f5r-4foi » 4few
Atomistry »
  Sodium »
    PDB 4f5r-4foi »
      4few »

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

Go back to Sodium Binding Sites List in 4few
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

Go back to Sodium Binding Sites List in 4few
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

Go back to Sodium Binding Sites List in 4few
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

Go back to Sodium Binding Sites List in 4few
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

Go back to Sodium Binding Sites List in 4few
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

Go back to Sodium Binding Sites List in 4few
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

Go back to Sodium Binding Sites List in 4few
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy