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Sodium in PDB 4gki: Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1

Enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1

All present enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1, PDB code: 4gki was solved by P.J.Stogios, E.Evdokimova, Z.Wawrzak, G.Minasov, O.Egorova, R.Di Leo, T.Shakya, P.Spanogiannopoulos, N.Todorovic, A.Capretta, G.D.Wright, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.38 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 96.843, 97.103, 112.128, 103.24, 106.18, 112.66
R / Rfree (%) 16.6 / 21.6

Other elements in 4gki:

The structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

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 1-Nm-PP1 (pdb code 4gki). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1, PDB code: 4gki:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 4gki

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Sodium binding site 1 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:31.8
occ:0.74
 O A:HOH569 2.3 48.0 1.0
O A:THR76 2.4 30.2 1.0
O A:MSE79 2.4 35.1 1.0
O A:HOH659 2.5 45.1 1.0
OG1 A:THR76 2.5 36.7 1.0
O A:ACT307 2.5 64.1 1.0
C A:THR76 3.3 42.0 1.0
C A:MSE79 3.4 36.2 1.0
C A:ACT307 3.5 0.6 1.0
CA A:THR76 3.5 30.0 1.0
CB A:THR76 3.5 32.2 1.0
CA A:PRO80 3.8 32.0 1.0
N A:LEU81 3.9 30.1 1.0
N A:PRO80 4.0 36.7 1.0
CH3 A:ACT307 4.0 41.7 1.0
O A:HOH644 4.3 56.0 1.0
OXT A:ACT307 4.4 61.3 1.0
C A:PRO80 4.4 30.8 1.0
N A:MSE79 4.5 43.2 1.0
CG2 A:THR76 4.5 26.2 1.0
N A:ALA77 4.5 25.9 1.0
CA A:MSE79 4.6 33.8 1.0
O A:LEU81 4.8 29.7 1.0
CB A:LEU81 4.9 27.5 1.0
N A:THR76 4.9 25.4 1.0
CA A:LEU81 4.9 27.1 1.0

Sodium binding site 2 out of 14 in 4gki

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Sodium binding site 2 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:24.3
occ:0.77
 OD1 A:ASN234 2.3 28.5 1.0
O A:HOH402 2.4 22.9 1.0
O A:HOH424 2.4 23.4 1.0
O A:HOH458 2.6 28.9 1.0
O A:HOH445 2.6 26.9 1.0
CG A:ASN234 3.5 26.5 1.0
CZ3 A:TRP233 4.1 20.5 1.0
O A:HOH408 4.2 21.1 1.0
CA A:ASN234 4.2 24.3 1.0
O A:ASN234 4.3 16.4 1.0
N4 A:KAN301 4.4 19.9 1.0
ND2 A:ASN234 4.4 28.6 1.0
CB A:ASN234 4.4 18.1 1.0
OE2 A:GLU169 4.5 34.4 1.0
CG A:ASP167 4.5 29.4 1.0
OE1 A:GLU169 4.6 25.2 1.0
NE2 A:GLN244 4.7 20.5 1.0
OD1 A:ASP167 4.7 20.2 1.0
OD2 A:ASP167 4.7 20.9 1.0
C A:ASN234 4.7 14.5 1.0
CE3 A:TRP233 4.7 22.5 1.0
CB A:ASP167 4.8 22.5 1.0
CH2 A:TRP233 4.9 26.7 1.0
CD A:GLU169 5.0 36.1 1.0

Sodium binding site 3 out of 14 in 4gki

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Sodium binding site 3 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:39.1
occ:1.00
 O C:HOH537 2.3 43.5 1.0
O C:THR76 2.3 38.8 1.0
O C:MSE79 2.5 36.4 1.0
OG1 C:THR76 2.5 34.1 1.0
O C:HOH563 2.5 49.0 0.8
O C:ACT308 2.6 58.1 1.0
C C:THR76 3.2 44.2 1.0
CA C:THR76 3.5 30.4 1.0
CB C:THR76 3.5 32.8 1.0
C C:MSE79 3.5 32.7 1.0
C C:ACT308 3.6 92.0 1.0
CA C:PRO80 4.0 37.3 1.0
OXT C:ACT308 4.0 73.0 1.0
N C:LEU81 4.0 41.3 1.0
N C:PRO80 4.2 38.2 1.0
CG2 C:THR76 4.3 33.6 1.0
O C:HOH576 4.4 51.2 1.0
N C:ALA77 4.5 31.4 1.0
N C:MSE79 4.5 46.7 1.0
C C:PRO80 4.5 36.4 1.0
CA C:MSE79 4.6 38.5 1.0
CH3 C:ACT308 4.8 53.0 1.0
O C:LEU81 4.9 41.6 1.0
N C:THR76 4.9 25.7 1.0

Sodium binding site 4 out of 14 in 4gki

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Sodium binding site 4 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:37.6
occ:1.00
 OD1 C:ASN234 2.3 42.0 1.0
O C:HOH466 2.4 32.7 1.0
O C:HOH469 2.5 29.9 1.0
O C:HOH525 2.5 27.9 1.0
CG C:ASN234 3.5 30.0 1.0
CZ3 C:TRP233 3.9 20.4 1.0
O C:HOH443 4.2 28.5 1.0
CA C:ASN234 4.3 16.7 1.0
OE2 C:GLU169 4.3 31.8 1.0
ND2 C:ASN234 4.4 27.8 1.0
CB C:ASN234 4.4 21.6 1.0
O C:ASN234 4.4 22.2 1.0
OE1 C:GLU169 4.5 28.1 1.0
NE2 C:GLN244 4.6 20.2 1.0
CG C:ASP167 4.6 25.4 1.0
CE3 C:TRP233 4.6 16.0 1.0
O E:HOH531 4.6 50.2 1.0
OD2 C:ASP167 4.6 23.4 1.0
N4 C:KAN301 4.7 22.6 1.0
CH2 C:TRP233 4.7 27.4 1.0
OD1 C:ASP167 4.8 21.6 1.0
C C:ASN234 4.9 22.2 1.0
CB C:ASP167 4.9 21.6 1.0
CD C:GLU169 4.9 38.6 1.0

Sodium binding site 5 out of 14 in 4gki

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Sodium binding site 5 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:43.3
occ:1.00
 O D:HOH507 2.3 45.1 1.0
O D:HOH526 2.4 45.1 1.0
O D:THR76 2.4 28.5 1.0
O D:MSE79 2.4 24.0 1.0
O D:ACT304 2.6 60.5 1.0
OG1 D:THR76 2.6 36.4 1.0
C D:THR76 3.3 29.4 1.0
C D:ACT304 3.4 83.4 1.0
CA D:THR76 3.4 28.7 1.0
C D:MSE79 3.4 24.3 1.0
CB D:THR76 3.6 32.0 1.0
OXT D:ACT304 3.6 62.6 1.0
CA D:PRO80 3.9 31.0 1.0
N D:LEU81 4.0 24.8 1.0
N D:PRO80 4.1 25.5 1.0
C D:PRO80 4.4 34.4 1.0
N D:MSE79 4.4 26.0 1.0
CH3 D:ACT304 4.5 41.8 1.0
N D:ALA77 4.6 28.2 1.0
CA D:MSE79 4.6 25.8 1.0
CG2 D:THR76 4.6 26.9 1.0
N D:THR76 4.8 20.1 1.0
CG D:LEU81 4.8 41.8 1.0
O D:LEU81 4.9 28.6 1.0
CB D:LEU81 4.9 36.8 1.0
CA D:LEU81 5.0 29.1 1.0
O D:LEU75 5.0 24.2 1.0

Sodium binding site 6 out of 14 in 4gki

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Sodium binding site 6 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:28.4
occ:0.69
 O E:HOH467 2.3 37.5 1.0
O E:THR76 2.3 24.5 1.0
O E:HOH520 2.4 39.8 1.0
O E:ACT307 2.5 56.2 1.0
O E:MSE79 2.5 27.4 1.0
OG1 E:THR76 2.5 32.6 1.0
C E:THR76 3.2 22.2 1.0
C E:ACT307 3.4 0.8 1.0
CA E:THR76 3.4 22.3 1.0
C E:MSE79 3.5 29.2 1.0
CB E:THR76 3.5 24.7 1.0
CH3 E:ACT307 3.8 45.4 1.0
O E:HOH643 3.9 64.3 1.0
CA E:PRO80 3.9 29.9 1.0
N E:LEU81 4.0 27.1 1.0
N E:PRO80 4.2 27.5 1.0
OXT E:ACT307 4.4 66.8 1.0
N E:MSE79 4.4 28.1 1.0
CG2 E:THR76 4.4 28.8 1.0
N E:ALA77 4.4 19.1 1.0
C E:PRO80 4.5 34.8 1.0
CA E:MSE79 4.6 21.3 1.0
N E:THR76 4.9 19.5 1.0
O E:LEU81 4.9 30.7 1.0
O E:LEU75 5.0 18.8 1.0

Sodium binding site 7 out of 14 in 4gki

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Sodium binding site 7 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-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 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na303

b:53.6
occ:1.00
 O F:THR76 2.4 36.9 1.0
O F:HOH600 2.5 35.6 0.6
O F:MSE79 2.5 31.2 1.0
O F:HOH641 2.6 60.2 1.0
OG1 F:THR76 2.6 46.9 1.0
C F:THR76 3.3 33.2 1.0
CA F:THR76 3.4 29.1 1.0
C F:MSE79 3.6 33.2 1.0
CB F:THR76 3.6 34.6 1.0
CA F:PRO80 3.8 35.3 1.0
N F:LEU81 3.9 31.5 1.0
N F:PRO80 4.1 34.0 1.0
C F:PRO80 4.4 32.6 1.0
N F:ALA77 4.6 30.7 1.0
CG2 F:THR76 4.6 30.1 1.0
N F:MSE79 4.6 41.6 1.0
CA F:MSE79 4.7 28.9 1.0
CB F:LEU81 4.8 35.6 1.0
N F:THR76 4.8 27.5 1.0
O F:LEU81 4.8 36.5 1.0
CA F:LEU81 4.9 39.2 1.0
CG F:LEU81 4.9 35.4 1.0
O F:LEU75 5.0 26.7 1.0

Sodium binding site 8 out of 14 in 4gki

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Sodium binding site 8 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na303

b:34.8
occ:1.00
 O G:HOH541 2.3 39.3 1.0
O G:THR76 2.3 37.4 1.0
O G:MSE79 2.5 34.4 1.0
O G:HOH529 2.5 47.9 0.9
OG1 G:THR76 2.5 32.6 1.0
O G:HOH708 2.6 45.1 1.0
C G:THR76 3.2 42.3 1.0
C G:MSE79 3.5 30.8 1.0
CA G:THR76 3.5 30.6 1.0
CB G:THR76 3.5 31.2 1.0
CA G:PRO80 3.9 37.6 1.0
N G:LEU81 4.0 31.4 1.0
O G:HOH709 4.0 54.8 1.0
N G:PRO80 4.1 34.7 1.0
CG2 G:THR76 4.4 29.4 1.0
C G:PRO80 4.5 40.3 1.0
N G:MSE79 4.5 34.1 1.0
N G:ALA77 4.5 38.8 1.0
CA G:MSE79 4.6 31.8 1.0
N G:THR76 5.0 23.8 1.0
O G:LEU81 5.0 32.9 1.0

Sodium binding site 9 out of 14 in 4gki

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Sodium binding site 9 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na304

b:32.7
occ:1.00
 OD1 G:ASN234 2.4 35.0 1.0
O E:HOH533 2.4 21.1 1.0
O G:HOH426 2.5 23.1 1.0
O G:HOH530 2.5 21.2 1.0
O G:HOH516 2.6 29.9 1.0
CG G:ASN234 3.6 22.3 1.0
OD2 E:ASP254 3.6 47.2 1.0
O G:HOH423 4.0 21.2 1.0
CZ3 G:TRP233 4.0 25.5 1.0
O G:HOH567 4.2 47.6 1.0
CA G:ASN234 4.3 17.2 1.0
O G:ASN234 4.3 19.4 1.0
N4 G:KAN301 4.3 19.1 1.0
OE2 G:GLU169 4.4 28.7 1.0
ND2 G:ASN234 4.5 27.2 1.0
OE1 G:GLU169 4.5 23.3 1.0
CG G:ASP167 4.6 20.4 1.0
CB G:ASN234 4.6 13.9 1.0
CG E:ASP254 4.6 26.9 1.0
OD2 G:ASP167 4.6 23.5 1.0
NE2 G:GLN244 4.7 17.9 1.0
CH2 G:TRP233 4.7 23.5 1.0
OD1 G:ASP167 4.8 22.1 1.0
CE3 G:TRP233 4.8 23.1 1.0
C G:ASN234 4.8 18.8 1.0
CB G:ASP167 4.9 15.6 1.0
CD G:GLU169 4.9 39.3 1.0
OD1 E:ASP254 4.9 38.1 1.0

Sodium binding site 10 out of 14 in 4gki

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Sodium binding site 10 out of 14 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor 1-Nm-PP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:48.5
occ:1.00
 O H:HOH521 2.3 46.5 1.0
O H:THR76 2.4 20.8 1.0
O H:ACT304 2.5 55.5 1.0
O H:MSE79 2.5 25.9 1.0
OG1 H:THR76 2.5 37.1 1.0
O H:HOH628 2.7 46.0 1.0
C H:THR76 3.2 22.4 1.0
CA H:THR76 3.4 26.4 1.0
C H:ACT304 3.4 0.1 1.0
CB H:THR76 3.5 29.3 1.0
C H:MSE79 3.6 22.2 1.0
CH3 H:ACT304 3.8 47.1 1.0
CA H:PRO80 4.0 28.3 1.0
N H:LEU81 4.0 22.4 1.0
N H:PRO80 4.2 25.4 1.0
OXT H:ACT304 4.4 52.0 1.0
N H:ALA77 4.5 17.7 1.0
N H:MSE79 4.5 20.1 1.0
C H:PRO80 4.5 30.0 1.0
CG2 H:THR76 4.6 21.5 1.0
CA H:MSE79 4.7 21.3 1.0
N H:THR76 4.8 18.8 1.0
CB H:LEU81 4.9 45.1 1.0
O H:LEU75 4.9 18.0 1.0
O H:LEU81 5.0 26.0 1.0
CG H:LEU81 5.0 43.0 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 Aug 17 19:29:30 2025

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