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Sodium in PDB 2onj: Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp

Protein crystallography data

The structure of Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp, PDB code: 2onj was solved by R.J.P.Dawson, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.961, 104.447, 181.391, 90.00, 98.23, 90.00
R / Rfree (%) 25.4 / 27.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp (pdb code 2onj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp, PDB code: 2onj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2onj

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Sodium binding site 1 out of 4 in the Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na900

b:0.3
occ:1.00
O A:SER524 2.7 0.0 1.0
O A:ARG527 2.8 0.1 1.0
OG1 A:THR369 2.8 0.7 1.0
O A:GLY367 2.9 99.6 1.0
C A:GLY367 3.5 99.6 1.0
O A:GLU368 3.6 0.6 1.0
C A:GLU368 3.7 0.6 1.0
O A:LYS525 3.8 0.2 1.0
C A:SER524 3.8 0.0 1.0
OG1 A:THR529 3.8 87.6 1.0
C A:ARG527 3.9 0.1 1.0
N A:THR369 4.0 89.7 1.0
CB A:THR369 4.0 0.7 1.0
N A:ARG527 4.1 0.1 1.0
CA A:GLY367 4.1 99.6 1.0
N A:GLU368 4.2 0.6 1.0
CA A:THR369 4.2 89.7 1.0
C A:LYS525 4.3 0.2 1.0
CB A:THR529 4.3 87.6 1.0
CA A:GLU368 4.4 0.6 1.0
N A:THR529 4.5 0.4 1.0
CB A:SER524 4.5 0.0 1.0
CA A:SER524 4.5 0.0 1.0
CA A:ARG527 4.6 0.1 1.0
OD2 A:ASP543 4.7 0.7 1.0
N A:LYS525 4.8 0.2 1.0
N A:ASP526 4.9 0.2 1.0
CA A:LYS525 4.9 0.2 1.0
N A:THR528 4.9 95.0 1.0
C A:ASP526 5.0 0.2 1.0
CG2 A:THR369 5.0 0.7 1.0

Sodium binding site 2 out of 4 in 2onj

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Sodium binding site 2 out of 4 in the Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na911

b:63.3
occ:1.00
OG A:SER381 2.4 0.9 1.0
OE1 A:GLN422 2.5 0.0 1.0
O3G A:ANP701 2.8 80.9 1.0
N3B A:ANP701 2.9 80.9 1.0
PG A:ANP701 3.0 80.9 1.0
O2G A:ANP701 3.1 80.9 1.0
O A:HOH818 3.2 92.1 1.0
OD1 A:ASP502 3.4 0.4 1.0
OE2 A:GLU503 3.4 0.4 1.0
O2B A:ANP701 3.4 80.9 1.0
CD A:GLN422 3.6 0.0 1.0
CB A:SER381 3.8 0.9 1.0
OD2 A:ASP502 3.8 0.4 1.0
PB A:ANP701 3.9 80.9 1.0
CG A:ASP502 3.9 0.4 1.0
NE2 A:GLN422 4.3 0.0 1.0
CD A:GLU503 4.3 0.4 1.0
CB A:GLN422 4.4 0.0 1.0
N B:GLY480 4.5 86.3 1.0
O3A A:ANP701 4.5 80.9 1.0
CG A:GLN422 4.6 0.0 1.0
CA A:SER381 4.6 82.2 1.0
CG A:GLU503 4.6 0.4 1.0
O1G A:ANP701 4.7 80.9 1.0
N A:SER381 4.8 82.2 1.0
CG1 A:VAL532 5.0 94.8 1.0
CA B:GLY480 5.0 86.3 1.0

Sodium binding site 3 out of 4 in 2onj

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Sodium binding site 3 out of 4 in the Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na901

b:64.8
occ:1.00
OE1 B:GLN422 2.2 0.2 1.0
OG B:SER381 2.7 87.9 1.0
O B:HOH808 2.8 98.0 1.0
O3G B:ANP700 2.8 75.0 1.0
N3B B:ANP700 2.9 75.0 1.0
PG B:ANP700 3.1 75.0 1.0
O2G B:ANP700 3.1 75.0 1.0
OE2 B:GLU503 3.3 0.6 1.0
CD B:GLN422 3.3 0.2 1.0
O2B B:ANP700 3.5 75.0 1.0
OD1 B:ASP502 3.5 0.6 1.0
PB B:ANP700 3.9 75.0 1.0
NE2 B:GLN422 4.0 0.2 1.0
OD2 B:ASP502 4.0 0.6 1.0
CB B:SER381 4.0 87.9 1.0
CG B:ASP502 4.0 0.6 1.0
CD B:GLU503 4.1 0.6 1.0
CB B:GLN422 4.1 0.2 1.0
CG B:GLN422 4.3 0.2 1.0
N A:GLY480 4.4 71.1 1.0
O3A B:ANP700 4.5 75.0 1.0
CG B:GLU503 4.6 0.6 1.0
O1G B:ANP700 4.7 75.0 1.0
CA A:GLY480 4.8 71.1 1.0
CA B:SER381 4.9 67.8 1.0

Sodium binding site 4 out of 4 in 2onj

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Sodium binding site 4 out of 4 in the Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Multidrug Abc Transporter SAV1866 From S. Aureus in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na910

b:0.3
occ:1.00
O B:ARG527 2.5 0.1 1.0
O B:GLY367 2.8 95.7 1.0
O B:SER524 2.9 1.0 1.0
OG1 B:THR369 2.9 0.8 1.0
C B:GLY367 3.3 95.7 1.0
O B:GLU368 3.4 0.6 1.0
C B:GLU368 3.6 0.6 1.0
C B:ARG527 3.7 0.1 1.0
OG1 B:THR529 3.8 93.9 1.0
CA B:GLY367 3.9 95.7 1.0
O B:LYS525 3.9 0.0 1.0
N B:ARG527 3.9 0.1 1.0
C B:SER524 3.9 1.0 1.0
N B:GLU368 4.0 0.6 1.0
N B:THR369 4.0 98.5 1.0
CB B:THR369 4.1 0.8 1.0
CA B:THR369 4.2 98.5 1.0
CA B:GLU368 4.2 0.6 1.0
CB B:THR529 4.3 93.9 1.0
N B:THR529 4.3 0.3 1.0
C B:LYS525 4.4 0.0 1.0
CA B:ARG527 4.4 0.1 1.0
CA B:SER524 4.6 1.0 1.0
N B:THR528 4.7 0.9 1.0
CB B:SER524 4.7 0.9 1.0
OD2 B:ASP543 4.8 1.0 1.0
CA B:THR528 4.8 0.9 1.0
C B:ASP526 4.8 0.2 1.0
N B:GLY367 4.9 95.7 1.0
N B:ASP526 4.9 0.2 1.0
C B:THR528 4.9 0.9 1.0
N B:LYS525 4.9 0.0 1.0
CA B:THR529 4.9 0.3 1.0

Reference:

R.J.P.Dawson, K.P.Locher. Structure of the Multidrug Abc Transporter SAV1866 From Staphylococcus Aureus in Complex with Amp-Pnp. Febs Lett. V. 581 935 2007.
ISSN: ISSN 0014-5793
PubMed: 17303126
DOI: 10.1016/J.FEBSLET.2007.01.073
Page generated: Tue Dec 15 05:52:35 2020

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