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Sodium in PDB 4z9n: Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound

Protein crystallography data

The structure of Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound, PDB code: 4z9n was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.66 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.990, 76.930, 131.470, 90.00, 94.07, 90.00
R / Rfree (%) 15.2 / 18.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound (pdb code 4z9n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound, PDB code: 4z9n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4z9n

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Sodium binding site 1 out of 6 in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:12.7
occ:1.00
 OD1 A:ASP95 2.3 19.9 1.0
O A:ASP89 2.3 19.2 1.0
OD1 A:ASP89 2.4 17.9 1.0
OE1 A:GLN212 2.5 31.4 1.0
O A:LEU94 2.6 17.4 1.0
OD1 D:ASP219 2.9 37.6 1.0
OD2 D:ASP219 3.2 31.9 1.0
O A:HOH518 3.2 36.2 1.0
C A:ASP89 3.4 18.0 1.0
CG D:ASP219 3.4 30.2 1.0
CD A:GLN212 3.5 31.8 1.0
CG A:ASP95 3.5 18.7 1.0
CG A:ASP89 3.5 15.8 1.0
C A:LEU94 3.7 16.2 1.0
CG A:GLN212 3.8 25.0 1.0
CA A:ASP89 3.9 15.4 1.0
CA A:ASP95 4.0 15.3 1.0
O A:HOH638 4.1 16.4 1.0
CB A:ASP89 4.2 13.7 1.0
N A:ASP95 4.3 17.4 1.0
O A:HOH519 4.3 19.9 1.0
NH1 D:ARG222 4.3 27.1 1.0
OD2 A:ASP95 4.3 20.8 1.0
CB A:ASP95 4.3 17.0 1.0
OD2 A:ASP89 4.4 15.6 1.0
N A:THR90 4.5 16.3 1.0
NE2 A:GLN212 4.7 33.6 1.0
CB D:ALA215 4.8 26.9 1.0
N A:LEU94 4.9 23.0 1.0
CA A:LEU94 4.9 18.7 1.0
CA A:THR90 4.9 18.8 1.0
CB D:ASP219 5.0 19.6 1.0
O D:ALA215 5.0 21.5 1.0

Sodium binding site 2 out of 6 in 4z9n

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Sodium binding site 2 out of 6 in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:13.3
occ:1.00
 O D:ASP89 2.3 13.2 1.0
OD1 D:ASP95 2.3 20.6 1.0
OD1 D:ASP89 2.4 14.4 1.0
OE1 D:GLN212 2.5 24.4 1.0
O D:LEU94 2.6 18.8 1.0
OD1 A:ASP219 2.9 27.2 1.0
OD2 A:ASP219 3.1 22.2 1.0
C D:ASP89 3.3 12.1 1.0
CG A:ASP219 3.4 20.7 1.0
CG D:ASP89 3.4 13.7 1.0
CD D:GLN212 3.5 27.5 1.0
CG D:ASP95 3.5 20.5 1.0
C D:LEU94 3.7 17.5 1.0
CA D:ASP89 3.8 15.6 1.0
CG D:GLN212 3.9 27.4 1.0
CA D:ASP95 4.0 13.4 1.0
O D:HOH605 4.0 30.0 1.0
O D:HOH577 4.0 15.8 1.0
CB D:ASP89 4.1 12.4 1.0
N D:ASP95 4.3 13.8 1.0
NH1 A:ARG222 4.3 29.0 1.0
CB D:ASP95 4.3 16.1 1.0
OD2 D:ASP89 4.3 12.3 1.0
OD2 D:ASP95 4.4 25.1 1.0
O D:HOH566 4.4 20.1 1.0
N D:THR90 4.5 13.5 1.0
O D:HOH651 4.6 33.8 1.0
NE2 D:GLN212 4.7 25.3 1.0
CB A:ALA215 4.8 29.0 1.0
N D:LEU94 4.9 15.6 1.0
CA D:LEU94 4.9 17.5 1.0
CB A:ASP219 4.9 13.2 1.0
CA D:THR90 4.9 14.8 1.0
O A:ALA215 4.9 21.5 1.0

Sodium binding site 3 out of 6 in 4z9n

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Sodium binding site 3 out of 6 in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:13.3
occ:1.00
 O B:ASP89 2.3 13.2 1.0
OD1 B:ASP95 2.4 17.8 1.0
OE1 B:GLN212 2.4 19.9 1.0
OD1 B:ASP89 2.5 11.6 1.0
O B:LEU94 2.5 17.3 1.0
OD1 E:ASP219 2.7 17.7 1.0
OD2 E:ASP219 3.3 20.5 1.0
C B:ASP89 3.3 10.7 1.0
CG E:ASP219 3.4 20.2 1.0
CG B:ASP89 3.4 13.4 1.0
CD B:GLN212 3.5 20.5 1.0
CG B:ASP95 3.5 18.9 1.0
C B:LEU94 3.6 15.5 1.0
CA B:ASP89 3.8 10.4 1.0
CG B:GLN212 3.9 17.5 1.0
O B:HOH596 3.9 19.6 1.0
CA B:ASP95 4.0 10.8 1.0
O B:HOH625 4.0 15.1 1.0
CB B:ASP89 4.1 9.9 1.0
N B:ASP95 4.2 10.2 1.0
NH2 E:ARG222 4.2 20.3 1.0
OD2 B:ASP89 4.3 10.8 1.0
OD2 B:ASP95 4.3 17.2 1.0
CB B:ASP95 4.3 15.7 1.0
N B:THR90 4.5 12.1 1.0
O B:HOH515 4.5 24.9 1.0
NE2 B:GLN212 4.7 18.1 1.0
O E:ALA215 4.8 18.2 1.0
CB E:ALA215 4.8 21.9 1.0
N B:LEU94 4.8 13.8 1.0
CA B:LEU94 4.8 11.6 1.0
CB E:ASP219 4.9 13.3 1.0
CA B:THR90 4.9 16.9 1.0

Sodium binding site 4 out of 6 in 4z9n

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Sodium binding site 4 out of 6 in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:13.1
occ:1.00
 O E:ASP89 2.3 18.9 1.0
OD1 E:ASP95 2.3 18.6 1.0
OE1 E:GLN212 2.4 23.8 1.0
OD1 E:ASP89 2.4 15.5 1.0
O E:LEU94 2.5 18.0 1.0
OD1 B:ASP219 2.8 26.5 1.0
OD2 B:ASP219 3.1 23.8 1.0
CG B:ASP219 3.3 21.0 1.0
C E:ASP89 3.3 14.9 1.0
CD E:GLN212 3.4 25.3 1.0
CG E:ASP89 3.4 13.6 1.0
CG E:ASP95 3.5 20.3 1.0
C E:LEU94 3.7 13.6 1.0
O E:HOH623 3.7 25.9 1.0
CG E:GLN212 3.7 23.9 1.0
CA E:ASP89 3.8 13.4 1.0
CA E:ASP95 4.0 14.9 1.0
O E:HOH647 4.1 14.2 1.0
CB E:ASP89 4.2 12.7 1.0
NH1 B:ARG222 4.2 22.0 1.0
N E:ASP95 4.2 15.9 1.0
OD2 E:ASP95 4.3 20.3 1.0
OD2 E:ASP89 4.3 12.4 1.0
CB E:ASP95 4.3 14.8 1.0
O E:HOH521 4.5 21.5 1.0
N E:THR90 4.5 15.9 1.0
NE2 E:GLN212 4.6 24.2 1.0
CB B:ASP219 4.8 13.0 1.0
O B:ALA215 4.9 21.3 1.0
N E:LEU94 4.9 15.9 1.0
CA E:LEU94 4.9 14.5 1.0
CA E:THR90 4.9 19.1 1.0
CB B:ALA215 4.9 26.2 1.0

Sodium binding site 5 out of 6 in 4z9n

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Sodium binding site 5 out of 6 in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:15.3
occ:1.00
 O C:ASP89 2.3 18.9 1.0
OD1 C:ASP95 2.4 19.7 1.0
OD1 C:ASP89 2.4 16.2 1.0
OE1 C:GLN212 2.5 34.8 1.0
O C:LEU94 2.6 20.1 1.0
OD2 F:ASP219 2.9 32.4 1.0
OD1 F:ASP219 3.2 30.6 1.0
C C:ASP89 3.3 18.6 1.0
CG F:ASP219 3.4 29.2 1.0
CG C:ASP89 3.4 16.6 1.0
CD C:GLN212 3.5 32.0 1.0
CG C:ASP95 3.5 22.9 1.0
C C:LEU94 3.7 21.7 1.0
CG C:GLN212 3.8 28.2 1.0
CA C:ASP89 3.9 14.8 1.0
CA C:ASP95 4.0 15.8 1.0
O C:HOH617 4.0 18.6 1.0
O F:HOH676 4.1 35.2 1.0
CB C:ASP89 4.2 14.2 1.0
NH1 F:ARG222 4.2 29.9 1.0
N C:ASP95 4.3 16.3 1.0
OD2 C:ASP89 4.3 14.8 1.0
CB C:ASP95 4.4 21.6 1.0
O C:HOH545 4.4 21.7 1.0
OD2 C:ASP95 4.4 23.2 1.0
N C:THR90 4.5 16.3 1.0
NE2 C:GLN212 4.7 27.9 1.0
CB F:ALA215 4.8 33.0 1.0
O C:HOH584 4.8 43.9 1.0
O F:ALA215 4.9 22.1 1.0
CA C:THR90 4.9 17.6 1.0
CA C:LEU94 4.9 20.9 1.0
N C:LEU94 4.9 19.6 1.0
CB F:ASP219 4.9 20.3 1.0

Sodium binding site 6 out of 6 in 4z9n

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Sodium binding site 6 out of 6 in the Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Abc Transporter / Periplasmic Binding Protein From Brucella Ovis with Glutathione Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:16.1
occ:1.00
 OD1 F:ASP95 2.3 25.8 1.0
O F:ASP89 2.4 21.1 1.0
OD1 F:ASP89 2.4 16.9 1.0
OE1 F:GLN212 2.5 27.8 1.0
O F:LEU94 2.7 19.7 1.0
OD1 C:ASP219 2.9 32.7 1.0
O F:HOH615 3.2 35.9 1.0
OD2 C:ASP219 3.2 34.9 1.0
C F:ASP89 3.4 21.3 1.0
CG F:ASP89 3.4 18.5 1.0
CG F:ASP95 3.5 25.3 1.0
CD F:GLN212 3.5 31.3 1.0
CG C:ASP219 3.5 31.5 1.0
C F:LEU94 3.8 20.9 1.0
CG F:GLN212 3.8 29.9 1.0
CA F:ASP89 3.9 17.2 1.0
CA F:ASP95 4.0 19.7 1.0
O F:HOH641 4.1 18.2 1.0
CB F:ASP89 4.2 17.3 1.0
OD2 F:ASP95 4.3 27.5 1.0
N F:ASP95 4.3 18.3 1.0
OD2 F:ASP89 4.3 16.7 1.0
NH2 C:ARG222 4.3 29.7 1.0
CB F:ASP95 4.3 18.2 1.0
O C:HOH503 4.4 44.3 1.0
O F:HOH581 4.4 21.0 1.0
N F:THR90 4.6 22.2 1.0
CB C:ALA215 4.6 31.0 1.0
NE2 F:GLN212 4.7 30.0 1.0
O C:ALA215 4.9 27.4 1.0
CA F:THR90 4.9 22.7 1.0
CA F:LEU94 5.0 19.5 1.0
N F:LEU94 5.0 20.6 1.0
CB C:ASP219 5.0 25.4 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), Seattle Structural Genomics Center For Infectious Disease (Ssgcid). N/A N/A.
Page generated: Sun Aug 17 22:43:19 2025

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