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Sodium in PDB 3e83: Crystal Structure of the the Open Nak Channel Pore

Protein crystallography data

The structure of Crystal Structure of the the Open Nak Channel Pore, PDB code: 3e83 was solved by Y.Jiang, A.Alam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.81 / 1.80
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 68.056, 68.056, 89.326, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.6

Other elements in 3e83:

The structure of Crystal Structure of the the Open Nak Channel Pore also contains other interesting chemical elements:

Caesium (Cs) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the the Open Nak Channel Pore (pdb code 3e83). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the the Open Nak Channel Pore, PDB code: 3e83:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3e83

Go back to Sodium Binding Sites List in 3e83
Sodium binding site 1 out of 3 in the Crystal Structure of the the Open Nak Channel Pore


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 the Open Nak Channel Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3

b:44.7
occ:0.25
CS A:CS1 2.3 19.3 0.7
O A:VAL64 2.9 20.2 1.0
C A:VAL64 4.0 18.8 1.0
O A:HOH119 4.1 26.2 1.0
CA A:GLY65 4.2 17.3 1.0
O A:THR63 4.4 18.1 1.0
N A:GLY65 4.5 14.3 1.0
C A:GLY65 4.8 21.4 1.0

Sodium binding site 2 out of 3 in 3e83

Go back to Sodium Binding Sites List in 3e83
Sodium binding site 2 out of 3 in the Crystal Structure of the the Open Nak Channel Pore


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 the Open Nak Channel Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:20.3
occ:0.25
OG1 A:THR63 2.4 16.0 1.0
O A:HOH118 2.7 54.0 0.2
CB A:THR63 3.3 19.8 1.0
O A:THR63 4.2 18.1 1.0
CG2 A:THR63 4.2 18.1 1.0
C A:THR63 4.5 19.7 1.0
CA A:THR63 4.6 17.2 1.0
O A:THR62 4.8 15.9 1.0
CS A:CS1 5.0 19.3 0.7

Sodium binding site 3 out of 3 in 3e83

Go back to Sodium Binding Sites List in 3e83
Sodium binding site 3 out of 3 in the Crystal Structure of the the Open Nak Channel Pore


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 the Open Nak Channel Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4

b:34.7
occ:0.25
OG1 B:THR63 2.4 27.3 1.0
O B:HOH155 2.8 37.4 0.2
CB B:THR63 3.4 25.7 1.0
O B:THR63 4.0 25.6 1.0
CG2 B:THR63 4.3 19.8 1.0
C B:THR63 4.5 27.9 1.0
CA B:THR63 4.6 26.8 1.0
O B:THR62 4.7 22.8 1.0
CS B:CS2 4.8 34.2 0.6

Reference:

A.Alam, Y.Jiang. Structural Analysis of Ion Selectivity in the Nak Channel Nat.Struct.Mol.Biol. V. 16 35 2009.
ISSN: ISSN 1545-9993
PubMed: 19098915
DOI: 10.1038/NSMB.1537
Page generated: Tue Dec 15 06:09:33 2020

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