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Sodium in PDB 3e8g: Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex

Protein crystallography data

The structure of Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex, PDB code: 3e8g 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) 33.99 / 2.00
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 67.990, 67.990, 89.168, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.5

Other elements in 3e8g:

The structure of Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex also contains other interesting chemical elements:

Caesium (Cs) 2 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex (pdb code 3e8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex, PDB code: 3e8g:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3e8g

Go back to Sodium Binding Sites List in 3e8g
Sodium binding site 1 out of 4 in the Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex


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-Na+/CA2+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:36.5
occ:0.25
OG1 A:THR63 2.4 28.7 1.0
O A:HOH504 2.8 49.4 0.2
CB A:THR63 3.4 34.0 1.0
O A:THR63 3.9 31.0 1.0
CG2 A:THR63 4.3 30.8 1.0
C A:THR63 4.4 35.2 1.0
CA A:THR63 4.6 33.9 1.0
CS A:CS1 4.7 26.9 0.6
O A:THR62 4.8 30.2 1.0

Sodium binding site 2 out of 4 in 3e8g

Go back to Sodium Binding Sites List in 3e8g
Sodium binding site 2 out of 4 in the Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex


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-Na+/CA2+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na8

b:56.4
occ:0.25
CS A:CS1 2.9 26.9 0.6
O A:VAL64 3.2 26.6 1.0
O A:HOH532 3.6 51.7 1.0
CA A:GLY65 4.2 28.3 1.0
C A:VAL64 4.2 29.0 1.0
C A:GLY65 4.6 31.2 1.0
N A:GLY65 4.6 24.1 1.0
O A:GLY65 4.9 33.5 1.0

Sodium binding site 3 out of 4 in 3e8g

Go back to Sodium Binding Sites List in 3e8g
Sodium binding site 3 out of 4 in the Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex


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-Na+/CA2+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6

b:45.6
occ:0.25
OG1 B:THR63 2.5 38.6 1.0
O B:HOH503 3.0 48.6 0.2
CB B:THR63 3.5 41.8 1.0
O B:THR63 3.9 38.4 1.0
CG2 B:THR63 4.4 34.1 1.0
C B:THR63 4.4 41.9 1.0
CA B:THR63 4.6 41.0 1.0
O B:THR62 4.7 37.1 1.0
CS B:CS2 4.9 40.9 0.6

Sodium binding site 4 out of 4 in 3e8g

Go back to Sodium Binding Sites List in 3e8g
Sodium binding site 4 out of 4 in the Crystal Structure of the the Open Nak Channel-Na+/CA2+ Complex


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 the Open Nak Channel-Na+/CA2+ Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na7

b:61.1
occ:0.25
CS B:CS2 3.0 40.9 0.6
O B:VAL64 3.2 39.9 1.0
CA B:GLY65 4.2 46.3 1.0
C B:VAL64 4.3 39.3 1.0
C B:GLY65 4.6 48.1 1.0
N B:GLY65 4.7 42.5 1.0

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 06:09:36 2020

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