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Sodium in PDB 3e86: High Resolution Crystal Structure of the Open Nak Channel Pore

Protein crystallography data

The structure of High Resolution Crystal Structure of the Open Nak Channel Pore, PDB code: 3e86 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) 34.01 / 1.60
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 68.030, 68.030, 89.264, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.2

Other elements in 3e86:

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

Caesium (Cs) 2 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the High Resolution Crystal Structure of the Open Nak Channel Pore (pdb code 3e86). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the High Resolution Crystal Structure of the Open Nak Channel Pore, PDB code: 3e86:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3e86

Go back to Sodium Binding Sites List in 3e86
Sodium binding site 1 out of 4 in the High Resolution Crystal Structure of 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 High Resolution Crystal Structure of the Open Nak Channel Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:54.5
occ:0.25
CS A:CS1 2.4 19.5 0.7
O A:VAL64 2.9 20.0 1.0
C A:VAL64 4.0 18.4 1.0
O A:HOH510 4.0 29.6 1.0
CA A:GLY65 4.3 19.1 1.0
O A:THR63 4.5 17.5 1.0
N A:GLY65 4.6 16.4 1.0
C A:GLY65 4.8 21.8 1.0

Sodium binding site 2 out of 4 in 3e86

Go back to Sodium Binding Sites List in 3e86
Sodium binding site 2 out of 4 in the High Resolution Crystal Structure of 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 High Resolution Crystal Structure of the Open Nak Channel Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:20.9
occ:0.25
OG1 A:THR63 2.3 18.6 1.0
O A:HOH545 2.7 47.4 0.2
CB A:THR63 3.3 18.3 1.0
O A:HOH506 4.1 56.3 1.0
O A:THR63 4.1 17.5 1.0
CG2 A:THR63 4.2 18.1 1.0
C A:THR63 4.5 17.1 1.0
CA A:THR63 4.5 16.2 1.0
O A:HOH548 4.7 48.6 0.2
O A:THR62 4.8 18.5 1.0
CS A:CS1 4.9 19.5 0.7

Sodium binding site 3 out of 4 in 3e86

Go back to Sodium Binding Sites List in 3e86
Sodium binding site 3 out of 4 in the High Resolution Crystal Structure of 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 High Resolution Crystal Structure of the Open Nak Channel Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6

b:35.6
occ:0.25
OG1 B:THR63 2.4 29.9 1.0
O B:HOH566 2.7 50.6 0.2
CB B:THR63 3.4 28.9 1.0
O B:THR63 4.0 29.1 1.0
CG2 B:THR63 4.3 26.8 1.0
C B:THR63 4.5 29.3 1.0
CA B:THR63 4.6 28.0 1.0
O B:THR62 4.7 23.7 1.0
CS B:CS2 4.9 31.9 0.6

Sodium binding site 4 out of 4 in 3e86

Go back to Sodium Binding Sites List in 3e86
Sodium binding site 4 out of 4 in the High Resolution Crystal Structure of 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 4 of High Resolution Crystal Structure of the Open Nak Channel Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na7

b:46.0
occ:0.25
CS B:CS2 2.6 31.9 0.6
O B:VAL64 3.0 34.7 1.0
C B:VAL64 4.0 33.0 1.0
CA B:GLY65 4.2 37.1 1.0
N B:GLY65 4.5 34.6 1.0
O B:THR63 4.7 29.1 1.0
C B:GLY65 4.8 36.5 1.0

Reference:

A.Alam, Y.Jiang. High-Resolution Structure of the Open Nak Channel Nat.Struct.Mol.Biol. V. 16 30 2009.
ISSN: ISSN 1545-9993
PubMed: 19098917
DOI: 10.1038/NSMB.1531
Page generated: Tue Dec 15 06:09:35 2020

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