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Sodium in PDB 2q6a: Crystal Structure of Nak Channel D66E Mutant

Protein crystallography data

The structure of Crystal Structure of Nak Channel D66E Mutant, PDB code: 2q6a was solved by A.Alam, N.Shi, Y.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.979, 85.630, 130.134, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 28

Other elements in 2q6a:

The structure of Crystal Structure of Nak Channel D66E Mutant also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Nak Channel D66E Mutant (pdb code 2q6a). 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 Nak Channel D66E Mutant, PDB code: 2q6a:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2q6a

Go back to Sodium Binding Sites List in 2q6a
Sodium binding site 1 out of 3 in the Crystal Structure of Nak Channel D66E Mutant


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 Nak Channel D66E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na116

b:55.8
occ:0.50
OG1 A:THR63 2.6 56.4 1.0
OG1 B:THR63 2.7 43.9 1.0
NA A:NA117 3.2 89.6 0.5
O B:THR63 3.3 52.4 1.0
O A:THR63 3.4 54.9 1.0
CB A:THR63 3.5 45.1 1.0
CB B:THR63 3.5 38.1 1.0
C A:THR63 4.0 48.2 1.0
C B:THR63 4.0 45.3 1.0
CA A:CA115 4.3 33.1 0.5
CA A:THR63 4.4 44.3 1.0
CA B:THR63 4.5 31.1 1.0
CG2 A:THR63 4.6 44.2 1.0
CG2 B:THR63 4.6 30.9 1.0
O A:THR62 4.8 54.0 1.0
O B:THR62 4.8 52.0 1.0
N A:VAL64 4.9 48.8 1.0
N B:VAL64 5.0 39.2 1.0

Sodium binding site 2 out of 3 in 2q6a

Go back to Sodium Binding Sites List in 2q6a
Sodium binding site 2 out of 3 in the Crystal Structure of Nak Channel D66E Mutant


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 Nak Channel D66E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na117

b:89.6
occ:0.50
NA A:NA116 3.2 55.8 0.5
O B:HOH115 3.8 86.2 1.0
OG1 A:THR63 3.9 56.4 1.0
OG1 B:THR63 4.0 43.9 1.0
O A:HOH122 4.3 86.9 1.0
CB A:THR63 4.9 45.1 1.0
CB B:THR63 4.9 38.1 1.0

Sodium binding site 3 out of 3 in 2q6a

Go back to Sodium Binding Sites List in 2q6a
Sodium binding site 3 out of 3 in the Crystal Structure of Nak Channel D66E Mutant


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 Nak Channel D66E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na119

b:54.8
occ:0.50
O A:GLU66 4.2 51.1 1.0
O B:GLU66 4.2 54.5 1.0
CA A:GLY67 4.4 56.4 1.0
C A:GLU66 4.4 42.1 1.0
CA B:GLY67 4.5 56.1 1.0
C B:GLU66 4.5 44.6 1.0
N A:GLY67 4.6 47.7 1.0
N B:GLY67 4.6 54.4 1.0
C A:GLY65 4.7 49.9 1.0
C B:GLY65 4.7 51.7 1.0
O B:VAL64 4.8 54.2 1.0
O A:VAL64 4.8 50.0 1.0
N B:GLU66 4.9 56.4 1.0
O A:GLY65 4.9 58.2 1.0
CA B:GLY65 4.9 45.4 1.0
N A:GLU66 4.9 53.5 1.0
CA A:GLY65 4.9 44.9 1.0

Reference:

A.Alam, N.Shi, Y.Jiang. Structural Insight Into CA2+ Specificity in Tetrameric Cation Channels. Proc.Natl.Acad.Sci.Usa V. 104 15334 2007.
ISSN: ISSN 0027-8424
PubMed: 17878296
DOI: 10.1073/PNAS.0707324104
Page generated: Tue Dec 15 05:54:23 2020

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