Sodium in PDB 3k04: Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex

The structure of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex, PDB code: 3k04 was solved by Y.Jiang, M.G.Derebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.58
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	67.840, 67.840, 89.380, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 23.5

The binding sites of Sodium atom in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex (pdb code 3k04). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex, PDB code: 3k04:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ 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 Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2 b:16.3 occ:0.25 NA A:NA5 2.2 41.8 0.2 O A:THR63 2.3 17.6 1.0 C A:THR63 3.5 17.1 1.0 O A:VAL64 3.7 20.8 1.0 NA A:NA4 4.0 19.1 0.2 C A:VAL64 4.0 19.7 1.0 CA A:VAL64 4.2 17.5 1.0 N A:VAL64 4.3 16.6 1.0 OG1 A:THR63 4.4 17.2 1.0 CB A:THR63 4.4 17.2 1.0 CA A:THR63 4.5 17.1 1.0 N A:GLY65 4.8 18.1 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ 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 Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:19.1 occ:0.25 OG1 A:THR63 2.4 17.2 1.0 O A:HOH1 2.7 38.8 0.2 CB A:THR63 3.4 17.2 1.0 NA A:NA2 4.0 16.3 0.2 O A:THR63 4.1 17.6 1.0 CG2 A:THR63 4.2 19.6 1.0 C A:THR63 4.5 17.1 1.0 CA A:THR63 4.6 17.1 1.0 O A:THR62 4.7 18.9 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ 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 Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5 b:41.8 occ:0.25 NA A:NA2 2.2 16.3 0.2 O A:VAL64 2.8 20.8 1.0 NA A:NA7 3.5 81.6 0.2 O A:THR63 3.5 17.6 1.0 C A:VAL64 3.7 19.7 1.0 O A:GLY65 3.9 22.5 1.0 C A:GLY65 4.3 23.7 1.0 N A:GLY65 4.4 18.1 1.0 CA A:GLY65 4.4 19.9 1.0 CA A:VAL64 4.5 17.5 1.0 C A:THR63 4.6 17.1 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ 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 Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6 b:81.6 occ:0.25 O A:HOH114 2.3 35.0 1.0 NA A:NA7 2.4 81.6 0.2 O A:GLY65 4.1 22.5 1.0 O A:ASP66 4.7 27.4 1.0 O A:HOH123 4.7 45.8 1.0 CA A:ASP66 4.8 24.9 1.0 C A:ASP66 4.8 25.5 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7 b:81.6 occ:0.25 NA A:NA6 2.4 81.6 0.2 O A:GLY65 2.8 22.5 1.0 O A:HOH114 3.3 35.0 1.0 NA A:NA5 3.5 41.8 0.2 C A:GLY65 3.9 23.7 1.0 CA A:ASP66 4.3 24.9 1.0 O A:VAL64 4.4 20.8 1.0 N A:ASP66 4.5 22.1 1.0 CA A:GLY65 4.9 19.9 1.0 C A:ASP66 5.0 25.5 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8 b:81.6 occ:0.25 O A:HOH135 3.0 57.3 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:26.1 occ:0.25 O B:THR63 2.3 28.7 1.0 C B:THR63 3.5 27.9 1.0 O B:VAL64 3.8 33.1 1.0 NA B:NA3 4.0 24.4 0.2 C B:VAL64 4.1 31.8 1.0 CA B:VAL64 4.2 29.4 1.0 OG1 B:THR63 4.3 24.6 1.0 N B:VAL64 4.4 26.2 1.0 CB B:THR63 4.4 25.9 1.0 CA B:THR63 4.6 25.0 1.0 N B:GLY65 4.9 34.3 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Cng Mimicking Nak Mutant, Nak-Dtpp, Na+ Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:24.4 occ:0.25 OG1 B:THR63 2.5 24.6 1.0 O B:HOH117 2.7 36.2 0.2 CB B:THR63 3.4 25.9 1.0 NA B:NA1 4.0 26.1 0.2 O B:THR63 4.1 28.7 1.0 CG2 B:THR63 4.2 23.5 1.0 C B:THR63 4.6 27.9 1.0 CA B:THR63 4.6 25.0 1.0 O B:THR62 4.7 24.3 1.0

M.G.Derebe, W.Zeng, Y.Li, A.Alam, Y.Jiang. Structural Studies of Ion Permeation and CA2+ Blockage of A Bacterial Channel Mimicking the Cyclic Nucleotide-Gated Channel Pore. Proc.Natl.Acad.Sci.Usa V. 108 592 2011.
ISSN: ISSN 0027-8424
PubMed: 21187429
DOI: 10.1073/PNAS.1013643108