Sodium in PDB 7x5q: Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)

The structure of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak), PDB code: 7x5q was solved by S.Sanram, A.Aunkham, W.Suginta, R.C.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.085, 182.602, 196.808, 90, 90, 90
R / Rfree (%)	21.1 / 25.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) (pdb code 7x5q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak), PDB code: 7x5q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:26.0 occ:1.00 OE1 A:GLN146 2.2 27.9 1.0 OE1 A:GLN149 2.3 31.9 1.0 OD1 A:ASP174 2.5 30.4 1.0 OD2 A:ASP174 3.3 34.5 1.0 CG A:ASP174 3.3 35.2 1.0 CD A:GLN149 3.3 29.9 1.0 CD A:GLN146 3.4 31.0 1.0 OD1 A:ASP147 3.7 43.9 1.0 NE2 A:GLN149 3.8 38.2 1.0 O A:ARG148 3.9 28.9 1.0 CB A:GLN146 4.1 36.2 1.0 CG A:GLN146 4.3 30.6 1.0 NE2 A:GLN146 4.3 32.2 1.0 CA A:GLN146 4.4 27.9 1.0 N A:ASP147 4.4 28.1 1.0 O A:HOH519 4.5 26.1 1.0 CG A:GLN149 4.6 29.4 1.0 CG A:ASP147 4.7 38.8 1.0 CB A:ASP174 4.8 29.7 1.0 CB A:GLN149 4.9 28.9 1.0 C A:ARG148 4.9 29.8 1.0 CA A:GLN149 4.9 30.0 1.0 C A:GLN146 5.0 30.0 1.0

Sodium binding site 2 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:34.3 occ:1.00 OD2 A:ASP156 2.3 54.5 1.0 OD1 A:ASP167 2.5 45.6 1.0 CG A:ASP167 3.3 42.0 1.0 OD2 A:ASP167 3.4 42.1 1.0 CG A:ASP156 3.6 48.0 1.0 OG A:SER165 4.0 48.1 1.0 OD1 A:ASP156 4.4 34.8 1.0 CB A:ASP156 4.5 40.5 1.0 O A:HOH527 4.7 39.7 1.0 NE2 A:HIS191 4.7 42.0 1.0 CD2 A:HIS191 4.8 43.3 1.0 CB A:ASP167 4.8 32.6 1.0

Sodium binding site 3 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:34.7 occ:1.00 O A:PRO82 2.2 34.0 1.0 O A:HOH503 2.5 33.7 1.0 O A:GLY85 2.7 37.8 1.0 OD1 A:ASP81 2.8 34.9 1.0 C A:PRO82 3.1 29.9 1.0 O A:ASP81 3.6 24.6 1.0 CA A:SER83 3.7 32.5 1.0 C A:GLY85 3.8 34.0 1.0 N A:SER83 3.8 28.8 1.0 N A:GLY85 3.9 32.8 1.0 C A:ASP81 3.9 30.3 1.0 CG A:ASP81 3.9 39.3 1.0 N A:PRO82 4.1 28.3 1.0 C A:SER83 4.1 33.7 1.0 N A:PHE84 4.1 30.6 1.0 CA A:PRO82 4.2 29.4 1.0 O A:LEU50 4.3 37.0 1.0 CA A:GLY85 4.4 31.7 1.0 CA A:ASP81 4.6 31.0 1.0 CB A:ASP81 4.7 31.7 1.0 OD2 A:ASP81 4.8 36.2 1.0 OE1 A:GLN49 4.8 38.1 1.0 O A:GLY86 4.8 37.7 1.0 CD A:PRO82 4.8 26.7 1.0 O A:SER83 4.9 31.2 1.0 N A:GLY86 4.9 35.2 1.0 C A:PHE84 4.9 32.2 1.0 C A:GLY86 4.9 32.7 1.0

Sodium binding site 4 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:27.8 occ:1.00 OE1 B:GLN146 2.2 28.6 1.0 OE1 B:GLN149 2.4 36.3 1.0 OD1 B:ASP174 2.5 33.8 1.0 OD2 B:ASP174 2.6 43.4 1.0 CG B:ASP174 2.9 37.1 1.0 CD B:GLN149 3.3 34.0 1.0 CD B:GLN146 3.4 28.6 1.0 NE2 B:GLN149 3.9 32.9 1.0 CG B:GLN149 4.1 30.8 1.0 OD1 B:ASP147 4.2 51.5 1.0 NE2 B:GLN146 4.3 32.4 1.0 O B:ASP147 4.4 56.1 1.0 CB B:ASP174 4.4 24.8 1.0 CG B:GLN146 4.5 30.4 1.0 O B:ARG148 4.5 30.1 1.0 O B:HOH530 4.6 28.5 1.0 CB B:GLN146 4.6 28.9 1.0 N B:ASP147 4.9 36.3 1.0 CA B:GLN146 5.0 34.1 1.0

Sodium binding site 5 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:40.1 occ:1.00 OD1 B:ASP167 2.2 48.3 1.0 OD2 B:ASP156 2.5 44.4 1.0 CG B:ASP167 3.0 40.8 1.0 OD2 B:ASP167 3.1 40.2 1.0 CG B:ASP156 3.6 38.5 1.0 CB B:ASP156 4.0 35.7 1.0 O B:HOH539 4.3 46.2 1.0 O B:ILE166 4.3 38.0 1.0 CB B:ASP167 4.5 30.5 1.0 O B:SER157 4.5 47.2 1.0 NH2 B:ARG154 4.5 33.7 1.0 NE2 B:HIS191 4.5 41.9 1.0 CB B:SER165 4.6 43.2 1.0 OD1 B:ASP156 4.6 39.8 1.0 CA B:ASP156 4.6 39.0 1.0 OG B:SER165 4.8 54.2 1.0 CD2 B:HIS191 4.8 43.8 1.0 C B:ILE166 4.8 36.1 1.0 O B:HOH542 4.9 30.3 1.0

Sodium binding site 6 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:50.2 occ:1.00 O B:GLY85 2.4 44.2 1.0 O B:PRO82 2.6 40.2 1.0 OD1 B:ASP81 3.0 43.8 1.0 C B:GLY85 3.5 41.6 1.0 C B:PRO82 3.7 39.2 1.0 O F:GLY177 3.8 47.8 1.0 N B:GLY85 3.9 43.2 1.0 CG B:ASP81 3.9 46.3 1.0 OD1 F:ASN151 4.2 40.8 1.0 ND2 F:ASN151 4.2 35.8 1.0 CA B:SER83 4.3 38.1 1.0 CA B:GLY85 4.3 39.7 1.0 O B:ASP81 4.3 37.0 1.0 N B:PHE84 4.4 33.3 1.0 OD2 B:ASP81 4.4 51.2 1.0 N B:SER83 4.4 35.0 1.0 OE1 B:GLN49 4.4 41.8 1.0 C B:ASP81 4.5 39.5 1.0 O B:LEU50 4.5 43.9 1.0 C B:SER83 4.5 37.8 1.0 N B:GLY86 4.6 36.2 1.0 CG F:ASN151 4.6 35.9 1.0 CB F:SER150 4.6 36.1 1.0 N B:PRO82 4.7 39.1 1.0 CA B:GLY86 4.8 41.8 1.0 OG F:SER150 4.8 38.1 1.0 C F:GLY177 4.8 41.3 1.0 C B:GLY86 4.8 39.4 1.0 CA B:PRO82 4.8 37.5 1.0 O B:GLY86 4.9 39.9 1.0 C B:PHE84 5.0 42.3 1.0

Sodium binding site 7 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:43.7 occ:1.00 O F:GLY181 2.3 41.5 1.0 O B:GLY46 2.5 40.5 1.0 O B:ASN44 2.7 43.6 1.0 O B:ASP43 2.9 48.4 1.0 C F:GLY181 3.4 40.7 1.0 C B:ASN44 3.5 48.2 1.0 CA F:ASP182 3.7 48.1 1.0 C B:GLY46 3.7 35.6 1.0 CB F:ALA176 3.9 33.8 1.0 CA B:ASN44 4.0 45.1 1.0 N F:ASP182 4.0 43.7 1.0 C B:ASP43 4.0 47.5 1.0 CB F:ASP182 4.1 50.8 1.0 CA F:ALA176 4.2 36.7 1.0 CA B:GLY47 4.4 32.1 1.0 N B:ASN44 4.5 49.7 1.0 N B:GLY46 4.5 39.4 1.0 N B:GLY47 4.5 35.4 1.0 O F:ALA176 4.6 38.8 1.0 N B:LEU45 4.6 43.8 1.0 C B:LEU45 4.6 41.5 1.0 CA F:GLY181 4.7 40.9 1.0 N F:GLY181 4.7 41.6 1.0 CA B:GLY46 4.7 37.7 1.0 O B:HOH504 4.9 39.2 1.0 C F:ASP182 4.9 40.7 1.0 C F:ALA176 4.9 41.9 1.0 O B:LEU45 4.9 39.6 1.0

Sodium binding site 8 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:27.6 occ:1.00 O C:HOH533 2.2 39.1 1.0 O C:HOH515 2.2 35.1 1.0 O C:HOH521 2.2 33.9 1.0 OD1 C:ASP167 2.3 40.9 1.0 O C:HOH509 2.3 35.9 1.0 OD2 C:ASP156 2.5 34.0 1.0 CG C:ASP167 3.1 42.5 1.0 OD2 C:ASP167 3.4 40.1 1.0 CG C:ASP156 3.6 36.9 1.0 CB C:ASP156 4.1 38.9 1.0 NH2 C:ARG154 4.2 38.0 1.0 O C:HOH540 4.4 38.9 1.0 CB C:ASP167 4.5 36.0 1.0 O C:ILE166 4.5 40.8 1.0 CB C:SER165 4.6 42.6 1.0 OD1 C:ASP156 4.6 40.8 1.0 CA C:ASP156 4.7 39.0 1.0 NE2 C:HIS191 4.7 41.0 1.0 O C:SER157 4.8 39.5 1.0 CD2 C:HIS191 4.8 43.0 1.0 C C:ILE166 4.8 43.7 1.0 OG C:SER165 4.9 49.0 1.0 CA C:ASP167 5.0 37.7 1.0

Sodium binding site 9 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:28.1 occ:1.00 OD1 D:ASP174 2.3 30.0 1.0 OE1 D:GLN149 2.3 32.5 1.0 OE1 D:GLN146 2.4 29.6 1.0 OD2 D:ASP174 2.6 35.9 1.0 CG D:ASP174 2.8 27.0 1.0 CD D:GLN149 3.2 27.3 1.0 NE2 D:GLN149 3.5 33.2 1.0 CD D:GLN146 3.7 27.6 1.0 OD1 D:ASP147 3.9 40.7 1.0 O D:ARG148 4.1 36.0 1.0 CB D:ASP174 4.3 26.8 1.0 CG D:GLN146 4.5 24.7 1.0 CB D:GLN146 4.6 29.9 1.0 NE2 D:GLN146 4.6 35.5 1.0 CG D:GLN149 4.6 29.2 1.0 CA D:GLN146 4.9 34.9 1.0 N D:ASP147 4.9 32.7 1.0 CA D:ASP174 5.0 30.1 1.0

Sodium binding site 10 out of 16 in the Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Apo Truncated Vhchip (Delta 1-19) in Complex with Peptide (Dgansdaak) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:43.5 occ:1.00 OD1 D:ASP167 2.3 45.0 1.0 OD1 D:ASP156 2.3 42.3 1.0 CG D:ASP167 3.3 40.9 1.0 CG D:ASP156 3.5 35.9 1.0 OD2 D:ASP167 3.7 44.2 1.0 OG D:SER165 3.7 57.5 1.0 NH2 D:ARG154 4.1 32.8 1.0 CB D:ASP156 4.2 32.2 1.0 NE2 D:HIS191 4.2 49.4 1.0 O D:ILE166 4.3 40.2 1.0 OD2 D:ASP156 4.5 35.7 1.0 CB D:ASP167 4.6 31.8 1.0 CD2 D:HIS191 4.6 53.0 1.0 O D:SER157 4.8 39.9 1.0 CA D:ASP156 4.8 34.2 1.0 C D:ILE166 4.9 39.3 1.0

A.Aunkham, S.Sanram, W.Suginta, R.C.Robinson. Structure and Function of Truncated Vhchip To Be Published.