Sodium in PDB 7x5p: Truncated Vhchip (1-19AA) in Complex with Doxycycline

The structure of Truncated Vhchip (1-19AA) in Complex with Doxycycline, PDB code: 7x5p was solved by S.Sanram, C.R.Robinson, A.Aunkham, W.Suginta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.02 / 3.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	92.393, 92.5, 96.522, 101.11, 101.14, 109.72
R / Rfree (%)	18.2 / 25.8

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Truncated Vhchip (1-19AA) in Complex with Doxycycline (pdb code 7x5p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Truncated Vhchip (1-19AA) in Complex with Doxycycline, PDB code: 7x5p:
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 Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:37.5 occ:1.00 OD1 A:ASP167 2.3 53.0 1.0 OD2 A:ASP167 2.4 52.1 1.0 CG A:ASP167 2.7 53.2 1.0 OD1 A:ASP156 3.3 57.4 1.0 CG A:ASP156 3.5 52.3 1.0 CB A:ASP156 3.6 47.6 1.0 NH2 A:ARG154 4.1 53.4 1.0 CB A:ASP167 4.3 44.1 1.0 CA A:ASP156 4.3 38.0 1.0 OD2 A:ASP156 4.4 51.3 1.0 O A:ILE166 4.6 52.9 1.0 O A:SER157 4.7 63.1 1.0 N A:SER157 4.9 52.7 1.0 CE1 A:HIS191 4.9 63.2 1.0 C A:ASP156 4.9 41.5 1.0

Sodium binding site 2 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:45.2 occ:1.00 OD1 A:ASP81 2.8 54.8 1.0 O A:PRO82 2.9 49.7 1.0 O A:GLY85 3.0 48.6 1.0 OE1 A:GLN49 3.0 55.8 1.0 OD1 B:ASN151 3.3 49.8 1.0 O B:GLY177 3.4 40.7 1.0 ND2 B:ASN151 3.6 45.7 1.0 N A:GLY85 3.6 50.1 1.0 N A:PHE84 3.7 43.8 1.0 CA A:SER83 3.7 49.0 1.0 CG B:ASN151 3.9 48.5 1.0 C A:SER83 3.9 45.3 1.0 CG A:ASP81 3.9 60.3 1.0 C A:PRO82 3.9 46.6 1.0 CD A:GLN49 4.0 54.3 1.0 C A:GLY85 4.0 51.8 1.0 O A:LEU50 4.2 45.3 1.0 OD2 A:ASP81 4.2 63.5 1.0 CG A:GLN49 4.3 43.7 1.0 N A:SER83 4.3 48.6 1.0 CA A:GLY85 4.4 49.7 1.0 C B:GLY177 4.4 46.5 1.0 C A:PHE84 4.5 46.6 1.0 CA A:PHE84 4.5 44.5 1.0 CA B:GLY177 4.6 52.6 1.0 O A:SER83 4.6 43.9 1.0 CB A:SER83 4.9 42.0 1.0

Sodium binding site 3 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:27.2 occ:1.00 OD2 A:ASP174 2.0 42.3 1.0 NE2 A:GLN149 2.2 43.9 1.0 OE1 A:GLN146 2.4 50.9 1.0 CD A:GLN149 2.4 48.8 1.0 OD1 A:ASP174 2.6 47.1 1.0 CG A:ASP174 2.7 46.2 1.0 OE1 A:GLN149 2.7 50.2 1.0 CG A:GLN149 3.5 49.2 1.0 CD A:GLN146 3.6 49.1 1.0 CB A:ASP174 4.1 42.1 1.0 NE2 A:GLN146 4.4 50.8 1.0 OD1 A:ASP147 4.4 63.5 1.0 O A:HOH502 4.6 25.3 1.0 CB A:GLN146 4.7 46.9 1.0 CG A:GLN146 4.7 46.7 1.0 CB A:GLN149 4.9 45.7 1.0 CA A:GLN146 4.9 45.8 1.0 N A:ASP147 4.9 47.4 1.0 O A:ASP147 5.0 60.6 1.0

Sodium binding site 4 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:34.7 occ:1.00 OE1 B:GLN149 2.4 50.8 1.0 OD1 B:ASP174 2.6 45.0 1.0 OD2 B:ASP174 2.6 42.2 1.0 OE1 B:GLN146 2.9 53.4 1.0 CG B:ASP174 3.0 46.5 1.0 OD1 B:ASP147 3.0 60.6 1.0 CD B:GLN149 3.6 50.2 1.0 O B:ARG148 3.6 50.1 1.0 CG B:ASP147 4.1 62.0 1.0 CD B:GLN146 4.1 52.7 1.0 CG B:GLN149 4.2 48.1 1.0 N B:ASP147 4.5 43.2 1.0 OD2 B:ASP147 4.5 67.0 1.0 CB B:ASP174 4.5 49.1 1.0 C B:ARG148 4.5 48.8 1.0 NE2 B:GLN149 4.6 46.2 1.0 CB B:GLN146 4.8 48.1 1.0 N B:ARG148 4.9 50.1 1.0 CA B:GLN146 4.9 47.4 1.0 CA B:GLN149 5.0 46.8 1.0 NE2 B:GLN146 5.0 51.4 1.0

Sodium binding site 5 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:27.3 occ:1.00 OD1 B:ASP156 2.4 51.2 1.0 OD1 B:ASP167 2.6 47.7 1.0 OD2 B:ASP167 3.1 42.2 1.0 CG B:ASP167 3.3 46.7 1.0 CG B:ASP156 3.4 51.7 1.0 OD2 B:ASP156 4.0 53.9 1.0 O B:SER157 4.3 45.7 1.0 NH2 B:ARG154 4.4 51.0 1.0 CB B:ASP156 4.6 50.8 1.0 OG B:SER165 4.7 58.1 1.0 O B:ILE166 4.7 44.0 1.0 CB B:ASP167 4.8 43.7 1.0 N B:SER157 4.9 44.0 1.0 CB B:SER165 4.9 53.3 1.0 NE2 B:HIS191 4.9 47.2 1.0 CA B:ASP156 4.9 47.3 1.0 CD2 B:HIS191 5.0 48.5 1.0

Sodium binding site 6 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:26.4 occ:1.00 OE1 C:GLN149 2.2 39.7 1.0 OE1 C:GLN146 2.5 55.1 1.0 OD2 C:ASP174 2.8 43.5 1.0 OD1 C:ASP174 3.0 50.5 1.0 CG C:ASP174 3.3 45.3 1.0 CD C:GLN149 3.4 43.7 1.0 OD1 C:ASP147 3.5 53.3 1.0 CD C:GLN146 3.7 47.6 1.0 O C:ARG148 3.9 53.9 1.0 CG C:GLN149 4.2 42.1 1.0 NE2 C:GLN146 4.4 43.1 1.0 NE2 C:GLN149 4.4 47.2 1.0 CG C:ASP147 4.5 55.5 1.0 N C:ASP147 4.7 53.5 1.0 C C:ARG148 4.8 49.3 1.0 CB C:ASP174 4.8 43.4 1.0 CB C:GLN146 4.8 42.4 1.0 CG C:GLN146 4.9 39.0 1.0 OD2 C:ASP147 5.0 52.0 1.0

Sodium binding site 7 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:32.0 occ:1.00 OD1 C:ASP167 2.7 55.4 1.0 OD2 C:ASP156 2.7 53.9 1.0 OD2 C:ASP167 3.1 50.5 1.0 CG C:ASP167 3.3 54.3 1.0 CG C:ASP156 3.8 57.2 1.0 CB C:ASP156 4.1 55.4 1.0 OG C:SER165 4.1 49.4 1.0 NH2 C:ARG154 4.6 49.0 1.0 O C:SER157 4.7 57.7 1.0 CB C:SER165 4.7 50.7 1.0 CB C:ASP167 4.8 51.0 1.0 CE1 C:HIS191 4.8 58.1 1.0 OD1 C:ASP156 4.9 57.2 1.0 O C:ILE166 4.9 46.3 1.0 CA C:ASP156 5.0 52.2 1.0

Sodium binding site 8 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:50.0 occ:1.00 O C:GLY46 2.2 52.3 1.0 O C:ASN44 2.6 52.0 1.0 O F:GLY181 3.0 51.5 1.0 O C:ASP43 3.3 53.6 1.0 C C:GLY46 3.4 50.2 1.0 C C:ASN44 3.7 53.2 1.0 O F:ALA176 3.9 54.7 1.0 CB F:ALA176 3.9 52.0 1.0 CA C:GLY47 4.2 50.5 1.0 C F:GLY181 4.2 56.3 1.0 CA F:ALA176 4.2 51.4 1.0 N C:GLY47 4.2 47.3 1.0 N C:GLY46 4.4 50.9 1.0 CA C:ASN44 4.4 54.5 1.0 C C:ASP43 4.4 54.1 1.0 C C:LEU45 4.5 54.7 1.0 C F:ALA176 4.5 48.8 1.0 CA C:GLY46 4.5 48.0 1.0 CA F:ASP182 4.5 59.7 1.0 O C:LEU45 4.7 53.7 1.0 CA F:GLY179 4.7 52.6 1.0 N C:LEU45 4.8 55.2 1.0 N F:ASP182 4.8 62.2 1.0 CB F:ASP182 4.9 58.4 1.0 C C:GLY47 4.9 51.1 1.0 N C:ASN44 4.9 52.8 1.0

Sodium binding site 9 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:36.5 occ:1.00 OE1 D:GLN149 2.3 49.2 1.0 OD2 D:ASP174 2.3 43.7 1.0 NE2 D:GLN146 2.5 61.4 1.0 OD1 D:ASP174 2.9 44.6 1.0 CG D:ASP174 3.0 44.6 1.0 CD D:GLN146 3.4 57.4 1.0 CD D:GLN149 3.4 49.4 1.0 CG D:GLN146 3.4 53.5 1.0 OD1 D:ASP147 3.7 70.2 1.0 O D:ASP147 3.9 62.7 1.0 NE2 D:GLN149 4.0 50.6 1.0 O D:ARG148 4.1 50.7 1.0 N D:ASP147 4.5 50.0 1.0 CB D:ASP174 4.5 45.2 1.0 OE1 D:GLN146 4.6 46.3 1.0 CG D:GLN149 4.6 45.3 1.0 CB D:GLN146 4.7 50.5 1.0 C D:ASP147 4.7 59.3 1.0 CB D:GLN149 4.8 43.6 1.0 CA D:GLN149 4.8 47.7 1.0 C D:ARG148 4.8 52.0 1.0 CA D:GLN146 4.8 47.4 1.0 CG D:ASP147 4.9 70.3 1.0

Sodium binding site 10 out of 16 in the Truncated Vhchip (1-19AA) in Complex with Doxycycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Truncated Vhchip (1-19AA) in Complex with Doxycycline within 5.0Å range: probe atom residue distance (Å) B Occ D:Na405 b:29.6 occ:1.00 OD1 D:ASP167 2.5 42.4 1.0 OD2 D:ASP156 3.1 52.0 1.0 CG D:ASP167 3.3 43.0 1.0 OD2 D:ASP167 3.4 41.1 1.0 CB D:ASP156 3.9 51.5 1.0 CG D:ASP156 4.0 52.4 1.0 O D:SER157 4.3 42.0 1.0 NH2 D:ARG154 4.3 56.0 1.0 O D:ILE166 4.5 44.8 1.0 OG D:SER165 4.5 56.6 1.0 CA D:ASP156 4.7 46.5 1.0 CB D:ASP167 4.8 42.9 1.0 CB D:SER165 4.8 52.7 1.0 N D:SER157 4.9 46.0 1.0

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