Sodium in PDB 8xwo: Vibrio Harveyi Chitoporin in Complex with Minocycline

The structure of Vibrio Harveyi Chitoporin in Complex with Minocycline, PDB code: 8xwo was solved by S.Sanram, W.Suginta, R.C.Robinson, 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 (%)	18.3 / 26.2

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Vibrio Harveyi Chitoporin in Complex with Minocycline (pdb code 8xwo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Vibrio Harveyi Chitoporin in Complex with Minocycline, PDB code: 8xwo:
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 Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:37.4 occ:1.00 OD1 A:ASP167 2.4 58.8 1.0 OD2 A:ASP167 2.6 52.2 1.0 CG A:ASP167 2.8 58.4 1.0 OD1 A:ASP156 3.3 60.7 1.0 CG A:ASP156 4.0 55.8 1.0 CB A:ASP156 4.1 52.7 1.0 CB A:ASP167 4.4 50.5 1.0 NH2 A:ARG154 4.5 55.2 1.0 CE1 A:HIS191 4.6 63.1 1.0 CA A:ASP156 4.7 42.5 1.0 ND1 A:HIS191 4.7 63.3 1.0 O A:ILE166 4.8 58.4 1.0 O A:SER157 4.8 64.2 1.0 CB A:SER165 5.0 63.0 1.0

Sodium binding site 2 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:45.3 occ:1.00 OD1 B:ASN151 2.8 53.5 1.0 OD1 A:ASP81 2.9 59.0 1.0 NE2 A:GLN49 3.0 55.0 1.0 O A:PRO82 3.0 51.5 1.0 ND2 B:ASN151 3.4 50.8 1.0 CG B:ASN151 3.5 53.9 1.0 O A:GLY85 3.5 54.5 1.0 O B:GLY177 3.6 41.1 1.0 O A:LEU50 3.8 48.3 1.0 CA A:SER83 3.8 51.2 1.0 CD A:GLN49 4.0 54.3 1.0 C A:PRO82 4.0 49.6 1.0 N A:PHE84 4.0 47.2 1.0 CG A:ASP81 4.0 63.7 1.0 CG A:GLN49 4.1 43.5 1.0 C A:SER83 4.2 47.5 1.0 N A:GLY85 4.3 52.2 1.0 N A:SER83 4.4 51.4 1.0 OD2 A:ASP81 4.5 65.1 1.0 C B:GLY177 4.5 50.2 1.0 C A:GLY85 4.6 54.1 1.0 CA B:GLY177 4.6 56.1 1.0 CB B:SER150 4.7 46.7 1.0 O A:ASP81 4.8 51.2 1.0 CB A:SER83 4.8 43.8 1.0 C A:LEU50 5.0 48.1 1.0 CB B:ASN151 5.0 47.2 1.0 CA A:PHE84 5.0 47.6 1.0

Sodium binding site 3 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:32.5 occ:1.00 OD2 A:ASP174 2.2 50.5 1.0 NE2 A:GLN149 2.2 50.3 1.0 CD A:GLN149 2.5 57.8 1.0 OE1 A:GLN146 2.6 56.0 1.0 OD1 A:ASP174 2.6 53.5 1.0 CG A:ASP174 2.7 51.2 1.0 OE1 A:GLN149 2.9 56.8 1.0 CG A:GLN149 3.6 56.1 1.0 CD A:GLN146 3.8 52.9 1.0 O A:HOH502 4.2 24.4 1.0 CB A:ASP174 4.3 45.2 1.0 OD1 A:ASP147 4.3 66.9 1.0 NE2 A:GLN146 4.6 55.1 1.0 CB A:GLN146 4.7 48.1 1.0 CG A:GLN146 4.8 49.5 1.0 CA A:GLN146 4.9 50.4 1.0 N A:ASP147 4.9 51.2 1.0 CG A:ASP147 5.0 67.1 1.0 CB A:GLN149 5.0 52.5 1.0

Sodium binding site 4 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:36.8 occ:1.00 OE1 B:GLN149 2.5 53.8 1.0 OD2 B:ASP174 2.6 45.5 1.0 OD1 B:ASP174 2.6 50.3 1.0 OE1 B:GLN146 2.8 57.0 1.0 CG B:ASP174 2.9 50.1 1.0 OD1 B:ASP147 3.2 59.1 1.0 O B:ARG148 3.6 51.9 1.0 CD B:GLN149 3.7 53.5 1.0 CD B:GLN146 4.0 58.4 1.0 CG B:GLN149 4.3 50.6 1.0 CG B:ASP147 4.3 56.8 1.0 N B:ASP147 4.5 47.8 1.0 CB B:ASP174 4.5 52.0 1.0 C B:ARG148 4.5 52.0 1.0 CB B:GLN146 4.7 51.4 1.0 OD2 B:ASP147 4.8 54.6 1.0 NE2 B:GLN149 4.8 51.9 1.0 CA B:GLN146 4.8 51.5 1.0 NE2 B:GLN146 4.8 56.5 1.0 N B:ARG148 4.9 49.0 1.0 CG B:GLN146 5.0 52.2 1.0

Sodium binding site 5 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:33.4 occ:1.00 OD1 B:ASP156 2.3 57.8 1.0 OD1 B:ASP167 2.5 50.5 1.0 OD2 B:ASP167 3.2 41.6 1.0 CG B:ASP167 3.2 50.4 1.0 CG B:ASP156 3.4 53.8 1.0 OD2 B:ASP156 3.9 52.2 1.0 O B:SER157 4.3 49.0 1.0 NH2 B:ARG154 4.5 53.3 1.0 CB B:ASP156 4.5 51.8 1.0 OG B:SER165 4.6 62.4 1.0 O B:ILE166 4.7 46.4 1.0 CB B:ASP167 4.8 48.6 1.0 N B:SER157 4.8 50.3 1.0 CB B:SER165 4.8 57.5 1.0 CA B:ASP156 4.9 50.6 1.0 NE2 B:HIS191 4.9 53.1 1.0 CD2 B:HIS191 4.9 54.3 1.0

Sodium binding site 6 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:32.5 occ:1.00 OE1 C:GLN149 2.4 45.6 1.0 OE1 C:GLN146 2.7 60.8 1.0 OD2 C:ASP174 2.8 45.9 1.0 OD1 C:ASP174 2.8 53.1 1.0 CG C:ASP174 3.2 48.8 1.0 OD1 C:ASP147 3.4 62.7 1.0 CD C:GLN149 3.6 47.8 1.0 O C:ARG148 3.9 56.7 1.0 CD C:GLN146 3.9 53.6 1.0 CG C:GLN149 4.3 43.9 1.0 NE2 C:GLN149 4.6 52.8 1.0 CG C:ASP147 4.6 65.6 1.0 NE2 C:GLN146 4.6 46.9 1.0 CB C:ASP174 4.8 46.5 1.0 N C:ASP147 4.8 54.7 1.0 C C:ARG148 4.8 51.6 1.0 CB C:GLN146 4.9 51.8 1.0

Sodium binding site 7 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:32.1 occ:1.00 OD1 C:ASP167 2.6 57.6 1.0 OD2 C:ASP156 2.8 59.4 1.0 OD2 C:ASP167 3.2 49.3 1.0 CG C:ASP167 3.3 54.0 1.0 CG C:ASP156 3.8 61.7 1.0 CB C:ASP156 4.1 55.8 1.0 OG C:SER165 4.1 49.5 1.0 NH2 C:ARG154 4.7 53.3 1.0 CE1 C:HIS191 4.7 60.7 1.0 O C:SER157 4.7 59.8 1.0 CB C:SER165 4.8 51.2 1.0 CB C:ASP167 4.8 51.2 1.0 CA C:ASP156 4.9 48.5 1.0 ND1 C:HIS191 4.9 57.7 1.0 OD1 C:ASP156 4.9 60.9 1.0

Sodium binding site 8 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:52.4 occ:1.00 O C:GLY46 2.4 56.4 1.0 O C:ASN44 2.6 57.2 1.0 O C:ASP43 2.9 54.5 1.0 O F:GLY181 3.0 51.4 1.0 C C:GLY46 3.6 55.8 1.0 C C:ASN44 3.7 56.9 1.0 O F:ALA176 4.0 55.7 1.0 CB F:ALA176 4.0 51.2 1.0 C C:ASP43 4.1 53.7 1.0 C F:GLY181 4.2 56.4 1.0 CA F:ALA176 4.2 50.5 1.0 CA C:ASN44 4.2 57.4 1.0 CA C:GLY47 4.3 53.8 1.0 N C:GLY47 4.4 51.8 1.0 CA F:ASP182 4.4 64.6 1.0 N C:GLY46 4.5 54.2 1.0 C F:ALA176 4.6 50.7 1.0 C C:LEU45 4.6 56.6 1.0 N C:ASN44 4.7 54.3 1.0 CA C:GLY46 4.7 52.4 1.0 N C:LEU45 4.7 56.9 1.0 CB F:ASP182 4.7 59.1 1.0 N F:ASP182 4.8 64.3 1.0 O C:LEU45 4.8 53.4 1.0 CA F:GLY179 4.9 51.3 1.0 C C:GLY47 5.0 55.2 1.0

Sodium binding site 9 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:34.4 occ:1.00 OD2 D:ASP174 2.4 47.9 1.0 OE1 D:GLN149 2.6 54.2 1.0 OD1 D:ASP174 2.8 46.5 1.0 CG D:ASP174 3.0 46.5 1.0 CG D:GLN146 3.2 52.0 1.0 OD1 D:ASP147 3.7 75.6 1.0 CD D:GLN149 3.7 51.3 1.0 NE2 D:GLN146 3.8 58.7 1.0 CB D:GLN146 4.0 54.6 1.0 CD D:GLN146 4.0 55.8 1.0 O D:ARG148 4.2 51.5 1.0 O D:ASP147 4.2 68.3 1.0 NE2 D:GLN149 4.3 50.8 1.0 N D:ASP147 4.4 57.8 1.0 CA D:GLN146 4.4 54.4 1.0 CB D:ASP174 4.5 47.5 1.0 C D:GLN146 4.8 54.1 1.0 C D:ASP147 4.9 65.2 1.0 CG D:ASP147 4.9 72.2 1.0 CG D:GLN149 4.9 45.9 1.0 C D:ARG148 5.0 56.9 1.0

Sodium binding site 10 out of 16 in the Vibrio Harveyi Chitoporin in Complex with Minocycline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Vibrio Harveyi Chitoporin in Complex with Minocycline within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:33.8 occ:1.00 OD1 D:ASP167 2.4 43.8 1.0 OD2 D:ASP156 3.0 51.5 1.0 CG D:ASP167 3.2 44.0 1.0 OD2 D:ASP167 3.3 40.4 1.0 CG D:ASP156 3.9 52.2 1.0 CB D:ASP156 4.0 54.1 1.0 O D:SER157 4.3 47.7 1.0 OG D:SER165 4.4 56.0 1.0 O D:ILE166 4.5 46.3 1.0 CA D:ASP156 4.6 50.6 1.0 NH2 D:ARG154 4.7 55.4 1.0 CB D:ASP167 4.7 44.7 1.0 CB D:SER165 4.7 55.6 1.0 N D:SER157 4.8 52.0 1.0 CD2 D:HIS191 4.9 52.3 1.0 NE2 D:HIS191 4.9 55.2 1.0 C D:ASP156 5.0 51.3 1.0

S.Sanram, W.Suginta, R.C.Robinson. Vhchip in Complex with Minocycline To Be Published.