Sodium in PDB 7eqr: Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose

The structure of Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose, PDB code: 7eqr was solved by A.Aunkham, S.Sanram, S.Suginta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58, 131.226, 136.586, 65.8, 87.83, 86.9
R / Rfree (%)	18 / 22.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose (pdb code 7eqr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 18 binding sites of Sodium where determined in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose, PDB code: 7eqr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:33.3 occ:1.00 O A:HOH508 2.0 38.5 1.0 OD1 A:ASP174 2.2 38.0 1.0 OE1 A:GLN146 2.4 40.5 1.0 OE1 A:GLN149 2.6 37.3 1.0 OD2 A:ASP174 2.6 49.6 1.0 CG A:ASP174 2.7 38.2 1.0 CD A:GLN149 3.6 38.8 1.0 CD A:GLN146 3.6 37.6 1.0 NE2 A:GLN149 3.9 42.0 1.0 OD1 A:ASP147 4.2 38.8 1.0 CB A:ASP174 4.2 31.4 1.0 CG A:GLN146 4.5 32.6 1.0 CB A:GLN146 4.5 33.3 1.0 O A:ARG148 4.5 44.1 1.0 NE2 A:GLN146 4.6 30.2 1.0 CA A:GLN146 4.7 36.8 1.0 N A:ASP147 4.9 38.4 1.0 CG A:GLN149 4.9 33.1 1.0 CA A:ASP174 5.0 36.6 1.0

Sodium binding site 2 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:40.0 occ:1.00 OD1 A:ASP317 2.3 53.9 1.0 O A:PHE318 2.5 44.4 1.0 OD2 A:ASP338 2.5 53.5 1.0 OE2 A:GLU320 2.7 63.4 1.0 OD1 A:ASP338 2.9 45.5 1.0 CG A:ASP338 3.1 45.8 1.0 CG A:ASP317 3.5 50.0 1.0 CD A:GLU320 3.6 62.1 1.0 C A:PHE318 3.7 41.6 1.0 N A:PHE318 3.7 38.2 1.0 CG A:GLU320 3.9 57.3 1.0 OD2 A:ASP317 4.1 51.9 1.0 C A:ASP317 4.2 39.6 1.0 CA A:PHE318 4.3 39.0 1.0 CA A:ASP317 4.4 46.3 1.0 CB A:ASP317 4.6 47.7 1.0 C5 A:C8E404 4.6 61.3 1.0 O A:HOH539 4.6 34.4 1.0 CB A:ASP338 4.6 39.9 1.0 OE1 A:GLU320 4.7 66.3 1.0 N A:ASN319 4.8 42.0 1.0 O A:ASN319 4.8 42.8 1.0 O A:HOH530 4.8 38.8 1.0 C A:ASN319 4.8 46.1 1.0 O A:ASP317 5.0 40.6 1.0

Sodium binding site 3 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:43.4 occ:1.00 O C:GLY181 2.5 38.7 1.0 O A:GLY46 2.6 38.5 1.0 O A:ASP43 2.7 36.2 1.0 O A:ASN44 2.9 37.7 1.0 O A:HOH531 3.4 32.6 1.0 C C:GLY181 3.6 40.4 1.0 CA C:ASP182 3.6 38.1 1.0 C A:ASN44 3.6 39.2 1.0 C A:GLY46 3.8 34.0 1.0 C A:ASP43 3.8 43.9 1.0 CB C:ASP182 3.9 43.7 1.0 CB C:ALA176 4.0 29.8 1.0 CA A:ASN44 4.0 39.5 1.0 N C:ASP182 4.0 36.7 1.0 CA C:ALA176 4.3 37.6 1.0 N A:ASN44 4.4 44.1 1.0 N A:GLY46 4.4 33.4 1.0 N A:LEU45 4.6 35.5 1.0 CA A:GLY47 4.7 33.4 1.0 N A:GLY47 4.7 34.3 1.0 CA A:GLY46 4.8 30.9 1.0 C C:ASP182 4.8 38.2 1.0 C A:LEU45 4.8 29.7 1.0 CA C:GLY181 4.9 44.2 1.0 N C:GLY181 5.0 44.2 1.0 O C:ALA176 5.0 33.1 1.0

Sodium binding site 4 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:57.6 occ:1.00 O A:GLY85 2.2 46.0 1.0 O A:HOH529 2.7 32.9 1.0 OD1 A:ASP81 2.9 46.6 1.0 C A:GLY85 3.4 40.8 1.0 O A:PRO82 3.4 39.4 1.0 C A:GLY86 3.9 38.4 1.0 ND2 C:ASN151 4.0 30.7 1.0 O C:GLY177 4.0 39.8 1.0 CA A:GLY86 4.0 34.7 1.0 CG A:ASP81 4.1 47.2 1.0 O A:GLY86 4.1 43.7 1.0 N A:GLY86 4.2 38.0 1.0 CB C:SER150 4.3 33.1 1.0 N A:GLU87 4.3 38.9 1.0 N A:GLY85 4.4 39.8 1.0 CA A:GLY85 4.4 39.4 1.0 OG C:SER150 4.5 40.8 1.0 C A:PRO82 4.6 35.6 1.0 OD2 A:ASP81 4.7 47.3 1.0 C A:ASP81 4.8 32.7 1.0 C C:GLY177 4.8 37.4 1.0 N A:PRO82 4.9 33.1 1.0 OE1 A:GLU87 5.0 47.0 1.0 CA A:GLU87 5.0 38.8 1.0 CG C:ASN151 5.0 30.5 1.0

Sodium binding site 5 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:29.9 occ:1.00 O B:HOH507 2.0 39.8 1.0 O B:HOH504 2.2 35.2 1.0 OE1 B:GLN146 2.2 39.8 1.0 O B:HOH509 2.3 34.0 1.0 OD1 B:ASP174 2.3 34.9 1.0 OE1 B:GLN149 2.4 40.6 1.0 OD2 B:ASP174 2.7 38.6 1.0 CG B:ASP174 2.9 39.1 1.0 CD B:GLN149 3.2 35.1 1.0 CD B:GLN146 3.4 34.4 1.0 NE2 B:GLN149 3.9 32.3 1.0 CG B:GLN149 4.0 33.4 1.0 CB B:GLN146 4.0 33.3 1.0 CG B:GLN146 4.2 30.0 1.0 OD1 B:ASP147 4.4 40.9 1.0 CB B:ASP174 4.4 33.4 1.0 NE2 B:GLN146 4.4 30.9 1.0 CA B:GLN146 4.4 36.0 1.0 O B:HOH524 4.7 32.2 1.0 N B:ASP147 4.8 40.2 1.0 O B:ARG148 4.8 38.8 1.0

Sodium binding site 6 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:47.4 occ:1.00 O A:GLY181 2.4 47.7 1.0 O B:GLY46 2.6 45.7 1.0 O B:ASP43 2.7 46.7 1.0 O B:ASN44 2.9 42.9 1.0 C A:GLY181 3.5 43.3 1.0 CA A:ASP182 3.6 43.2 1.0 C B:ASN44 3.6 44.1 1.0 C B:GLY46 3.8 33.6 1.0 C B:ASP43 3.8 48.7 1.0 CB A:ALA176 3.9 33.9 1.0 CA B:ASN44 3.9 45.8 1.0 N A:ASP182 4.0 41.7 1.0 CB A:ASP182 4.0 42.3 1.0 CA A:ALA176 4.3 40.2 1.0 N B:ASN44 4.4 51.4 1.0 CA B:GLY47 4.5 31.5 1.0 N B:GLY47 4.6 29.3 1.0 N B:GLY46 4.6 38.0 1.0 C A:ASP182 4.7 39.9 1.0 N B:LEU45 4.7 42.1 1.0 C B:LEU45 4.8 34.2 1.0 CA A:GLY181 4.8 43.1 1.0 CA B:GLY46 4.8 37.3 1.0 O A:ALA176 4.8 39.1 1.0 N A:GLY181 4.9 45.9 1.0

Sodium binding site 7 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:37.2 occ:1.00 O B:HOH519 2.1 45.1 1.0 OD2 B:ASP338 2.1 47.9 1.0 OD1 B:ASP317 2.2 48.7 1.0 OE2 B:GLU320 2.2 55.1 1.0 OD1 B:ASP338 2.6 49.6 1.0 O B:PHE318 2.6 43.5 1.0 CG B:ASP338 2.7 46.9 1.0 CD B:GLU320 3.3 61.1 1.0 CG B:ASP317 3.4 49.4 1.0 N B:PHE318 3.7 40.0 1.0 C B:PHE318 3.7 38.6 1.0 CG B:GLU320 4.1 53.4 1.0 OD2 B:ASP317 4.1 53.6 1.0 C B:ASP317 4.1 42.6 1.0 CB B:ASP338 4.2 43.1 1.0 OE1 B:GLU320 4.2 63.9 1.0 CA B:ASP317 4.3 38.6 1.0 CA B:PHE318 4.3 40.0 1.0 CB B:ASP317 4.5 44.8 1.0 O B:ASN319 4.8 46.2 1.0 C B:ASN319 4.8 40.5 1.0 N B:ASN319 4.9 38.8 1.0 O B:ASP317 4.9 39.5 1.0

Sodium binding site 8 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


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 Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na408 b:27.9 occ:1.00 O C:HOH523 2.0 37.7 1.0 OD1 C:ASP174 2.1 36.4 1.0 O C:HOH503 2.2 35.1 1.0 OE1 C:GLN146 2.3 36.5 1.0 OE1 C:GLN149 2.5 41.5 1.0 CG C:ASP174 2.8 33.3 1.0 CD C:GLN149 2.8 27.6 1.0 OD2 C:ASP174 2.8 37.2 1.0 NE2 C:GLN149 3.2 25.4 1.0 CD C:GLN146 3.4 33.2 1.0 CG C:GLN149 3.6 35.2 1.0 CB C:GLN146 4.1 34.0 1.0 CG C:GLN146 4.2 29.6 1.0 CB C:ASP174 4.2 28.1 1.0 O C:ARG148 4.4 30.3 1.0 NE2 C:GLN146 4.5 28.8 1.0 OD1 C:ASP147 4.5 39.5 1.0 CA C:GLN146 4.7 33.0 1.0 CB C:GLN149 4.7 31.4 1.0 CA C:GLN149 4.8 32.1 1.0 CA C:ASP174 4.8 33.6 1.0 N C:ASP174 4.8 33.0 1.0 N C:ASP147 4.9 32.3 1.0

Sodium binding site 9 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na409 b:39.6 occ:1.00 OD1 C:ASP317 2.1 52.1 1.0 OE2 C:GLU320 2.2 53.0 1.0 OD2 C:ASP338 2.3 52.3 1.0 O C:PHE318 2.4 46.8 1.0 OD1 C:ASP338 2.9 48.5 1.0 CG C:ASP338 3.0 48.1 1.0 CD C:GLU320 3.3 59.2 1.0 CG C:ASP317 3.4 52.7 1.0 C C:PHE318 3.6 44.3 1.0 N C:PHE318 3.7 37.7 1.0 CG C:GLU320 3.8 55.2 1.0 OD2 C:ASP317 4.0 54.6 1.0 C C:ASP317 4.2 40.6 1.0 CA C:PHE318 4.2 40.9 1.0 OE1 C:GLU320 4.3 59.9 1.0 CA C:ASP317 4.4 42.4 1.0 CB C:ASP317 4.5 44.2 1.0 CB C:ASP338 4.5 41.9 1.0 N C:ASN319 4.7 44.5 1.0 C C:ASN319 4.8 48.3 1.0 O C:ASP317 4.9 36.3 1.0 CA C:ASN319 5.0 47.3 1.0 O C:ASN319 5.0 50.1 1.0

Sodium binding site 10 out of 18 in the Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Truncated (Delta 1-19) Chitoporin Vhchip From Vibrio Harveyi in Complex with Chitohexaose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:31.1 occ:1.00 O D:HOH501 1.9 28.5 1.0 OD1 D:ASP174 2.1 33.4 1.0 OE1 D:GLN146 2.3 35.7 1.0 OD2 D:ASP174 2.4 37.7 1.0 OE1 D:GLN149 2.5 33.7 1.0 CG D:ASP174 2.6 37.0 1.0 CD D:GLN149 3.4 35.5 1.0 CD D:GLN146 3.5 31.0 1.0 NE2 D:GLN149 3.7 35.0 1.0 CB D:ASP174 4.1 28.6 1.0 CG D:GLN146 4.4 26.8 1.0 NE2 D:GLN146 4.4 28.1 1.0 CB D:GLN146 4.4 33.0 1.0 OD1 D:ASP147 4.4 34.2 1.0 CA D:GLN146 4.7 31.1 1.0 O D:ARG148 4.7 30.7 1.0 CA D:ASP174 4.8 32.0 1.0 CG D:GLN149 4.8 28.9 1.0 N D:ASP147 5.0 32.8 1.0 N D:ASP174 5.0 37.2 1.0

A.Aunkham, S.Sanram, S.Suginta. Structure of Truncated Vhchip Complex with Chitohexaose To Be Published.