Sodium in PDB 8jur: Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)

The structure of Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites), PDB code: 8jur was solved by S.Sanram, W.Suginta, R.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.16 / 2.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.326, 134.103, 145.787, 90, 90, 90
R / Rfree (%)	20.3 / 26.6

The binding sites of Sodium atom in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) (pdb code 8jur). 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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites), PDB code: 8jur:
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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:31.4 occ:1.00 OE1 A:GLN146 2.4 33.6 1.0 OE1 A:GLN149 2.6 51.5 1.0 OD1 A:ASP174 2.8 48.7 1.0 OD1 A:ASP147 3.2 61.2 1.0 OD2 A:ASP174 3.2 56.0 1.0 CG A:ASP174 3.4 48.2 1.0 CD A:GLN149 3.6 37.2 1.0 CD A:GLN146 3.6 27.5 1.0 CB A:GLN146 3.9 35.5 1.0 O A:ARG148 4.1 29.6 1.0 NE2 A:GLN149 4.1 44.4 1.0 CG A:ASP147 4.2 49.2 1.0 N A:ASP147 4.2 38.8 1.0 CG A:GLN146 4.3 28.6 1.0 CA A:GLN146 4.3 20.0 1.0 OD2 A:ASP147 4.5 60.4 1.0 NE2 A:GLN146 4.6 34.9 1.0 CB A:GLN149 4.7 21.4 1.0 CG A:GLN149 4.7 29.6 1.0 C A:GLN146 4.9 26.3 1.0 CA A:GLN149 4.9 34.0 1.0 CB A:ASP174 4.9 40.3 1.0 C A:ARG148 4.9 34.4 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:32.6 occ:1.00 O A:ASN44 2.4 46.4 1.0 O A:GLY46 2.5 34.0 1.0 O A:ASP43 2.6 42.8 1.0 O C:GLY181 2.8 37.0 1.0 C A:ASN44 3.3 36.8 1.0 C A:GLY46 3.7 29.5 1.0 CA A:ASN44 3.7 42.0 1.0 C A:ASP43 3.8 46.2 1.0 C C:GLY181 3.9 47.6 1.0 CB C:ALA176 4.1 28.8 1.0 N A:ASN44 4.2 49.9 1.0 C A:LEU45 4.3 36.2 1.0 N A:LEU45 4.4 40.3 1.0 CA C:ASP182 4.4 31.7 1.0 N A:GLY46 4.4 37.8 1.0 CA A:GLY47 4.4 25.2 1.0 O A:LEU45 4.4 44.1 1.0 CA C:ALA176 4.4 39.9 1.0 N A:GLY47 4.5 29.9 1.0 N C:ASP182 4.6 48.7 1.0 CA A:GLY46 4.6 42.9 1.0 O C:ALA176 4.7 48.4 1.0 CB C:ASP182 4.8 39.4 1.0 CA A:LEU45 4.8 39.1 1.0 N C:GLY181 4.9 41.1 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:47.2 occ:1.00 OD2 A:ASP156 2.7 56.4 1.0 O A:ARG154 3.0 33.2 1.0 OE1 A:GLN107 3.1 50.3 1.0 O A:GLN107 3.3 35.5 1.0 N A:ARG109 3.4 33.3 1.0 CB A:ARG109 3.4 36.2 1.0 NE A:ARG109 3.5 66.9 1.0 CD A:ARG109 3.6 46.3 1.0 C A:VAL108 3.6 37.0 1.0 CG A:ASP156 3.6 48.2 1.0 C A:GLN107 3.6 42.1 1.0 CA A:VAL108 3.7 43.2 1.0 N A:ASP156 3.7 40.6 1.0 CZ A:ARG109 3.8 69.5 1.0 CB A:ASP156 3.8 41.2 1.0 CG A:GLN107 3.8 50.0 1.0 C A:ARG154 3.8 33.3 1.0 N A:VAL108 3.8 42.7 1.0 CD A:GLN107 3.9 55.9 1.0 CG A:ARG109 3.9 43.8 1.0 CA A:ARG109 4.0 41.1 1.0 CB A:GLN107 4.1 30.1 1.0 NH1 A:ARG109 4.1 66.6 1.0 O A:VAL108 4.2 39.3 1.0 C A:TRP155 4.3 34.8 1.0 CA A:TRP155 4.3 42.6 1.0 N A:TRP155 4.3 39.2 1.0 NH2 A:ARG109 4.4 63.0 1.0 CD A:ARG154 4.4 39.3 1.0 CA A:ASP156 4.4 44.0 1.0 CB A:ARG154 4.5 35.0 1.0 CA A:GLN107 4.5 45.1 1.0 CG A:ARG154 4.6 38.9 1.0 OD1 A:ASP156 4.7 49.5 1.0 CA A:ARG154 4.8 29.4 1.0 NE A:ARG154 4.9 63.4 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:56.2 occ:1.00 O B:PRO82 2.9 40.4 1.0 O B:GLY85 3.0 31.8 1.0 O A:GLY177 3.4 45.4 1.0 ND2 A:ASN151 3.5 37.9 1.0 OD2 B:ASP81 3.6 47.4 1.0 OD1 A:ASN151 3.6 36.1 1.0 C B:PRO82 3.9 31.6 1.0 CA B:SER83 3.9 42.8 1.0 CG A:ASN151 4.0 29.7 1.0 N B:PHE84 4.1 37.6 1.0 C B:GLY85 4.1 34.4 1.0 N B:GLY85 4.2 38.3 1.0 OE1 B:GLN49 4.2 33.5 1.0 N B:SER83 4.3 33.6 1.0 C B:SER83 4.3 27.6 1.0 C A:GLY177 4.3 44.0 1.0 O B:ASP81 4.4 31.9 1.0 CA A:GLY177 4.5 31.4 1.0 O B:LEU50 4.6 49.5 1.0 CG B:ASP81 4.8 51.0 1.0 CA B:GLY85 4.8 40.3 1.0 CB A:SER150 4.9 42.0 1.0 C B:ASP81 4.9 37.4 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:50.9 occ:1.00 O B:GLY46 2.8 46.6 1.0 O B:ASN44 3.0 37.2 1.0 O A:ALA176 3.4 39.5 1.0 O A:GLY181 3.6 42.6 1.0 C B:GLY46 3.6 35.9 1.0 CB A:ALA176 3.9 48.5 1.0 O B:LEU45 4.0 32.8 1.0 CA A:ALA176 4.0 40.6 1.0 CA B:GLY47 4.0 24.5 1.0 C A:ALA176 4.0 31.8 1.0 N B:GLY47 4.2 29.1 1.0 O B:ASP43 4.2 42.4 1.0 NE2 B:GLN49 4.2 38.9 1.0 C B:ASN44 4.2 41.5 1.0 C B:LEU45 4.3 28.5 1.0 C B:GLY47 4.5 27.2 1.0 N B:GLY46 4.6 37.0 1.0 CA B:GLY46 4.7 34.7 1.0 O B:MET48 4.7 25.2 1.0 C A:GLY181 4.8 45.8 1.0 CG B:GLN49 4.8 35.5 1.0 CA A:GLY179 4.8 35.8 1.0 N B:MET48 5.0 40.1 1.0 CA B:LEU45 5.0 36.2 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:27.8 occ:1.00 NE2 B:GLN146 2.8 29.7 1.0 OD1 B:ASP174 2.9 31.6 1.0 NE2 B:GLN149 3.1 52.7 1.0 OE1 B:GLN149 3.5 28.6 1.0 CD B:GLN149 3.5 40.8 1.0 OD2 B:ASP174 3.7 43.6 1.0 CG B:ASP174 3.7 35.5 1.0 N B:ASP147 3.9 49.4 1.0 CD B:GLN146 3.9 23.8 1.0 CB B:GLN146 3.9 41.2 1.0 O B:ARG148 4.1 37.4 1.0 CA B:GLN146 4.2 31.6 1.0 OD2 B:ASP147 4.2 56.4 1.0 CG B:GLN146 4.4 29.2 1.0 CB B:GLN149 4.6 27.3 1.0 C B:GLN146 4.6 37.6 1.0 CG B:GLN149 4.6 29.5 1.0 CB B:ASP147 4.7 44.7 1.0 CG B:ASP147 4.7 57.4 1.0 CA B:ASP147 4.8 44.6 1.0 OE1 B:GLN146 4.8 31.1 1.0 CA B:GLN149 4.9 37.2 1.0 C B:ARG148 5.0 34.3 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:34.2 occ:1.00 OE1 C:GLN149 2.6 52.2 1.0 OE1 C:GLN146 2.8 45.4 1.0 OD1 C:ASP174 3.0 33.6 1.0 OD2 C:ASP174 3.1 50.0 1.0 CG C:ASP174 3.4 40.9 1.0 OD2 C:ASP147 3.7 76.0 1.0 CD C:GLN149 3.7 38.2 1.0 CD C:GLN146 4.0 35.8 1.0 NE2 C:GLN149 4.2 36.5 1.0 N C:ASP147 4.3 46.2 1.0 O C:ARG148 4.4 39.7 1.0 CB C:GLN146 4.4 34.1 1.0 CG C:ASP147 4.5 63.7 1.0 CA C:GLN146 4.6 39.2 1.0 CG C:GLN146 4.7 34.0 1.0 CB C:ASP174 4.9 27.2 1.0 CG C:GLN149 4.9 34.2 1.0 NE2 C:GLN146 5.0 40.6 1.0 CB C:ASP147 5.0 41.5 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites)


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 Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:41.7 occ:1.00 O C:GLY46 2.3 44.6 1.0 O C:ASN44 2.7 40.9 1.0 O C:ASP43 2.8 36.4 1.0 O B:GLY181 2.8 40.9 1.0 C C:GLY46 3.5 22.6 1.0 C C:ASN44 3.6 42.9 1.0 C B:GLY181 3.9 34.9 1.0 C C:ASP43 4.0 44.0 1.0 CA C:ASN44 4.1 46.8 1.0 CA B:ASP182 4.1 45.0 1.0 CA C:GLY47 4.2 26.4 1.0 CB B:ALA176 4.2 40.0 1.0 N C:GLY47 4.2 25.0 1.0 N C:GLY46 4.3 37.3 1.0 CB B:ASP182 4.3 57.1 1.0 C C:LEU45 4.4 37.1 1.0 O C:LEU45 4.4 29.3 1.0 CA B:ALA176 4.5 44.3 1.0 O B:ALA176 4.5 34.9 1.0 CA C:GLY46 4.5 32.2 1.0 N B:ASP182 4.5 44.1 1.0 N C:ASN44 4.5 48.6 1.0 N C:LEU45 4.6 42.9 1.0 C B:ALA176 4.9 31.2 1.0 CA C:LEU45 5.0 40.3 1.0

S.Sanram, W.Suginta. Crystal Structure of Chitoporin From Vibrio Harveyi in Complex with Gentamicin C1A (Multiple Binding Sites) To Be Published.