Sodium in PDB 8xua: Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp)

The structure of Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp), PDB code: 8xua was solved by P.Meesrikaew, S.Sanram, R.Robinson, W.Suginta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.21 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.54, 77.089, 143.062, 90, 95.09, 90
R / Rfree (%)	20.9 / 26.8

The binding sites of Sodium atom in the Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp) (pdb code 8xua). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp), PDB code: 8xua:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na310 b:21.5 occ:1.00 OD1 B:ASN62 2.2 34.6 1.0 O B:THR63 2.2 35.0 1.0 OD1 A:ASN62 2.2 36.8 1.0 O A:HOH408 2.3 33.0 1.0 O B:HOH415 2.3 31.2 1.0 O A:THR63 2.3 35.0 1.0 CG B:ASN62 3.3 34.9 1.0 CG A:ASN62 3.3 38.7 1.0 C B:THR63 3.4 36.0 1.0 C A:THR63 3.5 39.5 1.0 ND2 A:ASN62 3.8 40.5 1.0 ND2 B:ASN62 3.8 35.1 1.0 N B:THR63 4.0 35.4 1.0 C B:ASN62 4.3 37.5 1.0 N A:THR63 4.3 36.0 1.0 OE1 A:GLN49 4.3 37.6 1.0 N B:THR64 4.3 31.8 1.0 O A:HOH411 4.4 24.4 1.0 CA B:THR64 4.4 32.1 1.0 N A:THR64 4.4 37.8 1.0 CA B:THR63 4.4 33.0 1.0 C A:ASN62 4.4 38.1 1.0 CA A:THR64 4.4 36.7 1.0 CG2 B:THR64 4.4 31.3 1.0 OE1 B:GLN49 4.4 30.2 1.0 O B:HOH419 4.5 23.9 1.0 CA A:THR63 4.6 39.4 1.0 CB B:ASN62 4.6 31.9 1.0 CG2 A:THR64 4.6 28.4 1.0 O B:ASN62 4.6 42.8 1.0 CB A:ASN62 4.6 31.4 1.0 O A:ASN62 4.7 36.2 1.0 CA B:ASN62 4.7 30.0 1.0 CA A:ASN62 4.8 37.9 1.0 O A:HOH406 4.8 35.2 1.0

Sodium binding site 2 out of 2 in the Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na306 b:57.7 occ:1.00 OD1 D:ASN62 2.2 60.9 1.0 O C:THR63 2.3 64.6 1.0 O D:THR63 2.4 74.8 1.0 OD1 C:ASN62 2.4 70.9 1.0 CG D:ASN62 3.3 68.0 1.0 CG C:ASN62 3.5 70.8 1.0 NE2 D:GLN49 3.5 73.1 1.0 C C:THR63 3.5 62.7 1.0 C D:THR63 3.5 70.0 1.0 O D:HOH402 3.6 54.7 1.0 ND2 D:ASN62 3.8 67.3 1.0 OE1 C:GLN49 3.8 67.2 1.0 ND2 C:ASN62 4.0 73.0 1.0 O C:HOH405 4.1 57.1 1.0 CA D:THR64 4.2 68.3 1.0 CA C:THR64 4.3 59.1 1.0 N D:THR63 4.3 66.0 1.0 N C:THR64 4.3 60.5 1.0 N D:THR64 4.3 66.2 1.0 CG2 C:THR64 4.4 60.6 1.0 N C:THR63 4.4 64.8 1.0 C D:ASN62 4.5 68.3 1.0 O C:HOH402 4.6 59.3 1.0 CA D:THR63 4.6 66.6 1.0 C C:ASN62 4.6 69.0 1.0 CB D:ASN62 4.6 69.9 1.0 CA C:THR63 4.6 68.3 1.0 CG2 D:THR64 4.6 65.7 1.0 CD D:GLN49 4.7 69.5 1.0 CA D:ASN62 4.8 70.1 1.0 CB C:ASN62 4.8 70.9 1.0 CD D:PRO65 4.9 73.8 1.0 O C:ASN62 4.9 71.4 1.0 O D:ASN62 5.0 70.4 1.0 CD C:GLN49 5.0 65.4 1.0 CB D:THR64 5.0 71.9 1.0

P.Meesrikaew, S.Sanram, R.Robinson, W.Suginta. Oligogalacturonate-Specific Porin From Vibrio Harveyi (Vhgalp) To Be Published.