Sodium in PDB 2jbw: Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase.

The structure of Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase., PDB code: 2jbw was solved by C.Schleberger, P.Sachelaru, R.Brandsch, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.570, 57.020, 152.697, 90.00, 103.35, 90.00
R / Rfree (%)	18.1 / 23.8

The binding sites of Sodium atom in the Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase. (pdb code 2jbw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase., PDB code: 2jbw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase.


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 the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1368 b:53.6 occ:1.00 O A:LEU203 2.1 73.0 1.0 OD1 A:ASN208 2.5 71.9 1.0 O A:ILE206 2.6 74.0 1.0 O A:LEU200 2.7 68.6 1.0 C A:LEU203 3.3 73.6 1.0 O A:THR201 3.3 75.2 1.0 CG A:ASN208 3.5 77.2 1.0 C A:ILE206 3.6 72.8 1.0 C A:THR201 3.7 73.2 1.0 C A:LEU200 3.9 67.1 1.0 ND2 A:ASN208 3.9 76.5 1.0 N A:ILE206 4.0 72.2 1.0 CB A:ILE206 4.0 68.9 1.0 CA A:THR201 4.0 71.2 1.0 CA A:ILE206 4.0 70.7 1.0 N A:LEU203 4.1 72.7 1.0 CA A:GLU204 4.1 78.0 1.0 N A:GLU204 4.1 75.6 1.0 CA A:LEU203 4.2 72.4 1.0 C A:GLU204 4.4 77.0 1.0 C A:LYS202 4.4 74.1 1.0 N A:THR201 4.4 68.4 1.0 N A:LYS202 4.4 72.5 1.0 N A:ASN208 4.5 75.9 1.0 CG2 A:ILE206 4.5 67.6 1.0 O A:GLU204 4.6 78.6 1.0 O A:LYS202 4.7 76.1 1.0 CB A:ASN208 4.7 78.4 1.0 N A:ARG207 4.8 72.2 1.0 CA A:ASN208 4.8 75.9 1.0 N A:ALA205 4.9 75.0 1.0 CB A:LEU203 4.9 69.6 1.0 CA A:LYS202 4.9 74.2 1.0 C A:ARG207 5.0 73.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase.


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 the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1367 b:56.4 occ:1.00 O B:LEU203 2.2 86.4 1.0 OD1 B:ASN208 2.5 81.0 1.0 O B:LEU200 2.6 78.2 1.0 O B:ILE206 2.8 79.7 1.0 O B:HOH2096 2.9 62.4 1.0 O B:THR201 2.9 90.5 1.0 C B:LEU203 3.2 88.6 1.0 C B:THR201 3.3 86.7 1.0 CG B:ASN208 3.6 83.4 1.0 C B:LEU200 3.7 76.5 1.0 CA B:THR201 3.7 82.6 1.0 C B:ILE206 3.8 77.2 1.0 N B:LEU203 3.9 87.1 1.0 C B:LYS202 4.0 90.9 1.0 CA B:GLU204 4.0 87.5 1.0 N B:GLU204 4.0 85.3 1.0 N B:LYS202 4.0 86.6 1.0 CA B:LEU203 4.2 87.3 1.0 N B:ILE206 4.2 76.9 1.0 N B:THR201 4.2 78.0 1.0 ND2 B:ASN208 4.2 88.2 1.0 CA B:ILE206 4.3 75.0 1.0 O B:LYS202 4.3 94.7 1.0 CB B:ILE206 4.3 72.2 1.0 C B:GLU204 4.5 85.1 1.0 CA B:LYS202 4.5 90.6 1.0 O B:GLU204 4.8 86.4 1.0 N B:ASN208 4.8 79.3 1.0 CG2 B:ILE206 4.8 71.1 1.0 CB B:LEU203 4.9 83.0 1.0 CB B:ASN208 4.9 82.5 1.0 N B:ALA205 5.0 81.9 1.0 N B:ARG207 5.0 76.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase.


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 the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1367 b:36.3 occ:1.00 O C:LEU203 2.0 30.9 1.0 O C:ILE206 2.4 25.6 1.0 O C:HOH2167 2.5 48.2 1.0 O C:LEU200 2.6 31.3 1.0 OD1 C:ASN208 2.6 33.0 1.0 O C:THR201 2.8 30.7 1.0 C C:LEU203 3.2 31.1 1.0 C C:ILE206 3.4 25.9 1.0 C C:THR201 3.4 31.6 1.0 CG C:ASN208 3.7 32.6 1.0 C C:LEU200 3.7 30.1 1.0 N C:LEU203 3.8 32.4 1.0 CA C:ILE206 3.9 24.4 1.0 CA C:THR201 3.9 31.4 1.0 CB C:ILE206 3.9 24.5 1.0 N C:ILE206 3.9 24.9 1.0 CA C:LEU203 4.0 31.8 1.0 O C:HOH2171 4.1 44.6 1.0 ND2 C:ASN208 4.2 36.8 1.0 O C:HOH2164 4.2 32.9 1.0 N C:GLU204 4.2 31.1 1.0 N C:THR201 4.2 30.6 1.0 C C:LYS202 4.3 32.9 1.0 O C:HOH2161 4.4 56.5 1.0 N C:LYS202 4.4 32.7 1.0 CA C:GLU204 4.4 31.7 1.0 N C:ARG207 4.5 26.1 1.0 C C:GLU204 4.5 30.6 1.0 CB C:LEU203 4.5 31.7 1.0 CG2 C:ILE206 4.7 21.6 1.0 N C:ASN208 4.7 27.8 1.0 O C:GLU204 4.7 29.7 1.0 O C:LYS202 4.8 32.7 1.0 CA C:LYS202 4.9 33.2 1.0 CA C:ARG207 5.0 27.2 1.0 CG1 C:ILE206 5.0 24.3 1.0 CB C:ASN208 5.0 29.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase.


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 the 2,6-Dihydroxy-Pseudo-Oxynicotine Hydrolase. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1367 b:20.6 occ:1.00 O D:ILE206 2.1 16.7 1.0 OD1 D:ASN208 2.3 23.8 1.0 O D:LEU203 2.4 21.5 1.0 O D:LEU200 2.6 17.8 1.0 C D:ILE206 3.2 18.4 1.0 C D:LEU203 3.4 21.2 1.0 CG D:ASN208 3.5 23.0 1.0 C D:LEU200 3.8 18.9 1.0 CA D:ILE206 3.8 18.5 1.0 N D:ILE206 3.9 18.5 1.0 CB D:ILE206 3.9 18.7 1.0 CA D:THR201 3.9 21.0 1.0 N D:LEU203 3.9 20.9 1.0 C D:THR201 4.1 21.6 1.0 ND2 D:ASN208 4.1 19.2 1.0 N D:ASN208 4.2 22.2 1.0 CA D:LEU203 4.2 20.6 1.0 N D:THR201 4.3 19.0 1.0 N D:ARG207 4.3 20.0 1.0 N D:GLU204 4.4 22.8 1.0 O D:THR201 4.4 22.6 1.0 N D:LYS202 4.5 22.0 1.0 CG2 D:ILE206 4.5 17.5 1.0 CA D:GLU204 4.5 22.9 1.0 CA D:ASN208 4.6 22.9 1.0 C D:GLU204 4.6 22.3 1.0 CB D:ASN208 4.6 22.1 1.0 C D:ARG207 4.6 21.8 1.0 O D:GLU204 4.6 20.4 1.0 O D:HOH2279 4.7 37.1 1.0 CB D:LEU203 4.7 20.4 1.0 CA D:ARG207 4.8 22.4 1.0 C D:LYS202 4.9 21.8 1.0

C.Schleberger, P.Sachelaru, R.Brandsch, G.E.Schulz. Structure and Action of A Cc Bond Cleaving Alpha/Beta-Hydrolase Involved in Nicotine Degration. J.Mol.Biol. V. 367 409 2007.
ISSN: ISSN 0022-2836
PubMed: 17275835
DOI: 10.1016/J.JMB.2006.12.068