Sodium in PDB 2h5f: Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity

The structure of Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity, PDB code: 2h5f was solved by J.Pawlak, R.M.Kini, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.910, 34.038, 54.377, 90.00, 118.36, 90.00
R / Rfree (%)	20.2 / 23.8

The structure of Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity (pdb code 2h5f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity, PDB code: 2h5f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:22.1 occ:1.00 N A:ASN20 2.9 11.8 1.0 O A:HOH394 3.0 30.0 1.0 O A:HOH345 3.5 36.4 1.0 CA A:SER19 3.5 12.4 1.0 O A:HOH340 3.5 26.0 1.0 C A:SER19 3.7 12.1 1.0 O A:HOH429 3.7 28.0 1.0 CB A:SER19 3.8 10.9 1.0 O A:HOH408 3.8 22.9 1.0 CB A:ASN20 3.8 11.3 1.0 CA A:ASN20 3.9 11.4 1.0 O A:HOH323 4.2 17.6 1.0 O A:HOH350 4.3 25.9 1.0 O A:ASN20 4.5 11.8 1.0 C A:ASN20 4.7 10.7 1.0 OG A:SER19 4.8 10.2 1.0 N A:SER19 4.8 10.6 1.0 O A:TRP18 4.8 12.0 1.0 O A:SER19 4.9 9.1 1.0 O A:HOH396 4.9 52.4 1.0

Sodium binding site 2 out of 2 in the Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Denmotoxin: A the Three-Finger Toxin From Colubrid Snake Boiga Dendrophila with Bird-Specific Activity within 5.0Å range: probe atom residue distance (Å) B Occ B:Na307 b:19.1 occ:1.00 N B:ASN20 2.9 11.1 1.0 CA B:SER19 3.6 11.1 1.0 O B:HOH364 3.6 19.1 1.0 CB B:ASN20 3.6 12.5 1.0 C B:SER19 3.7 9.5 1.0 CA B:ASN20 3.8 12.2 1.0 CB B:SER19 3.8 11.1 1.0 O B:ASN20 4.2 11.2 1.0 C B:ASN20 4.4 11.0 1.0 O B:HOH318 4.8 24.9 1.0 O B:SER19 4.9 9.4 1.0 N B:SER19 4.9 11.1 1.0 OG B:SER19 4.9 8.5 1.0

J.Pawlak, S.P.Mackessy, B.G.Fry, M.Bhatia, G.Mourier, C.Fruchart-Gaillard, D.Servent, R.Menez, E.Stura, A.Menez, R.M.Kini. Denmotoxin, A Three-Finger Toxin From the Colubrid Snake Boiga Dendrophila (Mangrove Catsnake) with Bird-Specific Activity. J.Biol.Chem. V. 281 29030 2006.
ISSN: ISSN 0021-9258
PubMed: 16864572
DOI: 10.1074/JBC.M605850200