Sodium in PDB 3r0l: Crystal Structure of Crotoxin

All present enzymatic activity of Crystal Structure of Crotoxin:
3.1.1.4;

The structure of Crystal Structure of Crotoxin, PDB code: 3r0l was solved by F.A.Saul, G.Faure, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.33 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.664, 65.309, 37.429, 90.00, 103.90, 90.00
R / Rfree (%)	16.5 / 18.9

The structure of Crystal Structure of Crotoxin also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Crotoxin (pdb code 3r0l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Crotoxin, PDB code: 3r0l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Crotoxin


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 Crotoxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na124 b:11.2 occ:1.00 O D:TYR110 2.3 12.6 1.0 O D:GLY25 2.3 9.0 1.0 O D:HOH157 2.4 14.8 1.0 O D:HOH131 2.5 10.2 1.0 OD1 D:ASP112 2.5 12.9 1.0 O D:PHE23 2.6 11.0 1.0 C D:PHE23 3.4 11.0 1.0 C D:TYR110 3.4 13.2 1.0 C D:GLY25 3.5 9.9 1.0 CG D:ASP112 3.6 15.3 1.0 CB D:TYR110 4.0 12.4 1.0 CA D:PHE23 4.0 11.0 1.0 O D:HOH175 4.0 15.5 1.0 CA D:TYR110 4.1 12.6 1.0 C D:TYR24 4.1 8.9 1.0 O D:TYR24 4.1 9.6 1.0 N D:GLY25 4.2 8.9 1.0 N D:TYR110 4.2 12.8 1.0 N D:ASP112 4.2 15.3 1.0 N D:TYR24 4.3 9.3 1.0 OD2 D:ASP112 4.3 17.3 1.0 CB D:PHE23 4.4 11.9 1.0 N D:CYS26 4.4 9.0 1.0 CA D:GLY25 4.4 9.1 1.0 CA D:CYS26 4.5 11.8 1.0 O D:HOH243 4.5 17.8 1.0 N D:PRO111 4.5 13.5 1.0 C D:PRO111 4.5 14.3 1.0 CA D:ASP112 4.7 16.0 1.0 CA D:TYR24 4.7 9.5 1.0 CA D:PRO111 4.7 14.6 1.0 CB D:ASP112 4.7 15.4 1.0 CL B:CL126 4.7 17.8 1.0 CD2 D:TYR110 4.7 15.1 1.0 C D:CYS26 4.8 11.2 1.0 CG D:TYR110 4.9 14.6 1.0 O D:CYS28 5.0 12.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Crotoxin


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 Crotoxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na125 b:17.5 occ:1.00 O D:TYR27 2.2 10.2 1.0 O D:GLY31 2.3 18.0 1.0 O D:GLY29 2.5 13.8 1.0 O D:HOH247 2.5 36.8 1.0 OD2 D:ASP48 2.7 26.1 1.0 OD1 D:ASP48 3.1 26.1 1.0 CG D:ASP48 3.3 20.9 1.0 C D:TYR27 3.3 9.7 1.0 C D:GLY31 3.5 15.9 1.0 C D:GLY29 3.6 12.7 1.0 O D:HOH277 3.7 29.1 1.0 N D:GLY31 3.9 17.6 1.0 C D:TRP30 4.0 16.5 1.0 N D:GLY29 4.0 12.1 1.0 CA D:TYR27 4.1 10.7 1.0 O D:TRP30 4.1 16.8 1.0 C D:CYS28 4.1 11.9 1.0 CA D:GLY31 4.3 17.8 1.0 N D:CYS28 4.4 9.3 1.0 CA D:GLY29 4.4 12.4 1.0 OXT D:ACT127 4.4 20.7 1.0 O D:HOH168 4.5 34.7 1.0 N D:TRP30 4.5 15.0 1.0 CA D:CYS28 4.5 10.5 1.0 N D:GLY32 4.5 16.7 1.0 O D:HOH175 4.5 15.5 1.0 CB D:TYR27 4.5 10.6 1.0 CA D:TRP30 4.6 15.0 1.0 O D:CYS28 4.6 12.9 1.0 CA D:GLY32 4.7 15.8 1.0 CB D:ASP48 4.7 14.7 1.0 CD2 D:TYR27 4.9 11.7 1.0 O D:CYS44 4.9 10.2 1.0

G.Faure, H.Xu, F.A.Saul. Crystal Structure of Crotoxin Reveals Key Residues Involved in the Stability and Toxicity of This Potent Heterodimeric Beta-Neurotoxin J.Mol.Biol. V. 412 176 2011.
ISSN: ISSN 0022-2836
PubMed: 21787789
DOI: 10.1016/J.JMB.2011.07.027