Sodium in PDB 1v6p: Crystal Structure of Cobrotoxin

The structure of Crystal Structure of Cobrotoxin, PDB code: 1v6p was solved by X.Lou, X.Tu, J.Wang, M.Teng, L.Niu, Q.Liu, Q.Huang, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 0.87
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.808, 47.287, 90.018, 90.00, 90.00, 90.00
R / Rfree (%)	11.9 / 15.3

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

Copper	(Cu)	18 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Cobrotoxin (pdb code 1v6p). 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 Cobrotoxin, PDB code: 1v6p:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Cobrotoxin


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 Cobrotoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:8.2 occ:0.48 NA A:NA501 0.0 8.2 0.5 NA A:NA501 1.1 40.5 0.5 O A:HOH1214 3.2 13.4 1.0 OD1 A:ASN62 3.5 17.5 0.3 CG A:ASN62 3.5 8.0 0.7 OD1 A:ASN62 3.5 8.8 0.7 CB A:ASN62 3.6 8.3 0.7 CG A:ASN62 3.7 11.5 0.3 O A:HOH1303 3.7 35.6 0.5 ND2 A:ASN62 3.9 9.1 0.7 CB A:ASN62 4.0 12.5 0.3 O A:HOH1289 4.1 15.4 1.0 ND2 A:ASN62 4.3 13.9 0.3 CG A:PRO12 4.3 10.4 1.0 CU A:CU302 4.3 6.4 0.6 O A:HOH1321 4.4 13.6 0.4 CU A:CU302 4.4 7.7 0.2 CA A:ASN62 4.6 10.5 0.3 CA A:ASN62 4.6 7.7 0.7 O A:ASN62 4.7 9.0 0.7 C A:ASN62 4.7 11.7 0.3 O A:HOH1303 4.9 12.8 0.3 O A:ASN62 4.9 15.9 0.3 O A:HOH1329 5.0 14.5 0.2 CU A:CU302 5.0 9.7 0.1

Sodium binding site 2 out of 4 in the Crystal Structure of Cobrotoxin


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 Cobrotoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:40.5 occ:0.52 NA A:NA501 0.0 40.5 0.5 NA A:NA501 1.1 8.2 0.5 O A:HOH1214 2.8 13.4 1.0 OD1 A:ASN62 2.8 8.8 0.7 OD1 A:ASN62 2.9 17.5 0.3 CG A:ASN62 3.1 8.0 0.7 CU A:CU302 3.4 7.7 0.2 CU A:CU302 3.4 6.4 0.6 CG A:PRO12 3.5 10.4 1.0 CG A:ASN62 3.5 11.5 0.3 CB A:ASN62 3.6 8.3 0.7 ND2 A:ASN62 3.7 9.1 0.7 CB A:ASN62 4.0 12.5 0.3 CU A:CU302 4.1 9.7 0.1 ND2 A:ASN62 4.3 13.9 0.3 O A:HOH1289 4.3 15.4 1.0 CA A:ASN62 4.3 10.5 0.3 CA A:ASN62 4.4 7.7 0.7 O A:HOH1303 4.5 35.6 0.5 CB A:PRO12 4.5 9.6 1.0 CU A:CU302 4.6 26.6 0.2 CD A:PRO12 4.6 10.5 1.0 O A:HOH1321 4.6 13.6 0.4 NE2 A:HIS4 4.7 8.2 1.0 C A:ASN62 4.7 11.7 0.3 O A:ASN62 4.7 9.0 0.7 O A:ASN62 4.8 15.9 0.3 O A:HOH1329 5.0 14.5 0.2

Sodium binding site 3 out of 4 in the Crystal Structure of Cobrotoxin


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 Cobrotoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:10.1 occ:0.33 NA A:NA502 0.0 10.1 0.3 NA A:NA502 0.7 10.8 0.3 OG1 A:THR14 2.9 9.3 1.0 CB A:THR14 3.7 8.2 1.0 CD A:ARG59 3.8 7.8 1.0 CE1 A:HIS4 4.1 8.6 1.0 O A:HOH1227 4.5 19.0 1.0 ND1 A:HIS4 4.6 7.8 1.0 N A:THR14 4.6 7.6 1.0 CG2 A:THR14 4.6 8.9 1.0 CG A:ARG59 4.7 7.9 1.0 C A:THR13 4.8 7.1 1.0 NE A:ARG59 4.8 8.0 1.0 O A:PRO12 4.8 8.3 1.0 CA A:THR14 4.8 7.6 1.0 CA A:THR13 4.9 7.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Cobrotoxin


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 Cobrotoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:10.8 occ:0.31 NA A:NA502 0.0 10.8 0.3 NA A:NA502 0.7 10.1 0.3 OG1 A:THR14 3.2 9.3 1.0 CB A:THR14 3.8 8.2 1.0 O A:HOH1227 3.9 19.0 1.0 N A:THR14 4.4 7.6 1.0 CD A:ARG59 4.4 7.8 1.0 O A:PRO12 4.5 8.3 1.0 C A:THR13 4.6 7.1 1.0 CE1 A:HIS4 4.6 8.6 1.0 CA A:THR13 4.6 7.6 1.0 CA A:THR14 4.8 7.6 1.0 CG2 A:THR14 4.8 8.9 1.0 ND1 A:HIS4 4.9 7.8 1.0 C A:PRO12 5.0 7.4 1.0

X.Lou, Q.Liu, X.Tu, J.Wang, M.Teng, L.Niu, D.J.Schuller, Q.Huang, Q.Hao. The Atomic Resolution Crystal Structure of Atratoxin Determined By Single Wavelength Anomalous Diffraction Phasing J.Biol.Chem. V. 279 39094 2004.
ISSN: ISSN 0021-9258
PubMed: 15252034
DOI: 10.1074/JBC.M403863200