Sodium in PDB 7by5: Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F)

All present enzymatic activity of Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F):
3.4.24.68;

The structure of Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F), PDB code: 7by5 was solved by C.M.Zhang, Y.Imoto, Y.Fukuda, E.Yamashita, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.28 / 2.27
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.542, 145.542, 129.038, 90, 90, 120
R / Rfree (%)	18.6 / 23.3

The structure of Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F) (pdb code 7by5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F), PDB code: 7by5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1410 b:83.5 occ:1.00 O A:HOH1963 2.5 63.2 1.0 O A:HOH2030 2.6 62.9 1.0 OD1 A:ASN506 2.8 66.2 1.0 O A:HOH2134 2.9 72.9 1.0 OE1 A:GLU362 3.3 63.6 1.0 CG A:ASN506 3.7 67.8 1.0 CD A:GLU362 3.8 61.5 1.0 O A:TYR507 3.8 64.0 1.0 O A:TYR356 3.9 58.8 1.0 ND2 A:ASN506 4.0 71.1 1.0 OE2 A:GLU362 4.0 61.9 1.0 O A:HOH1724 4.1 51.0 1.0 CG2 A:THR359 4.1 48.9 1.0 O A:HOH1863 4.2 68.2 1.0 O A:HOH2254 4.5 73.5 1.0 O A:HOH1624 4.6 71.7 1.0 C A:TYR507 4.7 54.4 1.0 N A:TYR507 4.8 53.1 1.0 OG1 A:THR359 4.8 46.9 1.0 N A:GLY277 5.0 47.8 1.0 CG A:GLU362 5.0 53.9 1.0

Sodium binding site 2 out of 3 in the Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1411 b:64.1 occ:1.00 O A:ALA585 2.3 58.1 1.0 O A:ASN588 2.3 81.6 1.0 O A:LYS591 2.4 57.3 1.0 O A:HOH1897 2.5 60.7 1.0 O A:HOH1625 2.5 52.5 1.0 C A:ALA585 3.4 63.3 1.0 C A:ASN588 3.5 74.5 1.0 C A:LYS591 3.6 58.2 1.0 O A:HOH1618 3.8 68.8 1.0 CA A:ALA585 3.9 63.8 1.0 CA A:SER589 4.0 73.2 1.0 N A:LYS591 4.1 59.9 1.0 C A:SER589 4.1 70.3 1.0 N A:SER589 4.2 73.9 1.0 CB A:ALA585 4.2 62.1 1.0 O A:SER589 4.3 67.2 1.0 CA A:LYS591 4.3 59.6 1.0 O A:LYS568 4.3 61.2 1.0 CD1 A:ILE592 4.4 63.3 1.0 O A:ALA566 4.5 52.6 1.0 O A:HOH2150 4.5 83.9 1.0 N A:LEU586 4.5 65.1 1.0 N A:THR590 4.6 66.1 1.0 N A:ILE592 4.6 56.2 1.0 CA A:ASN588 4.6 73.6 1.0 N A:ASN588 4.7 75.6 1.0 CB A:LYS591 4.8 61.1 1.0 CA A:ILE592 4.9 55.2 1.0 CA A:LEU586 4.9 66.4 1.0 C A:LEU586 4.9 69.2 1.0

Sodium binding site 3 out of 3 in the Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Tetanus Neurotoxin Mutant-(H233A/E234Q/H237A/Y375F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1412 b:79.3 occ:1.00 O A:HOH1839 2.1 28.8 0.3 OE1 A:GLU201 2.2 82.5 1.0 OH A:TYR77 3.3 56.7 1.0 CD A:GLU201 3.4 79.5 1.0 CA A:PHE87 3.6 49.5 1.0 N A:PHE87 3.6 51.2 1.0 NH2 A:ARG86 3.8 85.0 1.0 CB A:PHE87 3.8 49.0 1.0 CZ A:TYR77 4.0 54.5 1.0 CZ A:ARG86 4.0 83.7 1.0 C A:ARG86 4.1 53.6 1.0 NE A:ARG86 4.1 77.9 1.0 CE1 A:TYR77 4.2 54.9 1.0 CG A:GLU201 4.2 69.8 1.0 O A:ASP83 4.2 55.1 1.0 CD1 A:PHE87 4.3 48.9 1.0 OE2 A:GLU201 4.3 79.5 1.0 CB A:ARG86 4.4 58.8 1.0 O A:ARG86 4.4 48.0 1.0 CG A:PRO200 4.5 44.8 1.0 CG A:PHE87 4.6 50.0 1.0 CG A:ARG86 4.6 67.4 1.0 OG1 A:THR90 4.8 42.4 1.0 NH1 A:ARG86 4.8 86.0 1.0 CA A:ARG86 4.8 54.2 1.0 CD A:PRO200 4.8 47.1 1.0 C A:PHE87 5.0 51.6 1.0

C.M.Zhang, T.Inoue. 2.3 A Crystal Structure of Tetanus Neurotoxin Light Chain To Be Published.