Sodium in PDB 3typ: The Crystal Structure of the Inorganic Triphosphatase NE1496

The structure of The Crystal Structure of the Inorganic Triphosphatase NE1496, PDB code: 3typ was solved by V.V.Lunin, T.Skarina, O.Onopriyenko, T.A.Binkowski, A.Joachimiak, A.M.Edwards, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.60 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.282, 52.282, 252.484, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 27

The binding sites of Sodium atom in the The Crystal Structure of the Inorganic Triphosphatase NE1496 (pdb code 3typ). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the The Crystal Structure of the Inorganic Triphosphatase NE1496, PDB code: 3typ:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na154 b:36.1 occ:1.00 O A:HOH186 2.2 38.8 1.0 O A:PHE132 2.3 28.0 1.0 O A:HOH240 2.3 37.1 1.0 O A:HOH246 2.3 44.9 1.0 O A:HOH173 2.5 30.5 1.0 O A:PRO130 2.6 29.5 1.0 O A:HOH250 3.3 39.6 1.0 C A:PHE132 3.5 27.0 1.0 C A:PRO130 3.6 29.9 1.0 CA A:PRO130 4.1 30.1 1.0 O A:HOH195 4.1 39.6 1.0 N A:PHE132 4.2 23.5 1.0 O A:HOH229 4.3 36.6 1.0 CA A:GLY133 4.4 27.2 1.0 CB A:ALA12 4.4 30.3 1.0 N A:GLY133 4.4 27.6 1.0 O A:PRO129 4.4 28.3 1.0 CA A:PHE132 4.4 24.2 1.0 C A:TRP131 4.5 24.6 1.0 O A:HOH272 4.6 53.2 1.0 N A:TRP131 4.6 28.6 1.0 CA A:TRP131 4.9 26.1 1.0 C A:GLY133 5.0 27.0 1.0 CB A:PHE132 5.0 25.0 1.0

Sodium binding site 2 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na155 b:31.9 occ:1.00 O A:ALA148 2.3 21.6 1.0 O A:SER150 2.3 29.7 1.0 O A:HOH177 2.4 26.6 1.0 O A:HOH182 2.5 28.4 1.0 O A:GLY80 2.6 23.3 1.0 C A:GLY80 3.2 22.3 1.0 C A:ALA148 3.5 23.8 1.0 C A:SER150 3.6 32.1 1.0 NE2 A:HIS106 3.9 31.0 1.0 N A:ARG81 3.9 21.3 1.0 C A:LEU149 3.9 29.8 1.0 CA A:GLY80 4.0 24.4 1.0 N A:SER150 4.0 30.7 1.0 CA A:ARG81 4.0 21.2 1.0 N A:ARG82 4.0 20.6 1.0 CA A:LEU149 4.2 28.6 1.0 O A:LEU149 4.2 29.1 1.0 O A:LEU147 4.2 23.3 1.0 O A:ARG82 4.2 19.7 1.0 N A:LEU149 4.2 27.1 1.0 O A:HOH283 4.3 35.5 1.0 N A:ILE151 4.5 35.0 1.0 CA A:SER150 4.5 31.5 1.0 CA A:ALA148 4.5 23.7 1.0 O A:HOH179 4.5 40.3 1.0 CG2 A:ILE151 4.5 41.0 1.0 CA A:ILE151 4.5 38.6 1.0 C A:ARG81 4.5 21.0 1.0 CE1 A:HIS106 4.6 30.6 1.0 OG A:SER150 4.7 32.6 1.0 CD2 A:HIS106 4.7 29.3 1.0 N A:GLY80 4.9 24.7 1.0

Sodium binding site 3 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na156 b:47.9 occ:1.00 O A:SER108 2.4 21.8 1.0 O A:HOH265 2.4 56.4 1.0 O A:HIS106 2.5 22.0 1.0 O A:HOH193 2.5 48.4 1.0 O A:HOH261 2.6 33.0 1.0 C A:HIS106 3.4 21.6 1.0 C A:SER108 3.6 21.2 1.0 CA A:HIS106 3.9 23.2 1.0 O A:HOH248 4.2 37.4 1.0 N A:SER108 4.3 21.4 1.0 CA A:SER108 4.4 21.6 1.0 C A:LEU107 4.4 21.1 1.0 N A:LEU107 4.4 19.7 1.0 O A:GLY105 4.5 23.5 1.0 N A:PRO109 4.5 21.9 1.0 CD A:PRO109 4.5 23.0 1.0 CB A:HIS106 4.6 24.3 1.0 CA A:LEU107 4.7 19.3 1.0 CB A:SER108 4.8 21.6 1.0 O A:LEU107 4.8 21.1 1.0 O A:HOH202 5.0 39.6 1.0

Sodium binding site 4 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na157 b:50.1 occ:1.00 O A:HOH354 2.1 31.0 0.5 O A:ASP94 2.6 33.4 1.0 C A:ASP94 3.5 34.6 1.0 CA A:ASP94 4.1 34.8 1.0 O A:HOH234 4.4 44.4 1.0 CB A:ASP94 4.4 35.3 1.0 N A:GLY95 4.5 34.2 1.0 CA A:GLY95 4.9 33.3 1.0

Sodium binding site 5 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na154 b:35.2 occ:1.00 O B:HOH290 2.2 41.7 1.0 O B:PHE132 2.2 27.3 1.0 O B:HOH176 2.2 43.2 1.0 O B:HOH174 2.3 30.3 1.0 O B:HOH242 2.4 42.4 1.0 O B:PRO130 2.6 29.5 1.0 C B:PHE132 3.5 27.4 1.0 C B:PRO130 3.6 29.0 1.0 CA B:PRO130 4.0 28.8 1.0 O B:HOH178 4.2 35.6 1.0 N B:PHE132 4.2 25.1 1.0 O B:PRO129 4.3 29.7 1.0 O B:HOH230 4.3 35.1 1.0 N B:GLY133 4.3 27.6 1.0 CA B:GLY133 4.4 28.2 1.0 CB B:ALA12 4.4 30.2 1.0 CA B:PHE132 4.4 25.3 1.0 O B:HOH252 4.6 52.5 1.0 C B:TRP131 4.6 25.7 1.0 N B:TRP131 4.6 28.3 1.0 CB B:PHE132 4.9 25.5 1.0 C B:GLY133 4.9 28.2 1.0 CA B:TRP131 5.0 26.6 1.0

Sodium binding site 6 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na155 b:33.5 occ:1.00 O B:ALA148 2.2 23.0 1.0 O B:SER150 2.3 29.1 1.0 O B:HOH163 2.4 25.0 1.0 O B:HOH167 2.4 10.7 0.5 O B:GLY80 2.6 23.6 1.0 C B:GLY80 3.2 22.9 1.0 C B:ALA148 3.4 23.5 1.0 C B:SER150 3.6 32.7 1.0 NE2 B:HIS106 3.9 29.1 1.0 N B:ARG81 3.9 22.6 1.0 N B:ARG82 3.9 20.7 1.0 CA B:ARG81 4.0 21.8 1.0 C B:LEU149 4.0 28.4 1.0 N B:SER150 4.0 30.0 1.0 CA B:GLY80 4.0 24.6 1.0 O B:ARG82 4.1 18.9 1.0 O B:LEU147 4.2 23.9 1.0 N B:LEU149 4.2 25.8 1.0 CA B:LEU149 4.2 27.9 1.0 O B:LEU149 4.3 26.9 1.0 CA B:ALA148 4.3 23.5 1.0 O B:HOH312 4.4 21.3 0.5 C B:ARG81 4.4 21.3 1.0 CA B:SER150 4.5 30.8 1.0 O B:HOH193 4.5 37.4 1.0 N B:ILE151 4.5 35.8 1.0 CE1 B:HIS106 4.6 27.2 1.0 CD2 B:HIS106 4.7 25.4 1.0 CA B:ILE151 4.8 40.5 1.0 OG B:SER150 4.8 29.1 1.0 N B:GLY80 5.0 24.3 1.0 C B:ARG82 5.0 18.3 1.0

Sodium binding site 7 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na156 b:41.8 occ:1.00 O B:SER108 2.3 21.5 1.0 O B:HIS106 2.5 21.2 1.0 O B:HOH196 2.5 49.1 1.0 O B:HOH259 2.5 48.3 1.0 C B:HIS106 3.4 22.0 1.0 C B:SER108 3.5 20.6 1.0 CA B:HIS106 3.9 22.4 1.0 N B:SER108 4.2 21.0 1.0 CA B:SER108 4.3 20.9 1.0 C B:LEU107 4.3 21.3 1.0 O B:GLY105 4.4 23.8 1.0 CD B:PRO109 4.4 22.8 1.0 N B:LEU107 4.4 19.4 1.0 N B:PRO109 4.5 21.5 1.0 CB B:HIS106 4.7 24.6 1.0 CA B:LEU107 4.7 19.8 1.0 CB B:SER108 4.7 21.9 1.0 O B:LEU107 4.8 20.3 1.0 O B:HOH244 4.9 38.3 1.0

Sodium binding site 8 out of 8 in the The Crystal Structure of the Inorganic Triphosphatase NE1496


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of the Inorganic Triphosphatase NE1496 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na157 b:51.1 occ:1.00 O B:HOH331 2.1 49.2 1.0 O B:ASP94 2.5 32.4 1.0 C B:ASP94 3.5 33.3 1.0 CA B:ASP94 4.1 33.1 1.0 O B:HOH206 4.3 48.7 1.0 N B:GLY95 4.5 32.6 1.0 CB B:ASP94 4.6 34.0 1.0 CA B:GLY95 4.9 31.5 1.0

D.Delvaux, M.R.V.S.Murty, V.Gabelica, B.Lakaye, V.V.Lunin, T.Skarina, O.Onopriyenko, G.Kohn, P.Wins, E.De Pauw, L.Bettendorff. A Specific Inorganic Triphosphatase From Nitrosomonas Europaea: Structure and Catalytic Mechanism. J.Biol.Chem. V. 286 34023 2011.
ISSN: ISSN 0021-9258
PubMed: 21840996