Sodium in PDB 7at6: Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane

The structure of Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane, PDB code: 7at6 was solved by I.Martiel, M.Marsh, L.Vera, C.Y.Huang, V.Olieric, P.Leonarski, K.Nass, C.Padeste, A.Karpik, M.Wang, B.Pedrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.35 / 1.46
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.6, 58.6, 151.5, 90, 90, 90
R / Rfree (%)	15.9 / 17.7

The binding sites of Sodium atom in the Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane (pdb code 7at6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane, PDB code: 7at6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:39.8 occ:1.00 OD1 A:ASP113 2.7 33.0 1.0 OG1 A:THR202 2.8 32.3 1.0 O A:ARG200 2.9 31.5 1.0 O A:HOH582 3.0 50.7 1.0 O A:ASP113 3.4 31.5 1.0 C A:ARG200 3.5 31.2 1.0 N A:THR202 3.6 28.9 1.0 CB A:THR202 3.6 29.8 1.0 CG A:ARG200 3.6 33.2 1.0 CG A:ASP113 3.7 32.8 1.0 CB A:ARG200 3.8 31.7 1.0 C A:ASP113 3.8 32.8 1.0 CB A:ASP113 3.9 30.4 1.0 CD A:ARG200 4.0 37.8 1.0 N A:SER115 4.0 29.9 1.0 O A:HOH581 4.1 56.8 1.0 C A:VAL201 4.1 30.8 1.0 N A:VAL201 4.1 30.4 1.0 CA A:VAL201 4.2 29.2 1.0 CB A:SER115 4.2 31.5 1.0 CA A:THR202 4.2 28.6 1.0 CA A:ARG200 4.3 31.5 1.0 OG A:SER115 4.3 32.7 1.0 N A:PHE114 4.4 30.4 1.0 CA A:PHE114 4.5 30.2 1.0 CA A:ASP113 4.5 29.7 1.0 C A:PHE114 4.6 32.4 1.0 CA A:SER115 4.7 30.3 1.0 OD2 A:ASP113 4.8 34.9 1.0 CG2 A:THR202 4.9 31.2 1.0 O A:VAL201 5.0 31.4 1.0

Sodium binding site 2 out of 5 in the Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:36.5 occ:1.00 N A:LYS106 2.8 30.3 1.0 O A:THR85 2.8 30.4 1.0 O A:SER103 2.8 29.8 1.0 O A:GLY107 3.1 31.1 1.0 CA A:LYS106 3.3 30.1 1.0 C A:ASN104 3.3 28.3 1.0 N A:ILE105 3.3 29.6 1.0 CA A:ASN104 3.3 29.0 1.0 C A:LYS106 3.4 30.4 1.0 C A:SER103 3.4 30.2 1.0 CB A:LYS106 3.4 29.3 1.0 N A:GLY107 3.5 29.8 1.0 CD1 A:LEU87 3.6 32.4 1.0 N A:ASN104 3.7 28.6 1.0 CG A:LEU87 3.7 29.2 1.0 O A:ASN104 3.9 30.9 1.0 C A:ILE105 3.9 30.3 1.0 C A:THR85 3.9 28.7 1.0 O A:LYS106 4.0 31.1 1.0 C A:GLY107 4.1 30.3 1.0 OG A:SER103 4.1 30.3 1.0 N A:LEU87 4.1 29.2 1.0 CA A:ILE105 4.2 28.9 1.0 CB A:LEU87 4.2 29.9 1.0 CA A:THR86 4.4 27.3 1.0 CA A:GLY107 4.4 27.8 1.0 CB A:SER103 4.5 29.5 1.0 CG A:LYS106 4.5 33.4 1.0 C A:THR86 4.6 30.1 1.0 OG1 A:THR85 4.6 32.3 1.0 CA A:SER103 4.6 28.8 1.0 N A:THR86 4.6 29.0 1.0 CB A:ASN104 4.8 29.2 1.0 CA A:LEU87 4.8 27.5 1.0 CB A:ILE105 4.9 29.4 1.0

Sodium binding site 3 out of 5 in the Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:38.3 occ:1.00 O A:THR86 2.7 31.1 1.0 N A:ALA52 2.8 28.6 1.0 OD1 A:ASN109 2.9 29.6 1.0 N A:THR86 3.6 29.0 1.0 O A:ALA52 3.6 31.1 1.0 CB A:TRP51 3.7 27.8 1.0 C A:THR86 3.7 30.1 1.0 CB A:ALA52 3.7 29.5 1.0 CA A:ALA52 3.7 28.0 1.0 CA A:TRP51 3.7 27.4 1.0 CB A:THR86 3.7 30.0 1.0 C A:TRP51 3.8 29.7 1.0 CG A:ASN109 3.8 29.6 1.0 CE A:MET112 3.8 30.7 0.5 CA A:THR86 3.9 27.3 1.0 ND2 A:ASN109 4.0 30.9 1.0 C A:ALA52 4.1 29.5 1.0 OG1 A:THR86 4.2 29.2 1.0 CE A:MET112 4.3 29.2 0.5 C A:THR85 4.4 28.7 1.0 O A:VAL110 4.5 30.9 1.0 CB A:VAL110 4.5 30.4 1.0 CE1 A:PHE203 4.5 31.9 1.0 CA A:THR85 4.6 28.0 1.0 N A:VAL110 4.6 28.0 1.0 CG A:TRP51 4.8 30.2 1.0 N A:LEU87 4.9 29.2 1.0 CB A:THR85 4.9 30.5 1.0 O A:TRP51 5.0 29.6 1.0 CD1 A:PHE203 5.0 30.4 1.0 CG2 A:VAL110 5.0 32.9 1.0 CD1 A:TRP51 5.0 30.2 1.0

Sodium binding site 4 out of 5 in the Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:39.7 occ:1.00 OG A:SER170 2.7 29.3 1.0 O A:HOH611 2.8 40.2 1.0 OG A:SER182 2.9 30.8 1.0 C A:SER170 3.2 30.6 1.0 O A:SER170 3.3 31.1 1.0 CB A:SER170 3.3 31.7 1.0 N A:ARG171 3.4 29.9 1.0 CA A:ARG171 3.6 30.2 1.0 CB A:LYS174 3.8 29.7 1.0 CD1 A:TYR183 3.9 31.5 1.0 CA A:SER170 3.9 28.9 1.0 CB A:PRO166 3.9 32.0 1.0 CB A:SER182 3.9 29.6 1.0 CG A:ARG171 4.0 31.9 1.0 CE1 A:TYR183 4.0 32.5 1.0 O A:HOH415 4.3 46.4 1.0 CG A:LYS174 4.3 30.3 1.0 CB A:ARG171 4.4 31.7 1.0 CA A:PRO166 4.6 30.6 1.0 O A:HOH620 4.7 46.3 1.0 OD2 A:ASP186 4.8 31.6 1.0 C A:ARG171 4.9 30.8 1.0 O A:THR167 4.9 30.8 1.0 OD1 A:ASP186 4.9 34.5 1.0 N A:THR167 4.9 30.8 1.0 CD A:LYS174 5.0 31.4 1.0 N A:SER170 5.0 29.9 1.0

Sodium binding site 5 out of 5 in the Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Thaumatin Collected By Femtosecond Serial Crystallography on A Coc Membrane within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:39.7 occ:1.00 O A:ASP179 2.8 36.7 1.0 O A:THR189 2.9 35.6 1.0 OG1 A:THR189 3.0 35.6 1.0 N A:ILE102 3.0 29.1 1.0 CB A:ASP101 3.4 32.5 1.0 CB A:THR189 3.4 33.0 1.0 O A:ILE102 3.5 31.4 1.0 CA A:ASP101 3.5 29.5 1.0 C A:THR189 3.6 35.0 1.0 C A:ASP101 3.8 29.6 1.0 C A:ASP179 3.9 33.9 1.0 CG1 A:VAL124 4.0 38.3 1.0 CA A:ILE102 4.0 26.6 1.0 CG2 A:VAL124 4.1 36.5 1.0 CA A:ALA180 4.1 29.0 1.0 CA A:THR189 4.1 33.4 1.0 CB A:VAL124 4.2 35.4 1.0 C A:ILE102 4.2 30.1 1.0 CB A:ILE102 4.4 27.4 1.0 N A:ALA180 4.4 31.4 1.0 OD1 A:ASP179 4.5 32.5 0.2 N A:THR190 4.5 34.4 1.0 CD1 A:PHE181 4.6 30.8 1.0 CG A:ASP101 4.6 32.2 1.0 CE1 A:PHE181 4.7 30.9 1.0 N A:PHE181 4.8 30.2 1.0 CG2 A:THR189 4.8 37.1 1.0 OD1 A:ASP101 4.8 31.9 1.0 C A:ALA180 4.8 31.1 1.0 N A:ASP101 4.9 28.9 1.0 CG A:ASP179 4.9 35.2 0.2 CA A:THR190 4.9 33.2 1.0 O A:ILE100 5.0 31.9 1.0 N A:THR189 5.0 34.4 1.0 O A:ASP101 5.0 29.5 1.0

I.Martiel, C.Pradervand, E.Panepucci, T.Zamofing, K.Nass, M.Marsh, L.Vera, C.Y.Hunag, V.Olieric, D.Buntschu, R.Kaelin, P.Leonarski, D.Ozerov, C.Padeste, A.Karpik, V.Thominet, J.Hora, N.Olieric, T.Weinert, M.Wranik, S.Brunle, J.Standfuss, O.Aurelius, J.John, M.Hogbom, L.Zhang, O.Einsle, G.Papp, S.Basu, F.Cipriani, P.Beaud, R.Mankowsky, W.Glettig, A.Mozzanica, S.Redford, B.Schmidt, O.Bunk, R.Abela, M.Wang, H.Lemke, B.Pedrini. Commissioning Results From the Swissmx Instrument For Fixed Target Macromolecular Crystallography at Swissfel To Be Published.