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

Protein crystallography data

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

Sodium Binding Sites:

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 7at6

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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 7at6

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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 7at6

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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 7at6

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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 7at6

Go back to Sodium Binding Sites List in 7at6
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

Reference:

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.
Page generated: Thu Nov 25 10:31:20 2021

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