Sodium in PDB 3l8m: Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86

The structure of Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86, PDB code: 3l8m was solved by J.Seetharaman, S.Lew, D.Wang, H.Janjua, K.Cunningham, L.Owens, R.Xiao, J.Liu, M.C.Baran, T.B.Acton, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.35 / 2.40
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	101.873, 101.873, 88.024, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 27.1

The binding sites of Sodium atom in the Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86 (pdb code 3l8m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86, PDB code: 3l8m:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86


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 A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8001 b:16.3 occ:1.00 OD1 A:ASP94 2.8 36.1 1.0 O A:ASN124 3.0 48.9 1.0 OD1 A:ASN124 3.1 74.2 1.0 O A:ILE93 3.3 25.2 1.0 CG A:ASN124 3.4 71.7 1.0 CG A:LYS126 3.6 35.2 1.0 N A:ILE93 3.7 33.2 1.0 CD A:LYS126 3.7 36.0 1.0 C A:ILE93 3.8 28.6 1.0 C A:ASN124 3.8 42.5 1.0 ND2 A:ASN124 3.9 81.8 1.0 CB A:LYS126 3.9 25.3 1.0 N A:LYS126 4.0 36.7 1.0 CG A:ASP94 4.1 34.6 1.0 CE A:LYS126 4.1 60.7 1.0 CB A:ASN124 4.2 56.8 1.0 C A:ASN92 4.2 39.1 1.0 CB A:ASN92 4.2 48.8 1.0 CA A:ASN92 4.2 40.3 1.0 CA A:ILE93 4.4 31.7 1.0 C A:ILE125 4.5 41.1 1.0 N A:ASP94 4.5 28.1 1.0 N A:ILE125 4.6 30.6 1.0 CA A:ILE125 4.6 32.8 1.0 CA A:LYS126 4.6 35.4 1.0 OD1 A:ASN92 4.6 73.7 1.0 CA A:ASN124 4.7 47.8 1.0 OD2 A:ASP94 4.7 28.4 1.0 CA A:ASP94 4.8 32.7 1.0 NZ A:LYS126 4.9 50.3 1.0 CG A:ASN92 4.9 66.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86


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 A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8003 b:14.3 occ:1.00 O A:HOH232 2.9 37.1 1.0 O B:HOH222 3.0 31.6 1.0 OD1 B:ASN11 3.3 26.0 1.0 ND2 A:ASN11 3.3 21.1 1.0 CA A:GLY100 3.6 27.4 1.0 OD1 A:ASN11 3.8 28.3 1.0 CA B:GLY100 3.9 39.8 1.0 CG A:ASN11 4.0 24.2 1.0 CG B:ASN11 4.1 30.1 1.0 ND2 B:ASN11 4.1 27.3 1.0 O A:HOH250 4.3 51.6 1.0 N A:GLY100 4.4 30.1 1.0 N B:GLY100 4.6 33.5 1.0 NH1 B:ARG10 4.7 68.7 1.0 O A:HOH220 4.8 25.2 1.0 C A:GLY100 4.8 30.4 1.0 N A:GLY101 4.8 24.7 1.0 O A:HOH237 5.0 32.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86


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 A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na8002 b:16.8 occ:1.00 NH1 B:ARG88 3.1 16.8 1.0 OH B:TYR90 3.3 30.4 1.0 CB B:GLN43 3.7 27.0 1.0 CD B:ARG88 3.7 27.6 1.0 CE2 B:TYR90 3.9 30.5 1.0 OE1 B:GLN43 4.0 30.3 1.0 CZ B:TYR90 4.1 25.6 1.0 CG B:GLN43 4.2 28.2 1.0 CZ B:ARG88 4.2 23.6 1.0 CD2 B:PHE44 4.2 31.0 1.0 NE B:ARG88 4.4 28.9 1.0 CE2 B:PHE44 4.5 25.9 1.0 CD B:GLN43 4.5 40.2 1.0 CA B:GLN43 4.8 25.7 1.0 O B:GLN43 5.0 23.8 1.0 CG B:ARG88 5.0 26.6 1.0 CB B:ARG88 5.0 29.9 1.0 C B:GLN43 5.0 34.6 1.0

J.Seetharaman, S.Lew, D.Wang, H.Janjua, K.Cunningham, L.Owens, R.Xiao, J.Liu, M.C.Baran, T.B.Acton, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium (Nesg). Crystal Structure of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id SYR86 To Be Published.