Sodium in PDB 6ter: Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose

The structure of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose, PDB code: 6ter was solved by T.Keenan, F.Parmeggiani, C.Q.Fontenelle, J.Malassis, J.Vendeville, W.A.Offen, P.Both, K.Huang, A.Marchesi, A.Heyam, C.Young, S.Charnock, G.J.Davies, B.Linclau, S.L.Flitsch, M.A.Fascione, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.60 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.320, 164.929, 113.630, 90.00, 94.97, 90.00
R / Rfree (%)	22.4 / 30.8

The structure of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose (pdb code 6ter). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose, PDB code: 6ter:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose


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 Galactokinase From Bifidobacterium Infantis in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na720 b:50.7 occ:1.00 OE1 B:GLU8 2.9 50.7 1.0 O B:PHE6 3.8 26.3 1.0 CD B:GLU8 3.9 35.9 1.0 CB B:PHE6 3.9 28.4 1.0 CB B:GLU8 4.0 29.6 1.0 O B:HOH967 4.2 36.1 1.0 C B:PHE6 4.2 24.7 1.0 CG B:GLU8 4.3 39.7 1.0 N B:GLU8 4.4 28.1 1.0 CA B:PHE6 4.6 26.7 1.0 CA B:GLU8 4.8 26.8 1.0 N B:PHE6 4.9 29.1 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose


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 Galactokinase From Bifidobacterium Infantis in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na721 b:37.8 occ:1.00 O B:HOH869 2.4 32.8 1.0 OD1 B:ASP236 2.4 20.6 1.0 O B:GLY136 2.8 33.1 1.0 CG B:ASP236 3.2 28.1 1.0 OD2 B:ASP236 3.3 36.1 1.0 C B:GLY136 3.3 37.6 1.0 CA B:SER137 3.5 30.8 1.0 CA B:GLN238 3.6 25.8 1.0 N B:SER137 3.7 33.5 1.0 N B:GLN238 3.7 21.0 1.0 NE2 B:GLN238 3.9 30.8 0.7 O B:HOH993 4.0 37.5 1.0 OG B:SER137 4.1 40.8 1.0 NE2 B:HIS241 4.2 53.9 1.0 CA B:GLY371 4.2 19.4 1.0 CB B:SER137 4.3 36.3 1.0 N B:GLY371 4.3 17.1 1.0 CA B:GLY136 4.4 41.0 1.0 C B:GLN238 4.4 27.4 1.0 C B:SER137 4.5 23.1 1.0 N B:ALA239 4.6 26.3 1.0 O B:LEU135 4.6 44.0 1.0 O B:GLY371 4.6 22.8 1.0 CB B:ASP236 4.6 23.4 1.0 CG B:GLN238 4.7 28.8 0.7 CD B:GLN238 4.7 29.3 0.7 C B:GLY371 4.7 19.6 1.0 CB B:GLN238 4.7 29.1 1.0 CD2 B:HIS241 4.8 50.8 1.0 NH2 B:ARG402 4.8 43.8 1.0 O B:ALA239 4.8 37.2 1.0 O B:SER137 4.8 19.1 1.0 C B:THR237 5.0 24.2 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose


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 Galactokinase From Bifidobacterium Infantis in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na722 b:40.2 occ:1.00 OE1 B:GLU415 2.7 26.2 1.0 CD B:GLU415 3.3 27.0 1.0 OE2 B:GLU415 3.6 27.5 1.0 O B:HOH868 3.7 30.5 1.0 O B:HOH1007 3.7 44.8 1.0 ND1 B:HIS12 3.7 34.9 1.0 OG B:SER413 4.1 19.8 1.0 CG B:HIS12 4.3 30.8 1.0 O B:ARG414 4.3 19.5 0.5 CE1 B:HIS12 4.4 33.8 1.0 O B:ARG414 4.4 22.8 0.5 CG B:GLU415 4.5 26.7 1.0 CB B:HIS12 4.5 25.8 1.0 CA B:GLU415 4.5 20.6 1.0 O B:HOH807 4.6 31.2 1.0 CB B:GLU415 4.8 24.3 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na612 b:48.5 occ:1.00 OD2 C:ASP391 2.5 47.9 1.0 CG C:ASP391 3.6 37.4 1.0 OD1 C:ASP391 4.0 42.0 1.0 NE2 C:GLN387 4.2 36.9 1.0 CG C:GLN387 4.4 33.6 1.0 CD C:GLN387 4.7 34.0 1.0 CB C:ASP391 4.9 27.1 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na609 b:42.9 occ:1.00 OD2 D:ASP352 2.3 37.6 1.0 CG D:ASP352 3.6 42.0 1.0 NH2 D:ARG392 4.2 28.1 1.0 OD1 D:ASP352 4.3 38.5 1.0 CB D:ASP352 4.6 30.7 1.0 CG1 D:ILE349 4.7 27.3 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na610 b:51.0 occ:1.00 OE1 D:GLU294 2.4 49.8 1.0 CD D:GLU294 3.4 49.9 1.0 CE D:LYS297 3.4 22.5 1.0 CB D:GLU294 3.4 36.0 1.0 CG D:GLU294 3.6 44.8 1.0 CA D:GLU294 3.8 32.4 1.0 CD D:LYS297 4.1 22.5 1.0 N D:GLU294 4.3 30.8 1.0 NZ D:LYS297 4.6 26.2 1.0 OE2 D:GLU294 4.6 46.4 1.0 O D:PRO292 4.6 37.8 1.0

T.Keenan, F.Parmeggiani, C.Q.Fontenelle, J.Malassis, J.Vendeville, W.A.Offen, P.Both, K.Huang, A.Marchesi, A.Heyam, G.J.Davies, B.Linclau, S.L.Flitsch, M.A.Fascione. Substrate Promiscuity of Wild-Type Sugar Kinases: Chemo-Enzymatic Synthesis of Multi-Fluorinated Monosaccharide-1-Phosphates. To Be Published.