Sodium in PDB 7p1s: Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.

The structure of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid., PDB code: 7p1s was solved by T.M.Gloster, S.A.Mcmahon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	179.01 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.646, 179.008, 97.292, 90, 104.04, 90
R / Rfree (%)	26 / 28.9

The binding sites of Sodium atom in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. (pdb code 7p1s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid., PDB code: 7p1s:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:37.5 occ:1.00 OD1 A:ASP90 1.9 35.4 1.0 O A:HOH625 2.2 37.1 1.0 O A:HOH698 2.5 37.6 1.0 O A:GLY121 2.5 37.9 1.0 OD1 A:ASN92 2.6 32.6 1.0 O A:HOH702 2.8 30.4 1.0 O A:GLY119 2.9 35.4 1.0 CG A:ASP90 2.9 30.9 1.0 OD2 A:ASP90 3.3 37.5 1.0 CG A:ASN92 3.6 31.4 1.0 C A:GLY121 3.7 34.5 1.0 C A:GLY119 3.8 33.2 1.0 ND2 A:ASN92 4.0 32.5 1.0 O D:HOH678 4.0 32.7 1.0 CB A:ASP90 4.3 30.9 1.0 O A:HIS123 4.3 24.1 1.0 CA A:GLY119 4.3 31.1 1.0 CA A:PRO122 4.3 30.2 1.0 N A:PRO122 4.4 31.0 1.0 N A:HIS123 4.5 25.6 1.0 N A:ILE91 4.5 28.7 1.0 CA A:ASP90 4.5 29.5 1.0 O A:THR120 4.6 34.1 1.0 C A:PRO122 4.6 27.5 1.0 O A:ILE91 4.6 23.9 1.0 C A:ASP90 4.6 30.3 1.0 C A:THR120 4.7 37.8 1.0 CD A:ARG82 4.7 39.8 1.0 N A:GLY121 4.8 35.6 1.0 C A:ILE91 4.8 25.8 1.0 N A:THR120 4.8 36.8 1.0 CA A:GLY121 4.9 35.6 1.0 NH1 A:ARG82 5.0 44.4 1.0 CB A:ASN92 5.0 30.4 1.0

Sodium binding site 2 out of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:23.0 occ:1.00 O B:HOH672 1.9 30.1 1.0 O B:GLY119 2.3 22.5 1.0 O B:GLY121 2.3 20.7 1.0 OD1 B:ASP90 2.5 15.4 1.0 O B:HOH759 2.5 36.2 1.0 OD1 B:ASN92 2.7 17.9 1.0 C B:GLY119 3.3 22.4 1.0 CG B:ASP90 3.5 16.0 1.0 C B:GLY121 3.6 19.6 1.0 CG B:ASN92 3.7 17.4 1.0 OD2 B:ASP90 3.9 16.8 1.0 CA B:GLY119 3.9 22.6 1.0 ND2 B:ASN92 4.0 18.9 1.0 O C:HOH602 4.0 22.6 1.0 O B:THR120 4.1 18.7 1.0 C B:THR120 4.1 21.5 1.0 N B:GLY121 4.3 20.2 1.0 N B:THR120 4.3 21.9 1.0 N B:PRO122 4.4 18.4 1.0 CA B:GLY121 4.5 20.8 1.0 CA B:PRO122 4.5 18.4 1.0 O B:HIS123 4.5 21.0 1.0 N B:HIS123 4.6 18.6 1.0 CA B:THR120 4.6 23.0 1.0 O B:ILE91 4.8 14.3 1.0 C B:PRO122 4.8 19.1 1.0 O B:HOH752 4.9 30.4 1.0 CB B:ASP90 4.9 14.8 1.0 N B:ILE91 5.0 14.0 1.0

Sodium binding site 3 out of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:22.7 occ:1.00 O C:HOH614 1.9 12.0 1.0 O C:HOH627 2.2 34.5 1.0 OD1 C:ASN92 2.3 18.9 1.0 OD1 C:ASP90 2.4 13.9 1.0 O C:GLY119 2.4 17.9 1.0 O C:GLY121 2.6 18.8 1.0 O C:HOH711 2.8 27.1 1.0 C C:GLY119 3.3 20.1 1.0 CG C:ASN92 3.3 19.2 1.0 CG C:ASP90 3.5 15.5 1.0 ND2 C:ASN92 3.7 19.3 1.0 CA C:GLY119 3.8 19.2 1.0 C C:GLY121 3.8 18.0 1.0 OD2 C:ASP90 4.0 16.8 1.0 O C:THR120 4.2 22.6 1.0 O B:HOH621 4.3 20.3 1.0 C C:THR120 4.3 21.8 1.0 O C:HIS123 4.3 15.7 1.0 N C:THR120 4.4 20.5 1.0 O C:ILE91 4.5 14.8 1.0 N C:GLY121 4.5 20.5 1.0 N C:HIS123 4.6 17.1 1.0 N C:PRO122 4.6 17.2 1.0 CA C:PRO122 4.7 17.0 1.0 CB C:ASN92 4.7 17.3 1.0 N C:ILE91 4.7 12.5 1.0 C C:ILE91 4.8 14.0 1.0 CA C:GLY121 4.8 19.8 1.0 CB C:ASP90 4.8 14.1 1.0 CA C:THR120 4.8 21.8 1.0 C C:PRO122 4.9 17.0 1.0 CD1 C:TRP125 4.9 17.3 1.0 CA C:ASP90 5.0 13.9 1.0 CA C:ASN92 5.0 17.1 1.0 C C:ASP90 5.0 13.7 1.0

Sodium binding site 4 out of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na502 b:31.0 occ:1.00 O D:HOH618 2.1 18.3 1.0 OD1 D:ASP90 2.1 28.3 1.0 OD1 D:ASN92 2.4 40.8 1.0 O D:GLY121 2.6 35.5 1.0 O D:GLY119 2.6 35.9 1.0 O D:HOH679 2.8 44.5 1.0 CG D:ASP90 3.2 29.3 1.0 CG D:ASN92 3.4 36.4 1.0 C D:GLY119 3.6 33.4 1.0 OD2 D:ASP90 3.6 33.7 1.0 C D:GLY121 3.8 31.2 1.0 ND2 D:ASN92 3.8 39.6 1.0 CA D:GLY119 4.0 32.9 1.0 O D:HIS123 4.3 25.7 1.0 O D:THR120 4.4 31.1 1.0 C D:THR120 4.5 36.4 1.0 CA D:PRO122 4.5 26.2 1.0 O D:ILE91 4.5 25.6 1.0 CB D:ASP90 4.5 28.2 1.0 N D:PRO122 4.6 27.0 1.0 N D:HIS123 4.6 23.9 1.0 N D:THR120 4.6 34.6 1.0 N D:ILE91 4.6 28.7 1.0 N D:GLY121 4.6 34.0 1.0 O D:HOH696 4.7 35.4 1.0 C D:PRO122 4.8 24.2 1.0 CA D:ASP90 4.8 26.9 1.0 C D:ILE91 4.8 26.6 1.0 CB D:ASN92 4.8 32.5 1.0 CD D:ARG82 4.8 44.6 1.0 CA D:GLY121 4.8 32.2 1.0 C D:ASP90 4.8 29.0 1.0

T.M.Gloster, S.A.Mcmahon. Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3-Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. To Be Published.