Sodium in PDB 8tx9: Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae

The structure of Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae, PDB code: 8tx9 was solved by D.M.Wood, C.R.Horne, S.Panjikar, R.C.J.Dobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.23 / 2.01
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	147.577, 147.577, 82.311, 90, 90, 90
R / Rfree (%)	21.1 / 27.1

The binding sites of Sodium atom in the Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae (pdb code 8tx9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae, PDB code: 8tx9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:66.8 occ:1.00 H A:SER225 2.1 113.7 1.0 HG12 A:ILE233 2.7 83.2 1.0 HB3 A:HIS224 2.7 116.3 1.0 HB3 A:SER97 2.8 86.0 1.0 N A:SER225 3.0 94.8 1.0 H A:GLN226 3.0 85.7 1.0 HA A:HIS224 3.2 105.0 1.0 OG A:SER225 3.2 76.7 1.0 HD2 A:HIS224 3.3 90.8 1.0 OG A:SER97 3.4 79.4 1.0 HG A:SER97 3.4 95.3 1.0 H A:ILE233 3.4 90.2 1.0 CB A:HIS224 3.4 97.0 1.0 CB A:SER97 3.4 71.6 1.0 HD11 A:ILE233 3.5 89.0 1.0 CG1 A:ILE233 3.5 69.3 1.0 CA A:HIS224 3.6 87.5 1.0 HG A:SER225 3.7 92.0 1.0 HA A:SER97 3.7 97.2 1.0 CD2 A:HIS224 3.8 75.6 1.0 C A:HIS224 3.8 95.5 1.0 N A:GLN226 3.8 71.4 1.0 HD13 A:ILE233 3.9 89.0 1.0 CG A:HIS224 3.9 88.1 1.0 CD1 A:ILE233 3.9 74.1 1.0 CA A:SER225 3.9 80.8 1.0 HG13 A:ILE233 3.9 83.2 1.0 HE3 A:MET101 3.9 95.3 1.0 CB A:SER225 4.0 73.2 1.0 HG2 A:GLN226 4.0 104.1 1.0 CA A:SER97 4.1 81.0 1.0 HA A:ARG232 4.2 81.8 1.0 HB2 A:GLN226 4.2 125.8 1.0 HB3 A:SER225 4.2 87.9 1.0 HG23 A:ILE233 4.2 96.2 1.0 HB2 A:SER97 4.3 86.0 1.0 N A:ILE233 4.3 75.2 1.0 HB2 A:HIS224 4.3 116.3 1.0 O A:SER97 4.3 67.2 1.0 C A:SER225 4.3 68.8 1.0 HG2 A:ARG232 4.4 98.9 1.0 C A:SER97 4.5 81.4 1.0 CB A:ILE233 4.7 74.5 1.0 CE A:MET101 4.7 79.4 1.0 CG A:GLN226 4.7 86.8 1.0 HA A:SER225 4.8 96.9 1.0 HE1 A:MET101 4.8 95.3 1.0 CB A:GLN226 4.8 104.9 1.0 HD12 A:ILE233 4.8 89.0 1.0 HB2 A:SER225 4.9 87.9 1.0 CG2 A:ILE233 4.9 80.1 1.0 HG3 A:GLN226 4.9 104.1 1.0 CA A:GLN226 4.9 104.0 1.0 NE2 A:HIS224 5.0 79.7 1.0 HB2 A:MET101 5.0 124.3 1.0 O A:HIS224 5.0 104.2 1.0 CA A:ARG232 5.0 68.2 1.0

Sodium binding site 2 out of 4 in the Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:31.1 occ:1.00 H C:SER225 2.5 50.1 1.0 H C:ILE233 2.8 39.9 1.0 HB3 C:HIS224 2.8 49.5 1.0 HD1 C:HIS224 2.9 50.1 1.0 HA C:ARG232 3.0 47.7 1.0 HG12 C:ILE233 3.0 43.2 1.0 H C:GLN226 3.0 44.3 1.0 HG C:SER97 3.0 58.2 1.0 HG2 C:GLN226 3.1 49.7 1.0 HB3 C:SER97 3.1 55.7 1.0 OG C:SER97 3.3 48.5 1.0 HB2 C:GLN226 3.3 57.9 1.0 N C:SER225 3.4 41.7 1.0 O C:HOH404 3.4 38.7 1.0 HG2 C:ARG232 3.5 50.8 1.0 N C:GLN226 3.5 36.9 1.0 HG23 C:ILE233 3.6 48.2 1.0 N C:ILE233 3.6 33.2 1.0 ND1 C:HIS224 3.6 41.8 1.0 CB C:HIS224 3.7 41.2 1.0 CB C:SER97 3.7 46.4 1.0 HG C:SER225 3.7 53.7 1.0 CG C:GLN226 3.7 41.4 1.0 HB3 C:ARG232 3.8 60.9 1.0 HG3 C:GLN226 3.8 49.7 1.0 CA C:ARG232 3.8 39.8 1.0 CB C:GLN226 3.9 48.2 1.0 HA C:HIS224 3.9 40.2 1.0 CG1 C:ILE233 3.9 36.0 1.0 OG C:SER225 4.0 44.8 1.0 CG C:HIS224 4.1 42.8 1.0 CA C:HIS224 4.1 33.5 1.0 CB C:ARG232 4.1 50.8 1.0 C C:SER225 4.2 46.3 1.0 C C:HIS224 4.2 32.1 1.0 CA C:SER225 4.2 45.6 1.0 C C:ARG232 4.2 37.3 1.0 CG C:ARG232 4.3 42.4 1.0 CA C:GLN226 4.3 46.6 1.0 HG13 C:ILE233 4.3 43.2 1.0 HB2 C:SER97 4.4 55.7 1.0 HB2 C:HIS224 4.4 49.5 1.0 CG2 C:ILE233 4.4 40.2 1.0 HA C:SER97 4.4 54.3 1.0 HE1 C:MSE101 4.5 46.1 0.6 CB C:ILE233 4.5 28.9 1.0 HE3 C:MSE101 4.6 46.0 0.9 HD13 C:ILE233 4.6 52.6 1.0 CA C:ILE233 4.6 26.9 1.0 CA C:SER97 4.7 45.2 1.0 O C:GLN231 4.7 42.9 1.0 O C:HOH439 4.7 46.6 1.0 HB3 C:GLN226 4.7 57.9 1.0 CB C:SER225 4.8 54.5 1.0 HG21 C:ILE233 4.8 48.2 1.0 CD1 C:ILE233 4.8 43.9 1.0 HE2 C:MSE101 4.8 46.1 1.0 O C:HOH457 4.8 61.0 1.0 CE1 C:HIS224 4.8 35.3 1.0 HE21 C:GLN226 4.9 50.3 1.0 HA C:GLN226 4.9 55.9 1.0 HG3 C:ARG232 4.9 50.8 1.0 N C:ARG232 4.9 32.6 1.0 HE1 C:MSE101 4.9 46.0 1.0 HD3 C:ARG232 5.0 54.6 1.0 HD11 C:ILE233 5.0 52.6 1.0

Sodium binding site 3 out of 4 in the Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:27.4 occ:1.00 H D:ILE233 2.6 35.4 1.0 H D:SER225 2.7 57.1 1.0 HG13 D:ILE233 2.7 42.5 1.0 HA D:ARG232 2.8 52.2 1.0 HB3 D:HIS224 2.9 49.5 1.0 H D:GLN226 3.0 42.5 1.0 HB3 D:SER97 3.0 47.0 1.0 HD1 D:HIS224 3.0 52.9 1.0 HG2 D:GLN226 3.2 40.6 1.0 HB2 D:GLN226 3.2 54.1 1.0 HD11 D:ILE233 3.2 49.3 1.0 OG D:SER97 3.3 39.1 1.0 N D:ILE233 3.4 29.5 1.0 N D:SER225 3.5 47.5 1.0 N D:GLN226 3.5 35.5 1.0 CG1 D:ILE233 3.6 35.5 1.0 HG2 D:ARG232 3.6 45.3 1.0 CB D:SER97 3.6 39.2 1.0 CA D:ARG232 3.7 43.5 1.0 ND1 D:HIS224 3.8 44.0 1.0 CB D:HIS224 3.8 41.2 1.0 CG D:GLN226 3.8 33.8 1.0 HB3 D:ARG232 3.8 53.1 1.0 HG3 D:GLN226 3.8 40.6 1.0 CB D:GLN226 3.9 45.1 1.0 CD1 D:ILE233 3.9 41.1 1.0 C D:ARG232 4.0 35.0 1.0 OG D:SER225 4.0 43.4 1.0 HA D:HIS224 4.0 48.9 1.0 HG D:SER97 4.1 46.9 1.0 CB D:ARG232 4.1 44.3 1.0 C D:SER225 4.2 43.1 1.0 HB D:ILE233 4.2 33.9 1.0 CG D:HIS224 4.2 52.0 1.0 HB2 D:SER97 4.2 47.0 1.0 HG12 D:ILE233 4.3 42.5 1.0 CA D:SER225 4.3 47.0 1.0 CA D:HIS224 4.3 40.7 1.0 CB D:ILE233 4.3 28.3 1.0 CA D:GLN226 4.3 33.3 1.0 CG D:ARG232 4.3 37.8 1.0 C D:HIS224 4.4 42.3 1.0 HB2 D:HIS224 4.4 49.5 1.0 CA D:ILE233 4.5 34.6 1.0 HA D:SER97 4.5 46.1 1.0 HD13 D:ILE233 4.5 49.3 1.0 HD12 D:ILE233 4.5 49.3 1.0 HG D:SER225 4.5 52.1 1.0 O D:GLN231 4.6 38.9 1.0 CA D:SER97 4.7 38.4 1.0 HB3 D:GLN226 4.7 54.1 1.0 CB D:SER225 4.7 52.4 1.0 O D:HOH442 4.7 55.3 1.0 HE3 D:MET101 4.8 51.9 1.0 N D:ARG232 4.8 35.1 1.0 HA D:GLN226 4.9 40.0 1.0 CE1 D:HIS224 4.9 37.3 1.0 HD3 D:ARG232 5.0 56.8 1.0 HA D:ILE233 5.0 41.5 1.0 O D:HOH422 5.0 44.8 1.0 HG3 D:ARG232 5.0 45.3 1.0

Sodium binding site 4 out of 4 in the Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Nan Regulatory Protein (Core Isomerase Domain) From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:57.4 occ:1.00 H B:GLN226 2.4 89.7 1.0 HB3 B:SER97 2.7 87.1 1.0 HG2 B:GLN226 2.8 84.3 1.0 HB2 B:GLN226 2.9 88.0 1.0 H B:ILE233 3.0 73.7 1.0 HB3 B:HIS224 3.0 95.8 1.0 OG B:SER97 3.0 77.5 1.0 HA B:ARG232 3.1 79.0 1.0 H B:SER225 3.1 109.8 1.0 HG12 B:ILE233 3.1 92.0 1.0 N B:GLN226 3.3 74.7 1.0 HD1 B:HIS224 3.3 74.3 1.0 CB B:SER97 3.3 72.6 1.0 CG B:GLN226 3.4 70.2 1.0 HG3 B:GLN226 3.4 84.3 1.0 HG21 B:ILE233 3.5 81.2 1.0 CB B:GLN226 3.5 73.4 1.0 N B:SER225 3.6 91.5 1.0 HG2 B:ARG232 3.6 76.9 1.0 HB2 B:SER225 3.6 102.0 1.0 N B:ILE233 3.7 61.4 1.0 HG B:SER97 3.8 93.0 1.0 CB B:HIS224 3.9 79.8 1.0 CA B:ARG232 3.9 65.8 1.0 HA B:HIS224 3.9 105.6 1.0 HB2 B:SER97 4.0 87.1 1.0 CA B:GLN226 4.0 74.0 1.0 HD11 B:ILE233 4.0 84.0 1.0 ND1 B:HIS224 4.0 74.3 1.0 CG1 B:ILE233 4.0 76.7 1.0 HA B:SER97 4.2 90.5 1.0 HB3 B:ARG232 4.2 70.9 1.0 C B:SER225 4.2 77.8 1.0 CA B:SER225 4.2 78.7 1.0 C B:HIS224 4.2 83.2 1.0 CA B:HIS224 4.3 88.0 1.0 CB B:SER225 4.3 85.0 1.0 CG B:ARG232 4.3 64.1 1.0 C B:ARG232 4.3 74.0 1.0 CB B:ARG232 4.3 59.1 1.0 CA B:SER97 4.4 75.4 1.0 HG3 B:ARG232 4.4 76.9 1.0 CG2 B:ILE233 4.4 67.7 1.0 HB3 B:GLN226 4.4 88.0 1.0 CG B:HIS224 4.4 71.1 1.0 HG B:SER225 4.5 101.7 1.0 OG B:SER225 4.5 84.8 1.0 HB2 B:HIS224 4.6 95.8 1.0 CD1 B:ILE233 4.6 70.0 1.0 CB B:ILE233 4.6 72.1 1.0 HA B:GLN226 4.6 88.8 1.0 HG13 B:ILE233 4.7 92.0 1.0 HE21 B:GLN226 4.8 112.9 1.0 CD B:GLN226 4.8 79.8 1.0 CA B:ILE233 4.8 68.2 1.0 HG22 B:ILE233 4.8 81.2 1.0 O B:GLN231 4.9 65.8 1.0 HG23 B:ILE233 5.0 81.2 1.0

D.M.Wood, R.C.J.Dobson. Structure of Isomerase Domain of the Nan-Regulatory Protein (Nanr) From Streptococcus Pneumoniae To Be Published.