Sodium in PDB 4igb: Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707

The structure of Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707, PDB code: 4igb was solved by A.Nylander, G.Svensater, D.B.Senadheera, D.G.Cvitkovitch, J.R.Davies, K.Persson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.07 / 2.09
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.131, 158.115, 164.265, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.5

The binding sites of Sodium atom in the Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707 (pdb code 4igb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707, PDB code: 4igb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707


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 the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:29.6 occ:1.00 O1 A:SO4502 2.3 23.4 0.7 O A:HOH1003 2.3 29.8 1.0 O A:THR271 2.4 28.5 1.0 OD1 A:ASP221 2.5 18.6 1.0 OD2 A:ASP223 2.6 28.5 1.0 O A:HOH1001 2.6 34.7 1.0 CG A:ASP221 3.3 33.0 1.0 CG A:ASP223 3.3 28.7 1.0 OD2 A:ASP221 3.4 20.6 1.0 OD1 A:ASP223 3.5 25.9 1.0 C A:THR271 3.6 27.8 1.0 S A:SO4502 3.6 36.8 0.7 OE1 A:GLU277 3.9 41.8 1.0 O3 A:SO4502 4.0 28.6 0.7 N A:THR271 4.1 26.1 1.0 OG1 A:THR271 4.2 17.4 1.0 O4 A:SO4502 4.3 35.6 0.7 CA A:THR271 4.4 25.7 1.0 N A:GLY272 4.5 28.7 1.0 CA A:GLY272 4.6 21.4 1.0 O2 A:SO4502 4.6 44.4 0.7 CB A:ASP223 4.6 21.4 1.0 CD A:GLU277 4.7 32.5 1.0 CG2 A:ILE270 4.7 36.4 1.0 CB A:ASP221 4.7 19.6 1.0 CG A:GLU277 4.7 24.6 1.0 CB A:THR271 4.9 24.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707


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 the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:31.9 occ:0.72 O B:HOH950 2.4 37.3 1.0 O3 B:SO4502 2.4 29.8 0.6 O B:THR271 2.6 33.4 1.0 OD1 B:ASP221 2.6 24.7 1.0 OD2 B:ASP223 2.7 28.9 1.0 OD2 B:ASP221 3.3 27.1 1.0 CG B:ASP221 3.3 31.5 1.0 CG B:ASP223 3.4 29.6 1.0 OD1 B:ASP223 3.6 23.7 1.0 S B:SO4502 3.7 51.1 0.6 C B:THR271 3.7 35.2 1.0 OE2 B:GLU277 4.0 46.5 1.0 O2 B:SO4502 4.0 42.3 0.6 N B:THR271 4.3 24.4 1.0 OG1 B:THR271 4.3 21.7 1.0 O4 B:SO4502 4.4 53.1 0.6 CA B:THR271 4.6 30.3 1.0 N B:GLY272 4.7 32.0 1.0 CA B:GLY272 4.7 29.8 1.0 CD B:GLU277 4.7 31.8 1.0 CB B:ASP223 4.7 21.2 1.0 CG2 B:ILE270 4.7 32.0 1.0 O1 B:SO4502 4.8 57.2 0.6 CB B:ASP221 4.8 17.5 1.0 CG B:GLU277 4.8 31.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707


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 the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:40.5 occ:0.64 O2 C:SO4502 2.0 54.4 0.8 OD1 C:ASP221 2.5 19.2 1.0 O C:THR271 2.6 32.5 1.0 OE2 C:GLU277 2.7 43.6 1.0 CG C:ASP221 3.1 30.6 1.0 OD2 C:ASP221 3.2 25.7 1.0 S C:SO4502 3.4 75.1 0.8 OD2 C:ASP223 3.5 30.5 1.0 CD C:GLU277 3.7 30.8 1.0 C C:THR271 3.7 32.2 1.0 O1 C:SO4502 3.9 65.9 0.8 CG C:GLU277 3.9 27.1 1.0 O3 C:SO4502 4.1 74.9 0.8 CA C:GLY272 4.1 30.3 1.0 CG C:ASP223 4.3 32.5 1.0 O4 C:SO4502 4.4 60.2 0.8 N C:GLY272 4.4 34.5 1.0 CB C:ASP221 4.4 14.7 1.0 OG1 C:THR271 4.5 22.7 1.0 OD1 C:ASP223 4.5 21.9 1.0 OE1 C:GLU277 4.8 34.5 1.0 CA C:THR271 4.9 31.2 1.0 N C:THR271 4.9 30.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707


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 the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na504 b:49.5 occ:0.91 O D:ASP221 2.8 21.2 1.0 OE2 D:GLU232 2.8 24.2 1.0 O D:SER303 2.9 23.9 1.0 OE1 D:GLU232 3.1 24.3 1.0 O D:HOH759 3.1 43.8 1.0 OD2 D:ASP221 3.3 25.6 1.0 CD D:GLU232 3.3 27.2 1.0 O3 D:SO4502 3.5 78.4 0.7 CG D:ASP221 3.9 29.1 1.0 OD1 D:ASP223 3.9 25.4 1.0 C D:SER303 3.9 26.1 1.0 C D:ASP221 4.0 21.9 1.0 O D:HOH648 4.1 31.9 1.0 O4 D:SO4502 4.2 43.2 0.7 S D:SO4502 4.2 70.6 0.7 CB D:ASP221 4.2 19.2 1.0 O1 D:SO4502 4.2 60.4 0.7 CA D:ALA304 4.3 19.4 1.0 O D:HOH698 4.3 25.2 1.0 N D:ALA304 4.5 24.4 1.0 CB D:ALA304 4.5 22.2 1.0 OH D:TYR296 4.7 23.2 1.0 OD1 D:ASP221 4.7 27.8 1.0 N D:ASP223 4.7 20.8 1.0 O D:HOH827 4.7 38.6 1.0 CA D:ASP221 4.8 18.8 1.0 N D:SER303 4.8 21.9 1.0 CG D:GLU232 4.8 21.5 1.0 O D:THR220 4.9 18.6 1.0 N D:ILE222 4.9 21.0 1.0 CA D:ILE222 4.9 17.2 1.0

A.Nylander, G.Svensater, D.B.Senadheera, D.G.Cvitkovitch, J.R.Davies, K.Persson. Structural and Functional Analysis of the N-Terminal Domain of the Streptococcus Gordonii Adhesin SGO0707 Plos One V. 8 63768 2013.
ISSN: ESSN 1932-6203
PubMed: 23691093
DOI: 10.1371/JOURNAL.PONE.0063768