Sodium in PDB 6jbv: Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative

The structure of Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative, PDB code: 6jbv was solved by A.K.Megta, A.K.Mishra, A.Palva, I.Von Ossowski, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.56 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.779, 63.936, 131.112, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.3

The binding sites of Sodium atom in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative (pdb code 6jbv). 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 Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative, PDB code: 6jbv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative


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 Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:21.2 occ:1.00 OD1 A:ASP221 2.3 24.0 1.0 O A:ARG296 2.3 20.1 1.0 O A:GLY294 2.3 22.7 1.0 OG1 A:THR293 2.4 17.9 1.0 O A:HOH726 2.4 23.1 1.0 N A:GLY294 3.2 21.5 1.0 CG A:ASP221 3.3 24.8 1.0 CB A:THR293 3.3 18.3 1.0 C A:GLY294 3.3 23.0 1.0 C A:THR293 3.4 20.7 1.0 C A:ARG296 3.5 21.9 1.0 CB A:ASP221 3.5 22.1 1.0 O A:HOH602 3.6 30.7 1.0 CA A:GLY294 3.8 21.2 1.0 CA A:THR293 3.8 19.0 1.0 CA A:ASP221 3.9 21.3 1.0 O A:THR293 4.0 18.9 1.0 N A:ARG296 4.1 23.5 1.0 C A:ASP221 4.3 20.0 1.0 C A:GLU295 4.4 25.2 1.0 OD1 A:ASN292 4.4 17.9 1.0 N A:GLU295 4.4 23.7 1.0 N A:PHE297 4.4 21.7 1.0 O A:HOH770 4.4 30.5 1.0 CA A:ARG296 4.4 22.6 1.0 OD2 A:ASP221 4.4 25.6 1.0 N A:THR293 4.5 19.2 1.0 CA A:PHE297 4.5 22.1 1.0 CG2 A:THR293 4.6 18.8 1.0 O A:GLY354 4.6 23.8 1.0 O A:HOH660 4.6 33.5 1.0 O A:PRO222 4.7 17.8 1.0 CA A:GLU295 4.8 27.4 1.0 O A:ASP221 4.8 19.6 1.0 O A:GLU295 4.8 24.8 1.0 N A:PRO222 4.9 19.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative


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 Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:39.1 occ:1.00 O A:HOH787 2.3 44.8 1.0 OG A:SER189 2.4 28.7 1.0 O A:HOH701 2.4 44.2 1.0 O A:GLN110 2.5 26.0 1.0 O A:HOH609 2.5 29.5 1.0 NE2 A:GLN110 2.7 52.0 1.0 CB A:SER189 3.4 24.9 1.0 C A:GLN110 3.6 27.4 1.0 CD A:GLN110 3.8 46.5 1.0 CA A:ASN111 4.2 27.1 1.0 CG A:GLN110 4.2 40.1 1.0 O A:HOH679 4.3 31.5 1.0 N A:ASN111 4.3 23.9 1.0 CA A:SER189 4.4 22.9 1.0 O A:MSE112 4.5 23.8 1.0 OD1 A:ASN111 4.6 41.4 1.0 CA A:GLN110 4.6 28.1 1.0 C A:ASN111 4.7 25.2 1.0 O A:HOH684 4.7 38.2 1.0 OE1 A:GLN110 4.8 53.0 1.0 CD A:PRO190 4.9 22.0 1.0 CB A:GLN110 4.9 32.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative


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 Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Selenium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:38.2 occ:1.00 OE1 A:GLN346 2.2 37.8 1.0 O A:HOH779 2.7 37.5 1.0 O A:HOH627 2.8 23.9 1.0 N A:ARG367 3.0 21.7 1.0 CD1 A:TYR365 3.2 20.8 1.0 CD A:GLN346 3.3 33.9 1.0 CA A:PRO366 3.7 21.8 1.0 O A:ARG367 3.7 21.8 1.0 C A:PRO366 3.8 20.7 1.0 CG A:ARG367 3.8 27.8 1.0 NE2 A:GLN346 3.8 28.3 1.0 CE1 A:TYR365 3.9 21.7 1.0 CA A:ARG367 3.9 23.1 1.0 CB A:ARG367 4.1 27.2 1.0 CB A:PRO366 4.2 22.9 1.0 CG A:TYR365 4.2 20.5 1.0 C A:ARG367 4.3 21.9 1.0 CB A:TYR365 4.4 20.6 1.0 CG A:GLN346 4.5 31.0 1.0 O A:HOH683 4.7 38.4 1.0 CA A:TYR365 4.8 19.8 1.0 OH A:TYR369 4.8 19.9 1.0 CB A:GLN346 4.9 27.9 1.0 N A:PRO366 4.9 21.6 1.0 O A:PRO366 5.0 19.3 1.0

A.K.Megta, A.K.Mishra, A.Palva, I.Von Ossowski, V.Krishnan. Crystal Structure of Basal Pilin Spae Reveals the Molecular Basis of Its Incorporation in the Lactobacillar Spafed Pilus. J.Struct.Biol. V. 207 74 2019.
ISSN: ESSN 1095-8657
PubMed: 31026587
DOI: 10.1016/J.JSB.2019.04.016