Sodium in PDB 8gyr: Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga

The structure of Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga, PDB code: 8gyr was solved by P.Kumar, M.Akif, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.92 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.219, 63.905, 171.839, 90, 90, 90
R / Rfree (%)	20.8 / 23.4

The structure of Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom
Potassium	(K)	5 atoms
Iodine	(I)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga (pdb code 8gyr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga, PDB code: 8gyr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:19.4 occ:1.00 N A:THR159 3.7 25.9 1.0 CE A:LYS108 3.7 24.0 1.0 CD A:LYS108 3.8 24.6 1.0 CA A:GLY158 3.9 24.0 1.0 OG1 A:THR159 4.0 32.3 1.0 CG2 A:THR159 4.1 30.3 1.0 C A:GLY158 4.3 25.5 1.0 CB A:THR159 4.5 31.1 1.0 CA A:THR159 4.7 29.1 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:6.4 occ:1.00 O1 A:EDO205 2.0 18.7 1.0 C1 A:EDO205 2.8 23.1 1.0 OG1 A:THR75 3.2 10.5 1.0 O A:SER73 3.4 11.1 1.0 N A:SER48 3.6 11.8 1.0 CB A:SER48 3.8 15.3 1.0 CA A:SER48 3.8 14.6 1.0 C A:SER47 3.9 11.6 1.0 CG A:LYS46 3.9 21.4 1.0 CE A:LYS46 4.0 26.1 1.0 CB A:THR75 4.0 10.2 1.0 C2 A:EDO205 4.1 24.3 1.0 C A:SER73 4.1 11.0 1.0 O A:LYS46 4.1 10.5 1.0 O A:HOH429 4.1 14.1 1.0 N A:THR75 4.2 9.9 1.0 CA A:SER47 4.3 12.4 1.0 CD A:LYS46 4.4 25.6 1.0 O A:SER47 4.4 13.1 1.0 C A:LYS46 4.4 12.1 1.0 C A:ILE74 4.5 10.3 1.0 N A:SER47 4.5 11.5 1.0 CA A:ILE74 4.6 10.4 1.0 N A:ILE74 4.6 10.2 1.0 CB A:SER73 4.6 12.0 1.0 O A:HOH383 4.7 25.1 1.0 CA A:THR75 4.8 9.3 1.0 OG A:SER48 4.8 13.1 1.0 NZ A:LYS46 4.8 27.6 1.0 CA A:SER73 5.0 12.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:35.6 occ:1.00 CB A:ALA68 3.8 13.5 1.0 CD A:LYS50 4.2 24.5 1.0 CB A:LYS50 4.3 18.7 1.0 N A:ALA51 4.3 12.8 1.0 CG A:LYS50 4.4 21.5 1.0 CA A:ALA51 4.5 12.3 1.0 CB A:ALA51 4.6 13.3 1.0 C A:LYS50 4.6 14.4 1.0 CA A:LYS50 5.0 14.7 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:10.3 occ:1.00 N B:ASN139 3.6 17.5 1.0 CB B:ASN139 4.1 21.4 1.0 ND2 B:ASN139 4.3 30.4 1.0 CG B:ASN139 4.4 26.1 1.0 CA B:ASN138 4.4 19.4 1.0 CA B:ASN139 4.4 19.6 1.0 OD1 B:ASN138 4.5 26.7 1.0 C B:ASN138 4.5 18.2 1.0 O B:HOH315 4.8 36.0 1.0 N B:SER140 4.9 21.0 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of A Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga


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 Variable Region Segment of Leptospira Host- Interacting Outer Surface Protein, Liga within 5.0Å range: probe atom residue distance (Å) B Occ B:Na210 b:15.1 occ:1.00 OE1 B:GLN42 2.2 19.6 0.5 O B:HOH450 2.3 43.2 1.0 O B:HOH403 2.5 32.1 1.0 CD B:GLN42 3.3 20.1 0.5 NE2 B:GLN42 3.7 19.6 0.5 CG2 B:ILE39 3.9 17.2 1.0 CD2 B:LEU78 3.9 24.2 1.0 CZ B:PHE31 4.2 23.2 1.0 CE2 B:PHE31 4.5 24.1 1.0 NZ B:LYS37 4.6 46.7 1.0 CG B:GLN42 4.6 20.4 0.5 CB B:ILE39 4.7 16.6 1.0 CD2 B:LEU5 4.7 17.7 1.0 CB B:GLN42 4.9 18.9 1.0 O B:HOH404 5.0 25.6 1.0 CD1 B:LEU5 5.0 16.8 1.0

P.Kumar, P.Vyas, S.M.Faisal, Y.F.Chang, M.Akif. Crystal Structure of A Variable Region Segment of Leptospira Host-Interacting Outer Surface Protein, Liga, Reveals the Orientation of Ig-Like Domains. Int.J.Biol.Macromol. 25445 2023.
ISSN: ISSN 0141-8130
PubMed: 37336372
DOI: 10.1016/J.IJBIOMAC.2023.125445