Sodium in PDB 8gr6: Crystal Structure of Pilus-Specific Sortase C From Streptococcus Sanguinis

The structure of Crystal Structure of Pilus-Specific Sortase C From Streptococcus Sanguinis, PDB code: 8gr6 was solved by S.Yadav, P.Parijat, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.33 / 2.06
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	140.019, 140.019, 103.625, 90, 90, 120
R / Rfree (%)	17.8 / 19.9

The structure of Crystal Structure of Pilus-Specific Sortase C From Streptococcus Sanguinis also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Pilus-Specific Sortase C From Streptococcus Sanguinis (pdb code 8gr6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Pilus-Specific Sortase C From Streptococcus Sanguinis, PDB code: 8gr6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Pilus-Specific Sortase C From Streptococcus Sanguinis


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 Pilus-Specific Sortase C From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2103 b:52.2 occ:1.00 O A:HOH2236 2.6 47.5 1.0 O A:GLU69 2.7 41.3 1.0 O A:HOH2233 2.8 43.0 1.0 O A:HOH2206 2.9 38.6 1.0 CD1 A:ILE197 3.7 42.2 1.0 C A:GLU69 3.7 42.6 1.0 CA A:PRO74 3.8 42.6 1.0 CG1 A:ILE197 4.1 38.1 1.0 O A:HOH2246 4.1 51.5 1.0 CB A:PRO74 4.1 42.1 1.0 O A:HOH2214 4.1 45.6 1.0 CB A:GLU69 4.3 51.7 1.0 CA A:GLU69 4.4 47.3 1.0 CG A:PRO74 4.5 42.0 1.0 N A:GLU69 4.5 49.4 1.0 O A:VAL72 4.6 37.0 1.0 CG2 A:VAL72 4.6 44.2 1.0 N A:PRO74 4.6 40.8 1.0 N A:ASN75 4.6 45.6 1.0 O A:GLY130 4.6 35.8 1.0 N A:LYS70 4.6 41.8 1.0 CB A:ILE197 4.8 37.2 1.0 C A:PRO74 4.8 43.7 1.0 N A:ILE197 4.8 38.4 1.0 CA A:LYS70 4.9 44.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Pilus-Specific Sortase C From Streptococcus Sanguinis


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 Pilus-Specific Sortase C From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2104 b:44.0 occ:1.00 O A:GLY139 2.7 39.9 1.0 O A:ASN65 2.8 46.2 1.0 OG A:SER132 2.9 34.5 1.0 C A:ASN65 3.4 44.2 1.0 CB A:ASN65 3.5 40.1 1.0 CA A:THR140 3.7 37.1 1.0 CB A:SER132 3.7 35.5 1.0 CA A:ASN65 3.8 42.2 1.0 CG2 A:THR140 3.8 44.0 1.0 C A:GLY139 3.8 39.5 1.0 CD1 A:ILE197 3.9 42.2 1.0 CD1 A:LEU68 4.0 35.7 1.0 CG2 A:ILE197 4.0 40.4 1.0 CG A:ASN65 4.0 39.3 1.0 CB A:THR140 4.2 38.6 1.0 CE A:LYS70 4.3 55.6 1.0 N A:THR140 4.3 38.9 1.0 CB A:LEU68 4.4 41.6 1.0 NZ A:LYS70 4.4 59.5 1.0 OD1 A:ASN65 4.5 37.1 1.0 CA A:SER132 4.5 34.7 1.0 N A:GLN66 4.5 44.3 1.0 CG A:LEU68 4.6 41.1 1.0 ND2 A:ASN65 4.6 38.4 1.0 N A:HIS141 4.7 37.5 1.0 CG1 A:ILE197 4.7 38.1 1.0 C A:THR140 4.8 38.3 1.0 CB A:ILE197 5.0 37.2 1.0

S.Yadav, P.Parijat, V.Krishnan. The Crystal Structure of Sortase C From An Early Colonizer of Dental Plaque, Streptococcus Sanguinis, Reveals An Active Open-Lid Conformation. Int.J.Biol.Macromol. 25183 2023.
ISSN: ISSN 0141-8130
PubMed: 37276901
DOI: 10.1016/J.IJBIOMAC.2023.125183