Sodium in PDB 5dxd: Crystal Structure of Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus

The structure of Crystal Structure of Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus, PDB code: 5dxd was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.43 / 1.70
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	52.390, 52.390, 223.350, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.9

The binding sites of Sodium atom in the Crystal Structure of Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus (pdb code 5dxd). 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 Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus, PDB code: 5dxd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus


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 Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na300 b:8.3 occ:1.00 O A:GLU31 2.3 11.4 1.0 OD1 A:ASP252 2.3 9.8 1.0 O A:ASP252 2.4 13.7 1.0 O A:SER82 2.4 7.7 1.0 OG A:SER82 2.4 17.6 1.0 O A:HOH423 2.5 10.0 1.0 CB A:SER82 3.4 15.8 1.0 C A:ASP252 3.4 12.4 1.0 C A:GLU31 3.4 8.4 1.0 C A:SER82 3.4 12.9 1.0 CG A:ASP252 3.5 8.4 1.0 CA A:ASP252 3.8 10.8 1.0 CA A:SER82 3.9 12.3 1.0 CA A:GLU31 4.1 13.7 1.0 CB A:ASP252 4.2 9.0 1.0 OD2 A:ASP252 4.3 12.7 1.0 CB A:GLU31 4.3 11.8 1.0 O A:HOH463 4.4 18.4 1.0 O A:HOH555 4.5 17.8 1.0 OE1 A:GLU31 4.5 13.5 1.0 OD1 A:ASP33 4.5 12.2 1.0 N A:TYR253 4.5 9.0 1.0 N A:PHE32 4.5 9.2 1.0 CB A:PHE32 4.6 11.9 1.0 N A:ASN83 4.6 12.9 1.0 OD1 A:ASN83 4.8 14.1 1.0 CB A:TYR253 4.8 6.1 1.0 C A:PHE32 4.8 12.5 1.0 CA A:PHE32 4.8 12.5 1.0 CA A:TYR253 4.9 5.9 1.0 O A:PHE32 4.9 13.3 1.0 CA A:ASN83 5.0 10.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus


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 Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abscessus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na300 b:10.1 occ:1.00 O B:HOH474 2.3 13.9 1.0 OG B:SER82 2.3 11.0 1.0 O B:SER82 2.3 14.0 1.0 O B:GLU31 2.4 9.2 1.0 OD1 B:ASP252 2.5 12.1 1.0 O B:ASP252 2.7 7.8 1.0 O B:HOH475 2.8 18.2 1.0 CB B:SER82 3.2 14.2 1.0 C B:SER82 3.3 14.5 1.0 C B:GLU31 3.5 12.2 1.0 C B:ASP252 3.6 7.7 1.0 CG B:ASP252 3.6 9.1 1.0 CA B:SER82 3.7 15.2 1.0 CA B:ASP252 4.0 11.0 1.0 CA B:GLU31 4.1 9.1 1.0 CB B:GLU31 4.3 12.1 1.0 CB B:ASP252 4.4 10.7 1.0 OD2 B:ASP252 4.4 12.7 1.0 OD1 B:ASP33 4.5 18.9 1.0 N B:ASN83 4.5 17.8 1.0 N B:PHE32 4.6 12.2 1.0 CB B:PHE32 4.7 10.6 1.0 OE1 B:GLU31 4.7 12.7 1.0 N B:TYR253 4.7 8.0 1.0 OD1 B:ASN83 4.7 16.6 1.0 C B:PHE32 4.8 13.3 1.0 CA B:PHE32 4.9 12.7 1.0 O B:PHE32 5.0 15.5 1.0 CA B:ASN83 5.0 16.7 1.0

J.Abendroth, D.R.Davies, D.D.Lorimer, T.E.Edwards. Crystal Structure of Putative Beta-Glucanase (RV0315 Ortholog) From Mycobacterium Abcesus To Be Published.