Sodium in PDB 3htl: Structure of the Corynebacterium Diphtheriae Major Pilin Spaa Points to A Modular Pilus Assembly with Stabilizing Isopeptide Bonds

The structure of Structure of the Corynebacterium Diphtheriae Major Pilin Spaa Points to A Modular Pilus Assembly with Stabilizing Isopeptide Bonds, PDB code: 3htl was solved by H.J.Kang, N.G.Paterson, A.H.Gaspar, H.Ton-That, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.22 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.780, 64.037, 199.192, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 24.2

The structure of Structure of the Corynebacterium Diphtheriae Major Pilin Spaa Points to A Modular Pilus Assembly with Stabilizing Isopeptide Bonds also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of the Corynebacterium Diphtheriae Major Pilin Spaa Points to A Modular Pilus Assembly with Stabilizing Isopeptide Bonds (pdb code 3htl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Corynebacterium Diphtheriae Major Pilin Spaa Points to A Modular Pilus Assembly with Stabilizing Isopeptide Bonds, PDB code: 3htl:

Sodium binding site 1 out of 1 in the Structure of the Corynebacterium Diphtheriae Major Pilin Spaa Points to A Modular Pilus Assembly with Stabilizing Isopeptide Bonds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Corynebacterium Diphtheriae Major Pilin Spaa Points to A Modular Pilus Assembly with Stabilizing Isopeptide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ X:Na487 b:47.5 occ:1.00 OD1 X:ASN482 2.2 38.2 1.0 O X:GLU454 2.6 28.6 1.0 OG1 X:THR449 2.7 27.7 1.0 CG X:ASN482 3.0 40.5 1.0 OE1 X:GLU446 3.3 27.1 1.0 CB X:THR449 3.3 25.3 1.0 CB X:ASN482 3.4 39.6 1.0 C X:GLU454 3.5 28.9 1.0 O X:HOH991 3.5 44.9 1.0 OE2 X:GLU446 3.6 27.2 1.0 CG2 X:THR449 3.6 27.3 1.0 CD X:GLU446 3.8 25.4 1.0 CB X:TYR453 3.8 29.8 1.0 N X:LEU455 4.1 27.8 1.0 N X:GLU454 4.2 29.4 1.0 CA X:LEU455 4.2 27.9 1.0 CA X:ASN482 4.2 39.8 1.0 CD1 X:LEU456 4.4 34.9 1.0 C X:TYR453 4.4 29.4 1.0 CA X:GLU454 4.5 29.6 1.0 NZ X:LYS363 4.5 26.4 1.0 CA X:THR449 4.7 25.9 1.0 N X:LYS483 4.8 43.3 1.0 CA X:TYR453 4.8 30.2 1.0 C X:LEU455 4.8 28.1 1.0 N X:LEU456 4.8 28.6 1.0 CG X:TYR453 4.8 29.3 1.0 O X:TYR453 4.9 29.7 1.0 C X:ASN482 4.9 41.4 1.0 CE X:LYS363 4.9 27.1 1.0 CE2 X:PHE365 5.0 26.6 1.0

H.J.Kang, N.G.Paterson, A.H.Gaspar, H.Ton-That, E.N.Baker. The Corynebacterium Diphtheriae Shaft Pilin Spaa Is Built of Tandem Ig-Like Modules with Stabilizing Isopeptide and Disulfide Bonds Proc.Natl.Acad.Sci.Usa V. 106 16967 2009.
ISSN: ISSN 0027-8424
PubMed: 19805181
DOI: 10.1073/PNAS.0906826106