Sodium in PDB 5vm6: The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T10

The structure of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T10, PDB code: 5vm6 was solved by S.Tabares-Da Rosa, G.Gonzalez-Sapienza, D.K.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.59 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.769, 36.387, 44.598, 90.00, 111.18, 90.00
R / Rfree (%)	17.2 / 19.3

The structure of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T10 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T10 (pdb code 5vm6). 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 The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T10, PDB code: 5vm6:

Sodium binding site 1 out of 1 in the The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Hapten Triclocarban Bound to the Single Domain Camelid Nanobody Vhh T10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:21.9 occ:1.00 OE2 A:GLU48 2.6 12.6 1.0 O4 A:SO4202 2.7 17.8 1.0 CD A:GLU48 3.4 11.2 1.0 OE1 A:GLU48 3.6 11.4 1.0 CG A:LYS45 3.8 6.6 1.0 S A:SO4202 4.0 15.4 1.0 O A:HOH358 4.0 18.7 1.0 CD A:LYS45 4.0 6.9 1.0 O A:HOH359 4.1 23.7 1.0 O2 A:SO4202 4.1 15.8 1.0 CB A:LYS45 4.3 6.6 1.0 CE A:LYS45 4.4 7.1 1.0 CD1 A:ILE42 4.5 8.1 1.0 O3 A:SO4202 4.8 17.9 1.0 CG A:GLU48 4.9 10.2 1.0 O1 A:SO4202 5.0 18.8 1.0 O A:HOH309 5.0 14.0 1.0

S.Tabares-Da Rosa, L.A.Wogulis, M.D.Wogulis, G.Gonzalez-Sapienza, D.K.Wilson. Structure and Specificity of Several Triclocarban-Binding Single Domain Camelid Antibody Fragments. J. Mol. Recognit. V. 32 E2755 2019.
ISSN: ISSN 1099-1352
PubMed: 30033524
DOI: 10.1002/JMR.2755