Sodium in PDB 7xld: Crystal Structure of Isdh Linker-NEAT3 Bound to A Nanobody (Vhh)

The structure of Crystal Structure of Isdh Linker-NEAT3 Bound to A Nanobody (Vhh), PDB code: 7xld was solved by J.M.M.Caaveiro, S.Valenciano-Bellido, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.90 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.13, 49.42, 53.94, 90, 99.54, 90
R / Rfree (%)	14.8 / 19.7

The structure of Crystal Structure of Isdh Linker-NEAT3 Bound to A Nanobody (Vhh) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Isdh Linker-NEAT3 Bound to A Nanobody (Vhh) (pdb code 7xld). 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 Crystal Structure of Isdh Linker-NEAT3 Bound to A Nanobody (Vhh), PDB code: 7xld:

Sodium binding site 1 out of 1 in the Crystal Structure of Isdh Linker-NEAT3 Bound to A Nanobody (Vhh)


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 Isdh Linker-NEAT3 Bound to A Nanobody (Vhh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:34.0 occ:0.50 OE1 A:GLU556 2.4 27.8 1.0 O A:GLU562 2.6 19.3 1.0 O A:HOH830 2.6 40.1 1.0 OG A:SER561 3.0 36.5 1.0 CD A:GLU556 3.4 24.7 1.0 C A:GLU562 3.7 15.6 1.0 CG A:GLU556 3.7 19.7 1.0 CB A:SER561 3.8 28.2 1.0 O B:HOH375 3.8 32.9 1.0 O A:HOH859 3.9 28.9 0.6 C A:SER561 4.1 17.8 1.0 N A:GLU562 4.1 17.6 1.0 O B:HOH328 4.2 23.9 1.0 O A:SER561 4.3 17.0 1.0 CA A:GLU562 4.5 17.2 1.0 OE2 A:GLU556 4.5 25.1 1.0 CA A:SER561 4.6 22.2 1.0 N A:SER563 4.6 15.1 1.0 MG B:MG201 4.7 15.2 1.0 CA A:SER563 4.9 14.1 1.0

S.Valenciano-Bellido, J.M.M.Caaveiro, M.Nakakido, D.Kuroda, I.Nakagawa, K.Tsumoto. Generation of A Specific Antibody Against the Linker-NEAT3 Region of the Isdh Protein of S. Aureus Inhibiting Bacterial Growth Under Iron Limiting Conditions To Be Published.