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Sodium in PDB 8p88: X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody C4

Protein crystallography data

The structure of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody C4, PDB code: 8p88 was solved by L.Broggini, S.Ricagno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.80 / 2.02
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 73.593, 121.953, 88.675, 90, 90, 90
R / Rfree (%) 22.2 / 23.3

Other elements in 8p88:

The structure of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody C4 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody C4 (pdb code 8p88). 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 X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody C4, PDB code: 8p88:

Sodium binding site 1 out of 1 in 8p88

Go back to Sodium Binding Sites List in 8p88
Sodium binding site 1 out of 1 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody C4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody C4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:51.5
occ:1.00
CL C:CL201 3.7 64.8 1.0
ND2 C:ASN31 3.7 47.9 1.0
CG C:ASN31 4.8 45.6 1.0

Reference:

L.Broggini, M.M.Barzago, V.Speranzini, T.Schulte, F.Sonzini, M.Giono, M.Romeo, P.Milani, S.Caminito, G.Mazzini, P.Rognoni, G.Merlini, C.Pappone, L.Anastasia, M.Nuvolone, G.Palladini, L.Diomede, S.Ricagno. Nanobodies Counteract the Toxicity of An Amyloidogenic Light Chain By Stabilizing A Partially Open Dimeric Conformation J.Mol.Biol. 2023.
ISSN: ESSN 1089-8638
DOI: 10.1016/J.JMB.2023.168320
Page generated: Mon Aug 18 15:00:03 2025

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