Sodium in PDB 5l6q: Refolded Al Protein From Cardiac Amyloidosis

The structure of Refolded Al Protein From Cardiac Amyloidosis, PDB code: 5l6q was solved by K.Annamalai, F.Liberta, M.-T.Vielberg, H.Lilie, K.-H.Guehrs, A.Schierhorn, R.Koehler, A.Schmidt, C.Haupt, O.Hegenbart, S.Schoenland, M.Groll, M.Faendrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.020, 105.810, 34.750, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 18.2

The structure of Refolded Al Protein From Cardiac Amyloidosis also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	7 atoms

The binding sites of Sodium atom in the Refolded Al Protein From Cardiac Amyloidosis (pdb code 5l6q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Refolded Al Protein From Cardiac Amyloidosis, PDB code: 5l6q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Refolded Al Protein From Cardiac Amyloidosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Refolded Al Protein From Cardiac Amyloidosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:15.1 occ:1.00 O B:HOH378 1.9 38.1 1.0 O A:HOH334 2.0 18.7 1.0 O1 B:CO3207 2.1 21.4 1.0 O B:HOH328 2.1 22.4 1.0 O B:HOH377 2.6 31.5 1.0 C B:CO3207 2.9 24.5 1.0 O2 B:CO3207 3.0 20.8 1.0 NA B:NA205 3.0 18.9 1.0 O A:HOH400 3.6 58.0 1.0 O3 B:CO3207 4.0 38.1 1.0 O B:HOH389 4.1 45.8 1.0 N A:LEU44 4.2 11.0 1.0 O B:PRO42 4.3 13.8 1.0 O A:LEU44 4.4 12.5 1.0 CB A:LEU44 4.5 15.7 1.0 CG1 A:VAL43 4.7 16.0 1.0 O B:HOH337 4.7 19.2 1.0 O A:HOH320 4.7 23.8 1.0 CA A:LEU44 4.8 11.6 1.0 CA B:VAL43 4.9 12.8 1.0 CG2 B:VAL43 4.9 16.4 1.0 CB A:PRO53 4.9 14.2 1.0 CA A:VAL43 5.0 14.2 1.0

Sodium binding site 2 out of 3 in the Refolded Al Protein From Cardiac Amyloidosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Refolded Al Protein From Cardiac Amyloidosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:18.9 occ:1.00 OE2 B:GLU81 2.1 18.7 1.0 OE1 B:GLU81 2.3 26.5 1.0 CD B:GLU81 2.5 22.1 1.0 O B:VAL106 3.6 17.7 1.0 CG B:GLU81 4.0 17.5 1.0 O B:HOH374 4.2 45.3 1.0 O B:HOH315 4.4 34.6 1.0 O B:HOH367 4.4 55.9 1.0 CG2 B:THR105 4.5 16.0 1.0 N B:VAL106 4.5 12.8 1.0 C B:VAL106 4.7 16.0 1.0 CB B:GLU81 4.7 15.0 1.0

Sodium binding site 3 out of 3 in the Refolded Al Protein From Cardiac Amyloidosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Refolded Al Protein From Cardiac Amyloidosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:18.9 occ:1.00 O B:HOH377 1.9 31.5 1.0 O B:HOH337 1.9 19.2 1.0 O2 B:CO3207 2.1 20.8 1.0 O A:HOH320 2.2 23.8 1.0 O B:HOH378 2.6 38.1 1.0 C B:CO3207 2.8 24.5 1.0 O1 B:CO3207 3.0 21.4 1.0 NA A:NA205 3.0 15.1 1.0 O3 B:CO3207 3.9 38.1 1.0 O A:HOH400 4.1 58.0 1.0 O A:HOH383 4.2 32.6 1.0 N B:LEU44 4.2 10.2 1.0 O A:PRO42 4.3 13.0 1.0 O B:LEU44 4.4 13.7 1.0 CB B:LEU44 4.4 15.5 1.0 CG1 B:VAL43 4.6 14.7 1.0 O B:HOH328 4.6 22.4 1.0 O A:HOH334 4.7 18.7 1.0 CA B:LEU44 4.8 10.8 1.0 CA B:VAL43 4.9 12.8 1.0 CA A:VAL43 4.9 14.2 1.0 CG2 A:VAL43 4.9 15.3 1.0 CB B:PRO53 5.0 13.1 1.0

K.Annamalai, F.Liberta, M.T.Vielberg, W.Close, H.Lilie, K.H.Guhrs, A.Schierhorn, R.Koehler, A.Schmidt, C.Haupt, U.Hegenbart, S.Schonland, M.Schmidt, M.Groll, M.Fandrich. Common Fibril Structures Imply Systemically Conserved Protein Misfolding Pathways in Vivo. Angew. Chem. Int. Ed. Engl. V. 56 7510 2017.
ISSN: ESSN 1521-3773
PubMed: 28544119
DOI: 10.1002/ANIE.201701761