Sodium in PDB 4nw9: Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V)

The structure of Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V), PDB code: 4nw9 was solved by R.K.Spencer, H.Li, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.54 / 1.66
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.220, 68.220, 92.990, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 20.9

The structure of Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V) (pdb code 4nw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V), PDB code: 4nw9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V)


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 Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:56.7 occ:1.00 O D:HOH213 2.4 57.1 1.0 HG3 L:ORN1 2.5 57.1 1.0 OD2 D:ASP8 2.8 54.6 1.0 HG23 D:ILE12 2.8 52.1 1.0 H1 L:ORN1 2.9 63.6 1.0 HD13 D:ILE12 3.3 47.9 1.0 CG L:ORN1 3.6 47.6 1.0 CG2 D:ILE12 3.7 43.4 1.0 CG D:ASP8 3.8 53.8 1.0 N L:ORN1 3.8 53.0 1.0 HB3 D:ASP8 3.8 52.2 1.0 H2 L:ORN1 4.0 63.6 1.0 HG2 L:ORN1 4.0 57.1 1.0 HG21 D:ILE12 4.0 52.1 1.0 HG22 D:ILE12 4.1 52.1 1.0 CD1 D:ILE12 4.2 39.9 1.0 HD12 D:ILE12 4.2 47.9 1.0 CB D:ASP8 4.2 43.5 1.0 HD3 L:ORN1 4.2 52.5 1.0 HB2 D:ASP8 4.3 52.2 1.0 CD L:ORN1 4.4 43.7 1.0 CB L:ORN1 4.4 43.8 1.0 HB3 L:ORN1 4.4 52.6 1.0 O D:HOH206 4.5 68.1 1.0 H3 L:ORN1 4.5 63.6 1.0 CA L:ORN1 4.5 47.4 1.0 HD2 L:ORN1 4.6 52.5 1.0 HA L:ORN1 4.6 56.9 1.0 HB D:ILE12 4.6 49.6 1.0 CB D:ILE12 4.7 41.3 1.0 OD1 D:ASP8 4.7 57.7 1.0 HD11 D:ILE12 4.8 47.9 1.0 CG1 D:ILE12 4.9 39.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Macrocycles Containing ABETA17-23 (Lvf(Mea)Aed) and ABETA30-36 (Aiigl(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ L:Na101 b:62.7 occ:1.00 HG3 L:GLU7 2.1 56.1 1.0 OE2 L:GLU7 2.3 58.7 1.0 HB2 L:GLU7 2.6 38.9 1.0 CG L:GLU7 2.7 46.8 1.0 CD L:GLU7 2.9 67.7 1.0 HD11 L:ILE11 3.0 35.5 1.0 HZ K:MEA5 3.1 51.3 1.0 CB L:GLU7 3.1 32.4 1.0 HD13 L:ILE11 3.5 35.5 1.0 HG2 L:GLU7 3.5 56.1 1.0 HB3 L:GLU7 3.6 38.9 1.0 CD1 L:ILE11 3.7 29.6 1.0 HE1 K:MEA5 4.0 66.8 1.0 CZ K:MEA5 4.0 42.8 1.0 HD12 L:ILE11 4.1 35.5 1.0 OE1 L:GLU7 4.1 61.4 1.0 HA L:GLU7 4.3 34.5 1.0 HB2 L:ORN9 4.3 47.6 1.0 CA L:GLU7 4.3 28.8 1.0 CE1 K:MEA5 4.4 55.7 1.0 HB3 L:ORN9 4.8 47.6 1.0 HG12 L:ILE11 4.9 35.5 1.0 CG1 L:ILE11 4.9 29.5 1.0

R.K.Spencer, H.Li, J.S.Nowick. X-Ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of A Peptide Derived From A Beta (17-36). J.Am.Chem.Soc. V. 136 5595 2014.
ISSN: ISSN 0002-7863
PubMed: 24669800
DOI: 10.1021/JA5017409