Sodium in PDB 4nw8: Crystal Structure of Macrocycles Containing ABETA17-23 (Lv(Phi)(Mea) Aed) and ABETA30-36 (Aiigl(Orn)V)

The structure of Crystal Structure of Macrocycles Containing ABETA17-23 (Lv(Phi)(Mea) Aed) and ABETA30-36 (Aiigl(Orn)V), PDB code: 4nw8 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)	29.74 / 2.02
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.680, 68.680, 93.840, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.7

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

Iodine	(I)	12 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Macrocycles Containing ABETA17-23 (Lv(Phi)(Mea) Aed) and ABETA30-36 (Aiigl(Orn)V) (pdb code 4nw8). 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 (Lv(Phi)(Mea) Aed) and ABETA30-36 (Aiigl(Orn)V), PDB code: 4nw8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Macrocycles Containing ABETA17-23 (Lv(Phi)(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 (Lv(Phi)(Mea) Aed) and ABETA30-36 (Aiigl(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:26.9 occ:1.00 HG21 C:ILE12 2.5 20.7 1.0 OD2 C:ASP8 2.5 20.3 1.0 O C:HOH203 2.6 26.2 0.9 HD13 C:ILE12 2.9 35.2 1.0 HG3 K:ORN1 3.1 29.4 1.0 H3 K:ORN1 3.3 26.0 1.0 CG2 C:ILE12 3.4 17.2 1.0 HB3 C:ASP8 3.5 23.7 1.0 CG C:ASP8 3.5 24.6 1.0 O C:HOH211 3.5 26.7 0.7 HG22 C:ILE12 3.8 20.7 1.0 HG23 C:ILE12 3.8 20.7 1.0 CD1 C:ILE12 3.9 29.3 1.0 CB C:ASP8 4.0 19.7 1.0 CG K:ORN1 4.1 24.5 1.0 N K:ORN1 4.2 21.7 1.0 HD12 C:ILE12 4.2 35.2 1.0 HB2 C:ASP8 4.3 23.7 1.0 H2 K:ORN1 4.3 26.0 1.0 HG2 K:ORN1 4.3 29.4 1.0 HB C:ILE12 4.3 21.2 1.0 CB C:ILE12 4.3 17.7 1.0 HD11 C:ILE12 4.4 35.2 1.0 HG12 C:ILE12 4.5 28.0 1.0 CG1 C:ILE12 4.5 23.4 1.0 OD1 C:ASP8 4.6 31.8 1.0 H1 K:ORN1 4.8 26.0 1.0 HD3 K:ORN1 4.9 31.8 1.0 O K:HOH201 5.0 9.7 0.6 CB K:ORN1 5.0 21.9 1.0 HB2 K:ORN1 5.0 26.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Macrocycles Containing ABETA17-23 (Lv(Phi)(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 (Lv(Phi)(Mea) Aed) and ABETA30-36 (Aiigl(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ K:Na102 b:26.9 occ:1.00 O K:ILE11 2.5 18.9 1.0 HB1 K:ALA10 2.9 30.9 1.0 O K:HOH213 3.1 47.0 1.0 HG22 K:ILE12 3.2 27.1 1.0 C K:ILE11 3.5 17.9 1.0 HA K:ILE12 3.6 18.0 1.0 HB3 K:ALA10 3.7 30.9 1.0 CB K:ALA10 3.7 25.8 1.0 HG23 K:ILE12 3.9 27.1 1.0 CG2 K:ILE12 4.0 22.6 1.0 H K:ILE11 4.0 25.5 1.0 N K:ILE11 4.1 21.2 1.0 N K:ILE12 4.3 15.4 1.0 CA K:ILE12 4.3 15.0 1.0 HB2 K:ALA10 4.3 30.9 1.0 CA K:ILE11 4.4 19.2 1.0 C K:ALA10 4.5 25.9 1.0 HG21 K:ILE12 4.7 27.1 1.0 CA K:ALA10 4.7 29.8 1.0 CB K:ILE12 4.7 18.4 1.0 CL K:CL101 4.8 57.3 1.0 HB K:ILE11 4.8 24.7 1.0 O K:HOH209 4.8 39.1 0.9

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