Sodium in PDB 4ntp: Crystal Structure of Macrocycles Containing A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(Orn)V)

The structure of Crystal Structure of Macrocycles Containing A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(Orn)V), PDB code: 4ntp was solved by J.S.Nowick, R.K.Spencer, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.09 / 1.99
Space group	H 3 1
Cell size a, b, c (Å), α, β, γ (°)	68.180, 68.180, 170.430, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.6

The structure of Crystal Structure of Macrocycles Containing A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(Orn)V) also contains other interesting chemical elements:

Iodine	(I)	16 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the Crystal Structure of Macrocycles Containing A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(Orn)V) (pdb code 4ntp). 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 A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(Orn)V), PDB code: 4ntp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Macrocycles Containing A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(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 A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:53.5 occ:1.00 O A:HOH216 2.8 50.4 1.0 HZ C:PHE5 2.8 28.7 1.0 HD13 A:ILE11 3.1 32.9 1.0 HZ D:PHE5 3.1 36.4 1.0 OE1 A:GLU7 3.3 49.4 1.0 CD A:GLU7 3.5 64.4 1.0 HE1 C:PHE5 3.5 40.7 1.0 CZ C:PHE5 3.5 23.9 1.0 OE2 A:GLU7 3.6 77.1 1.0 HD12 F:ILE11 3.6 49.2 1.0 CZ D:PHE5 3.7 30.4 1.0 HB2 A:GLU7 3.8 26.1 1.0 O F:HOH118 3.8 71.2 1.0 CE1 C:PHE5 3.9 33.9 1.0 CD F:GLU7 4.0 74.3 1.0 CD1 A:ILE11 4.0 27.4 1.0 OE2 F:GLU7 4.0 51.2 1.0 HB2 F:GLU7 4.1 29.6 1.0 OE1 F:GLU7 4.1 52.4 1.0 HE1 D:PHE5 4.2 56.8 1.0 HG3 A:GLU7 4.3 34.1 1.0 CG A:GLU7 4.3 28.4 1.0 CE1 D:PHE5 4.3 47.4 1.0 HD12 A:ILE11 4.4 32.9 1.0 HD11 A:ILE11 4.4 32.9 1.0 HG3 F:GLU7 4.4 60.1 1.0 CB A:GLU7 4.5 21.8 1.0 CE2 D:PHE5 4.5 53.4 1.0 CD1 F:ILE11 4.6 41.0 1.0 HE2 D:PHE5 4.6 64.0 1.0 O A:HOH214 4.6 38.4 1.0 CE2 C:PHE5 4.6 28.6 1.0 HG12 F:ILE11 4.6 43.4 1.0 CG F:GLU7 4.6 50.1 1.0 HG13 F:ILE11 4.7 43.4 1.0 CB F:GLU7 4.8 24.7 1.0 HE2 C:PHE5 4.8 34.3 1.0 HB3 A:GLU7 4.9 26.1 1.0 HG12 A:ILE11 4.9 47.4 1.0 HG13 A:ILE11 4.9 47.4 1.0 CG1 F:ILE11 4.9 36.1 1.0 CG1 A:ILE11 4.9 39.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Macrocycles Containing A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(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 A 17-23 (Lv(Phi)Faed) and A 30-36 (Aii(Sar)L(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na102 b:42.2 occ:1.00 HD21 E:LEU2 2.6 34.7 1.0 HD23 E:LEU2 2.6 34.7 1.0 HG E:LEU2 2.9 28.0 1.0 CD2 E:LEU2 2.9 28.9 1.0 OD1 D:ASP8 3.0 41.0 1.0 H L:ORN9 3.1 31.3 1.0 H1 L:ORN9 3.3 31.3 1.0 CG E:LEU2 3.5 23.3 1.0 N L:ORN9 3.7 26.1 1.0 CG D:ASP8 3.7 47.8 1.0 H2 E:ORN1 3.8 43.6 1.0 HD22 E:LEU2 3.8 34.7 1.0 C E:ORN1 4.1 19.2 1.0 OD2 D:ASP8 4.1 53.9 1.0 HD11 E:LEU2 4.2 46.0 1.0 HA E:ORN1 4.2 29.0 1.0 N E:LEU2 4.2 14.9 1.0 O E:ORN1 4.3 24.0 1.0 H2 L:ORN9 4.3 31.3 1.0 HA E:LEU2 4.3 20.7 1.0 HA L:ORN9 4.4 25.9 1.0 CD1 E:LEU2 4.5 38.3 1.0 H E:LEU2 4.5 17.9 1.0 CB E:LEU2 4.6 16.0 1.0 CA E:LEU2 4.6 17.2 1.0 HB2 D:ASP8 4.6 22.0 1.0 CA E:ORN1 4.6 24.2 1.0 N E:ORN1 4.6 36.3 1.0 HA D:ASP8 4.6 27.4 1.0 CB D:ASP8 4.7 18.3 1.0 CA L:ORN9 4.8 21.6 1.0 HG3 L:ORN9 4.8 41.5 1.0 HD12 E:LEU2 5.0 46.0 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