Sodium in PDB 4ntr: Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 30-36 (Aii(Sar)L(Orn)V)

The structure of Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 30-36 (Aii(Sar)L(Orn)V), PDB code: 4ntr 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)	34.36 / 1.70
Space group	H 3 1
Cell size a, b, c (Å), α, β, γ (°)	68.000, 68.000, 169.260, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22.6

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

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 30-36 (Aii(Sar)L(Orn)V) (pdb code 4ntr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 30-36 (Aii(Sar)L(Orn)V), PDB code: 4ntr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 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 Abeta 17-23 (Lvffaed) and Abeta 30-36 (Aii(Sar)L(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:65.0 occ:1.00 OE1 F:GLU7 3.1 71.4 1.0 HZ D:PHE5 3.2 41.9 1.0 OE2 A:GLU7 3.2 87.2 1.0 HZ C:PHE5 3.3 55.0 1.0 HD12 A:ILE11 3.5 58.5 1.0 CD A:GLU7 3.5 58.9 1.0 CD F:GLU7 3.5 64.1 1.0 OE1 A:GLU7 3.6 54.2 1.0 OE2 F:GLU7 3.7 70.7 1.0 HB2 F:GLU7 3.8 38.1 1.0 HB2 A:GLU7 3.8 35.1 1.0 CZ D:PHE5 3.9 34.9 1.0 CZ C:PHE5 4.0 45.9 1.0 HE1 C:PHE5 4.0 48.4 1.0 HD12 F:ILE11 4.2 79.2 1.0 O A:HOH214 4.3 59.0 1.0 CG A:GLU7 4.4 38.4 1.0 CE1 C:PHE5 4.4 40.3 1.0 HG3 A:GLU7 4.4 46.1 1.0 CD1 A:ILE11 4.4 48.7 1.0 CG F:GLU7 4.4 41.5 1.0 HE1 D:PHE5 4.5 53.0 1.0 HG3 F:GLU7 4.5 49.8 1.0 CB A:GLU7 4.5 29.3 1.0 CB F:GLU7 4.5 31.7 1.0 HE2 D:PHE5 4.6 43.2 1.0 CE1 D:PHE5 4.6 44.1 1.0 CE2 D:PHE5 4.6 36.0 1.0 HD11 A:ILE11 4.7 58.5 1.0 HG12 F:ILE11 4.8 61.1 1.0 HD13 A:ILE11 4.8 58.5 1.0 HB3 A:GLU7 4.8 35.1 1.0 HB3 F:GLU7 4.9 38.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 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 Abeta 17-23 (Lvffaed) and Abeta 30-36 (Aii(Sar)L(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:38.9 occ:1.00 HE1 B:ORN9 2.1 29.2 1.0 O A:ORN1 2.5 34.8 1.0 OE1 B:GLU7 2.9 36.2 1.0 NE B:ORN9 3.0 24.3 1.0 HG2 B:GLU7 3.0 31.9 1.0 HG2 B:ORN9 3.0 31.7 1.0 HG23 A:VAL3 3.2 31.6 1.0 O B:GLU7 3.2 26.0 1.0 O G:HOH211 3.2 46.6 1.0 HA B:ASP8 3.5 31.3 1.0 O G:HOH212 3.6 46.3 1.0 C B:GLU7 3.7 25.1 1.0 CG B:GLU7 3.7 26.6 1.0 CD B:GLU7 3.7 34.3 1.0 CD B:ORN9 3.8 30.4 1.0 C A:ORN1 3.8 41.0 1.0 HD3 B:ORN9 3.8 36.5 1.0 HA G:ORN9 3.8 34.7 1.0 CG B:ORN9 3.8 26.4 1.0 HA A:LEU2 3.8 30.8 1.0 H1 G:ORN9 3.9 41.0 1.0 HB3 B:GLU7 3.9 26.7 1.0 C B:ASP8 4.0 30.9 1.0 HD2 G:ORN9 4.0 32.3 1.0 CA B:ASP8 4.0 26.1 1.0 CG2 A:VAL3 4.0 26.3 1.0 N B:ASP8 4.1 22.1 1.0 HG21 A:VAL3 4.1 31.6 1.0 HB3 B:ORN9 4.1 28.0 1.0 H A:VAL3 4.2 27.4 1.0 H2 G:ORN9 4.2 41.0 1.0 H2 A:ORN1 4.2 48.5 1.0 CB B:GLU7 4.2 22.2 1.0 H3 A:ORN1 4.3 48.5 1.0 O A:HOH212 4.3 42.5 1.0 N G:ORN9 4.4 34.1 1.0 N A:VAL3 4.5 22.9 1.0 CA A:LEU2 4.5 25.7 1.0 CB B:ORN9 4.5 23.3 1.0 HG3 B:GLU7 4.5 31.9 1.0 N A:LEU2 4.6 28.8 1.0 HG22 A:VAL3 4.6 31.6 1.0 CA B:GLU7 4.6 20.6 1.0 N A:ORN1 4.6 40.4 1.0 C A:LEU2 4.6 24.2 1.0 HB A:VAL3 4.7 27.8 1.0 CA G:ORN9 4.7 28.9 1.0 HG3 B:ORN9 4.7 31.7 1.0 HB2 B:ORN9 4.7 28.0 1.0 H B:ASP8 4.7 26.6 1.0 HD2 B:ORN9 4.8 36.5 1.0 CA A:ORN1 4.8 35.8 1.0 CB A:VAL3 4.9 23.1 1.0 OE2 B:GLU7 4.9 37.9 1.0 O G:HOH213 5.0 40.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 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 3 of Crystal Structure of Macrocycles Containing Abeta 17-23 (Lvffaed) and Abeta 30-36 (Aii(Sar)L(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ M:Na101 b:74.9 occ:1.00 HZ N:PHE5 3.3 37.5 1.0 OE1 M:GLU7 3.4 72.0 1.0 OE2 M:GLU7 3.5 80.0 1.0 CD M:GLU7 3.6 69.3 1.0 CZ N:PHE5 3.9 31.3 1.0 O M:HOH215 4.0 54.6 1.0 HB2 M:GLU7 4.1 33.2 1.0 HD11 M:ILE11 4.1 60.1 1.0 HE1 N:PHE5 4.2 46.7 1.0 CE1 N:PHE5 4.4 38.9 1.0 O M:HOH210 4.5 45.6 1.0 CG M:GLU7 4.6 37.9 1.0 HG3 M:GLU7 4.7 45.5 1.0 CB M:GLU7 4.8 27.6 1.0 CE2 N:PHE5 4.9 33.5 1.0 HE2 N:PHE5 4.9 40.2 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