Sodium in PDB 5v64: Crystal Structure of Macrocycles Containing Abeta 15-21 (Qklv(Phi)Fa) and Abeta 30-36 (Aii(Sar)L(Orn)V)

The structure of Crystal Structure of Macrocycles Containing Abeta 15-21 (Qklv(Phi)Fa) and Abeta 30-36 (Aii(Sar)L(Orn)V), PDB code: 5v64 was solved by P.J.Salveson, R.K.Spencer, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.07 / 2.02
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	20.346, 22.029, 31.598, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.4

The structure of Crystal Structure of Macrocycles Containing Abeta 15-21 (Qklv(Phi)Fa) and Abeta 30-36 (Aii(Sar)L(Orn)V) also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Macrocycles Containing Abeta 15-21 (Qklv(Phi)Fa) and Abeta 30-36 (Aii(Sar)L(Orn)V) (pdb code 5v64). 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 Abeta 15-21 (Qklv(Phi)Fa) and Abeta 30-36 (Aii(Sar)L(Orn)V), PDB code: 5v64:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Macrocycles Containing Abeta 15-21 (Qklv(Phi)Fa) 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 15-21 (Qklv(Phi)Fa) and Abeta 30-36 (Aii(Sar)L(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:74.4 occ:0.50 OB1 A:FLC101 2.4 82.2 1.0 OB2 A:FLC101 3.0 84.5 1.0 CBC A:FLC101 3.1 81.7 1.0 HOB A:FLC101 4.1 79.3 1.0 CB A:FLC101 4.4 77.5 1.0 OHB A:FLC101 4.6 66.1 1.0 HA2 A:FLC101 4.9 0.8 1.0 OA2 A:FLC101 5.0 96.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Macrocycles Containing Abeta 15-21 (Qklv(Phi)Fa) 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 15-21 (Qklv(Phi)Fa) and Abeta 30-36 (Aii(Sar)L(Orn)V) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:78.1 occ:1.00 HE1 A:ORN9 2.8 21.6 1.0 OA1 A:FLC101 3.1 0.0 1.0 HG1 A:FLC101 3.3 94.8 1.0 HA A:ALA8 3.3 19.4 1.0 CAC A:FLC101 3.5 95.2 1.0 OA2 A:FLC101 3.5 96.8 1.0 NE A:ORN9 3.6 18.0 1.0 OB2 A:FLC101 3.9 84.5 1.0 HG2 A:FLC101 3.9 94.8 1.0 CG A:FLC101 4.0 79.0 1.0 CBC A:FLC101 4.0 81.7 1.0 HD2 A:ORN9 4.1 25.7 1.0 CA A:ALA8 4.2 16.2 1.0 HB1 A:ALA8 4.3 16.1 1.0 CB A:FLC101 4.4 77.5 1.0 C A:ALA8 4.4 15.2 1.0 CD A:ORN9 4.5 21.4 1.0 OB1 A:FLC101 4.5 82.2 1.0 CA A:FLC101 4.5 84.8 1.0 CB A:ALA8 4.7 13.4 1.0 HB2 A:ALA8 4.9 16.1 1.0 O A:PHE7 4.9 40.6 1.0

P.J.Salveson, R.K.Spencer, A.G.Kreutzer, J.S.Nowick. X-Ray Crystallographic Structure of A Compact Dodecamer From A Peptide Derived From A Beta 16-36. Org. Lett. V. 19 3462 2017.
ISSN: ISSN 1523-7052
PubMed: 28683555
DOI: 10.1021/ACS.ORGLETT.7B01445