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

Protein crystallography data

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

Other elements in 4ntp:

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

Sodium Binding Sites:

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 4ntp

Go back to Sodium Binding Sites List in 4ntp
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 4ntp

Go back to Sodium Binding Sites List in 4ntp
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

Reference:

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
Page generated: Tue Dec 15 06:55:56 2020

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