Atomistry » Sodium » PDB 4njk-4nwh » 4nw8
Atomistry »
  Sodium »
    PDB 4njk-4nwh »
      4nw8 »

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

Protein crystallography data

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

Other elements in 4nw8:

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

Sodium Binding Sites:

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 4nw8

Go back to Sodium Binding Sites List in 4nw8
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 4nw8

Go back to Sodium Binding Sites List in 4nw8
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

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 06:56:01 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy