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Sodium in PDB 4p4w: Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk

Protein crystallography data

The structure of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk, PDB code: 4p4w was solved by R.K.Spencer, A.Kreutzer, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.53 / 1.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.193, 58.193, 121.279, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 20.9

Other elements in 4p4w:

The structure of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk also contains other interesting chemical elements:

Iodine (I) 14 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk (pdb code 4p4w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk, PDB code: 4p4w:

Sodium binding site 1 out of 1 in 4p4w

Go back to Sodium Binding Sites List in 4p4w
Sodium binding site 1 out of 1 in the Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dodecamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Mva)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na102

b:29.9
occ:1.00
OE1 H:GLU8 2.2 23.7 1.0
OH H:TYR6 2.4 18.7 1.0
HH H:TYR6 2.9 22.5 1.0
HE2 H:TYR6 3.0 22.1 1.0
O H:HOH205 3.1 28.1 1.0
CD H:GLU8 3.3 27.5 1.0
CZ H:TYR6 3.4 17.6 1.0
CE2 H:TYR6 3.6 18.4 1.0
HG2 H:GLU8 3.8 29.4 1.0
CG H:GLU8 4.1 24.5 1.0
OE2 H:GLU8 4.3 33.0 1.0
HB1 H:ALA12 4.3 20.6 1.0
HG3 H:GLU8 4.4 29.4 1.0
O H:HOH206 4.6 38.4 1.0
CE1 H:TYR6 4.7 16.1 1.0
HB3 H:ALA12 4.7 20.6 1.0
HB2 H:ALA12 4.8 20.6 1.0
CB H:ALA12 4.8 17.1 1.0
CD2 H:TYR6 4.9 17.8 1.0
HE1 H:TYR6 5.0 19.4 1.0

Reference:

R.K.Spencer, A.G.Kreutzer, P.J.Salveson, H.Li, J.S.Nowick. X-Ray Crystallographic Structures of Oligomers of Peptides Derived From Beta 2-Microglobulin. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25915729
DOI: 10.1021/JACS.5B01673
Page generated: Tue Dec 15 06:57:44 2020

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