Sodium in PDB 4p4z: Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk

The structure of Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk, PDB code: 4p4z was solved by 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)	35.13 / 1.31
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.310, 63.310, 126.710, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.5

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

Iodine

(I)

12 atoms

The binding sites of Sodium atom in the Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk (pdb code 4p4z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk, PDB code: 4p4z:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:29.4 occ:1.00 OE1 B:GLU8 2.5 18.9 1.0 O B:HOH212 2.7 19.2 1.0 HB2 B:GLU8 2.8 20.9 1.0 O1 B:PO4102 2.9 35.2 0.5 HD2 B:LYS10 3.0 18.6 1.0 HB3 B:GLU8 3.0 20.9 1.0 CB B:GLU8 3.3 17.4 1.0 HB2 B:LYS10 3.3 13.8 1.0 CD B:GLU8 3.6 23.6 1.0 CD B:LYS10 3.9 15.4 1.0 CG B:GLU8 4.0 23.7 1.0 HG3 B:LYS10 4.0 17.7 1.0 HE3 B:LYS10 4.1 24.0 1.0 H B:LYS10 4.1 13.3 1.0 P B:PO4102 4.1 35.8 0.5 O B:HOH215 4.2 48.1 1.0 CB B:LYS10 4.2 11.5 1.0 CG B:LYS10 4.2 14.8 1.0 HZ1 B:LYS10 4.3 27.6 1.0 O B:HOH213 4.4 46.1 1.0 CE B:LYS10 4.4 20.0 1.0 O4 B:PO4102 4.4 35.9 0.5 O B:GLU8 4.5 16.7 1.0 HD3 B:LYS10 4.5 18.6 1.0 HG3 B:GLU8 4.6 28.4 1.0 CA B:GLU8 4.6 12.3 1.0 HG2 B:GLU8 4.6 28.4 1.0 O B:HOH222 4.7 24.1 0.9 O B:HOH217 4.7 44.8 1.0 O3 B:PO4102 4.7 35.7 0.5 OE2 B:GLU8 4.7 18.0 1.0 HB3 B:ORN9 4.8 18.5 1.0 HB3 B:LYS10 4.8 13.8 1.0 C B:GLU8 4.8 12.9 1.0 N B:LYS10 4.9 11.1 1.0 NZ B:LYS10 4.9 23.0 1.0

Sodium binding site 2 out of 3 in the Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:34.7 occ:1.00 OE2 E:GLU8 2.4 20.1 1.0 O K:HOH121 2.6 30.1 0.9 HG2 E:GLU8 2.7 22.4 1.0 O E:HOH209 2.7 16.8 1.0 HE2 K:LYS10 2.8 24.1 1.0 HG3 E:GLU8 2.8 22.4 1.0 CG E:GLU8 3.0 18.7 1.0 CD E:GLU8 3.1 20.8 1.0 HZ2 K:LYS10 3.2 24.8 1.0 HD2 D:TYR6 3.3 16.9 1.0 CD2 D:TYR6 3.4 14.0 1.0 CE K:LYS10 3.5 20.1 1.0 HE2 E:TYR6 3.6 21.7 1.0 HD3 K:LYS10 3.6 22.2 1.0 NZ K:LYS10 3.7 20.6 1.0 HB3 D:TYR6 3.7 12.3 1.0 CE2 D:TYR6 3.7 13.7 1.0 HZ3 K:LYS10 3.8 24.8 1.0 CE2 E:TYR6 3.9 18.1 1.0 HE2 D:TYR6 3.9 16.4 1.0 CG D:TYR6 3.9 12.5 1.0 HG1 E:THR12 4.0 16.6 1.0 HG2 K:LYS10 4.0 20.4 1.0 CD K:LYS10 4.1 18.5 1.0 HD2 E:TYR6 4.3 19.0 1.0 CD2 E:TYR6 4.3 15.8 1.0 CB D:TYR6 4.3 10.3 1.0 HE3 K:LYS10 4.3 24.1 1.0 OE1 E:GLU8 4.4 20.2 1.0 O E:HOH218 4.4 32.0 1.0 HH E:TYR6 4.4 22.0 1.0 CZ D:TYR6 4.5 15.2 1.0 O K:HOH123 4.5 35.6 1.0 CZ E:TYR6 4.5 16.9 1.0 CB E:GLU8 4.5 13.7 1.0 HZ1 K:LYS10 4.5 24.8 1.0 CD1 D:TYR6 4.6 12.0 1.0 CG K:LYS10 4.6 17.0 1.0 OG1 E:THR12 4.6 13.8 1.0 O E:HOH219 4.7 33.8 1.0 OH E:TYR6 4.8 18.3 1.0 HB2 D:TYR6 4.8 12.3 1.0 CE1 D:TYR6 4.8 13.6 1.0 HB3 E:GLU8 4.9 16.4 1.0 H E:GLU8 4.9 12.1 1.0 HD2 K:LYS10 4.9 22.2 1.0 HB2 E:GLU8 4.9 16.4 1.0

Sodium binding site 3 out of 3 in the Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Octomer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kvt(Mva)Tvk within 5.0Å range: probe atom residue distance (Å) B Occ H:Na101 b:36.1 occ:1.00 OE2 H:GLU8 2.5 19.7 1.0 O I:HOH120 2.5 31.0 0.9 HG3 H:GLU8 2.7 19.7 1.0 O H:HOH214 2.7 15.4 1.0 HE2 I:LYS10 2.8 18.1 1.0 HG2 H:GLU8 2.8 19.7 1.0 CG H:GLU8 3.0 16.4 1.0 CD H:GLU8 3.1 17.9 1.0 HZ1 I:LYS10 3.2 21.9 1.0 HE2 H:TYR6 3.5 22.3 1.0 CE I:LYS10 3.5 15.1 1.0 HD3 I:LYS10 3.6 16.9 1.0 NZ I:LYS10 3.7 18.2 1.0 HZ2 I:LYS10 3.8 21.9 1.0 CE2 H:TYR6 3.8 18.6 1.0 HG2 I:LYS10 4.0 15.0 1.0 CD I:LYS10 4.1 14.1 1.0 HG1 H:THR12 4.1 15.9 1.0 HD2 H:TYR6 4.2 17.2 1.0 CD2 H:TYR6 4.2 14.3 1.0 O H:HOH203 4.3 27.0 1.0 HE3 I:LYS10 4.3 18.1 1.0 O I:HOH111 4.4 46.7 1.0 OE1 H:GLU8 4.4 27.0 1.0 CB H:GLU8 4.4 14.3 1.0 CZ H:TYR6 4.5 16.4 1.0 HZ3 I:LYS10 4.5 21.9 1.0 CG I:LYS10 4.6 12.5 1.0 OG1 H:THR12 4.6 13.3 1.0 OH H:TYR6 4.7 17.8 1.0 HB2 H:GLU8 4.8 17.2 1.0 O H:HOH227 4.9 28.2 1.0 HB3 H:GLU8 4.9 17.2 1.0 HD2 I:LYS10 4.9 16.9 1.0 HG3 I:LYS10 5.0 15.0 1.0

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