Sodium in PDB 9bnh: X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide

The structure of X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide, PDB code: 9bnh was solved by V.T.Dang, A.Nguyen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.48 / 1.12
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	23.198, 25.261, 24.149, 90, 110.32, 90
R / Rfree (%)	12 / 14.5

The structure of X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Sodium atom in the X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide (pdb code 9bnh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide, PDB code: 9bnh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:17.2 occ:0.50 O B:ACY105 2.3 19.2 0.3 H A:TRP4 2.4 10.1 1.0 C B:ACY105 2.6 18.9 0.3 HD2 A:HIS3 2.8 11.1 1.0 HA A:HIS3 2.8 9.4 1.0 OXT B:ACY105 2.9 18.8 0.3 N A:TRP4 3.2 8.4 1.0 H3 B:ACY105 3.2 22.8 0.7 H1 B:ACY105 3.3 22.8 0.7 HB3 A:TRP4 3.4 10.7 1.0 H1 B:ACY105 3.6 22.8 0.3 CA A:HIS3 3.7 7.9 1.0 CD2 A:HIS3 3.7 9.3 1.0 CH3 B:ACY105 3.7 19.0 0.7 CH3 B:ACY105 3.8 19.0 0.3 C A:HIS3 3.9 8.3 1.0 O B:ACY105 4.0 19.2 0.7 CB A:TRP4 4.1 8.9 1.0 CA A:TRP4 4.1 8.0 1.0 O A:TRP2 4.2 9.5 1.0 O A:TRP4 4.2 9.5 1.0 HB2 A:TRP4 4.2 10.7 1.0 H3 B:ACY105 4.2 22.8 0.3 C B:ACY105 4.3 18.7 0.7 H2 B:ACY105 4.4 22.8 0.3 CG A:HIS3 4.4 8.7 1.0 H2 B:ACY105 4.6 22.8 0.7 CB A:HIS3 4.6 8.6 1.0 N A:HIS3 4.6 7.8 1.0 C A:TRP4 4.6 7.9 1.0 NE2 A:HIS3 4.7 9.5 1.0 C A:TRP2 4.8 8.5 1.0 HB2 A:HIS3 4.8 10.3 1.0 HE2 A:HIS3 4.9 11.4 1.0 HA A:TRP4 4.9 9.6 1.0 O B:HOH202 5.0 17.2 1.0

Sodium binding site 2 out of 2 in the X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of Cu-TZ4H Tryptophan Zipper Metallo-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:41.3 occ:1.00 O A:HOH215 2.8 13.4 1.0 H2 A:ACY102 3.4 14.5 0.3 H1 A:ACY102 3.4 14.5 0.7 CH3 A:ACY102 4.3 12.1 0.3 CU A:CU103 4.3 9.1 1.0 CH3 A:ACY102 4.4 12.1 0.7 H1 A:ACY102 4.4 14.5 0.3 H3 A:ACY102 4.6 14.5 0.7 H3 A:ACY102 4.6 14.5 0.3 O A:HOH201 4.7 25.0 1.0 H2 A:ACY102 4.8 14.5 0.7 HE1 A:HIS10 5.0 12.8 1.0

V.T.Dang, A.Engineer, D.Mcelheny, A.Drena, J.Telser, K.Tomczak, A.I.Nguyen. Crystallography Reveals Metal-Triggered Restructuring of Beta-Hairpins. Chemistry 02101 2024.
ISSN: ISSN 0947-6539
PubMed: 39152095
DOI: 10.1002/CHEM.202402101