Sodium in PDB 5nqm: Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus

The structure of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus, PDB code: 5nqm was solved by A.Basle, S.Platsaki, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 1.59
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.650, 106.680, 45.620, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 20.7

The structure of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus also contains other interesting chemical elements:

Copper

(Cu)

4 atoms

The binding sites of Sodium atom in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus (pdb code 5nqm). 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 Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus, PDB code: 5nqm:

Sodium binding site 1 out of 1 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:20.9 occ:1.00 O A:HOH329 1.9 18.2 1.0 OE2 A:GLU79 2.0 28.8 1.0 O A:ARG74 2.1 21.1 1.0 O A:HOH322 2.1 18.4 1.0 O A:HOH320 2.2 19.4 1.0 O A:HOH305 2.2 22.1 1.0 CD A:GLU79 3.1 44.7 1.0 C A:ARG74 3.3 17.9 1.0 OE1 A:GLU79 3.5 49.8 1.0 CA A:ALA75 4.0 26.1 1.0 N A:ALA75 4.0 21.7 1.0 O A:HOH330 4.1 26.6 1.0 O A:HOH316 4.2 24.8 1.0 CA A:ARG74 4.3 17.4 1.0 CB A:ARG74 4.3 16.4 1.0 O A:HOH318 4.4 19.7 1.0 CG A:GLU79 4.4 41.5 1.0 C A:ALA75 4.6 31.6 1.0 N A:ALA76 4.7 33.0 1.0 N A:GLY77 4.8 41.3 1.0 O A:HOH326 4.9 29.5 1.0

A.Basle, S.Platsaki, C.Dennison. Visualizing Biological Copper Storage: the Importance of Thiolate-Coordinated Tetranuclear Clusters. Angew. Chem. Int. Ed. Engl. V. 56 8697 2017.
ISSN: ESSN 1521-3773
PubMed: 28504850
DOI: 10.1002/ANIE.201703107