Sodium in PDB 4d0p: Crystal Structure of Human CSN4

The structure of Crystal Structure of Human CSN4, PDB code: 4d0p was solved by R.D.Bunker, G.M.Lingaraju, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.76 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.660, 63.530, 75.800, 90.00, 101.69, 90.00
R / Rfree (%)	17.89 / 19.29

The structure of Crystal Structure of Human CSN4 also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CSN4 (pdb code 4d0p). 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 Human CSN4, PDB code: 4d0p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human CSN4


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 Human CSN4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:36.8 occ:1.00 O A:HOH2297 2.2 47.4 1.0 O A:SER313 2.3 36.1 1.0 O A:TYR316 2.3 30.8 1.0 O A:HOH2299 2.4 43.4 1.0 HB2 A:PHE361 3.0 32.1 1.0 HB3 A:PHE361 3.2 34.4 1.0 C A:TYR316 3.5 29.9 1.0 C A:SER313 3.5 31.8 1.0 HA A:LYS314 3.6 32.1 1.0 HA A:ASN317 3.6 27.1 1.0 CB A:PHE361 3.6 33.2 1.0 H A:TYR316 3.8 25.9 1.0 C A:LYS314 4.1 34.3 1.0 N A:TYR316 4.1 25.4 1.0 CA A:LYS314 4.1 29.3 1.0 HD2 A:PHE361 4.2 32.3 1.0 O A:HOH2298 4.2 61.4 1.0 O A:LYS314 4.2 35.5 1.0 N A:LYS314 4.2 28.1 1.0 HA A:SER313 4.3 29.8 1.0 N A:ASN317 4.3 29.8 1.0 CA A:TYR316 4.4 25.9 1.0 CA A:ASN317 4.4 29.4 1.0 CG A:PHE361 4.5 32.0 1.0 OD1 A:ASN317 4.5 40.2 1.0 N A:LEU315 4.5 30.7 1.0 O A:PHE361 4.5 42.9 1.0 CA A:SER313 4.5 29.1 1.0 CD2 A:PHE361 4.6 31.7 1.0 C A:PHE361 4.6 42.3 1.0 C A:LEU315 4.7 33.8 1.0 H A:LEU315 4.7 31.6 1.0 HB2 A:SER313 4.8 30.3 1.0 CA A:PHE361 4.8 33.4 1.0 O A:HOH2333 4.8 52.4 1.0 CB A:GLU362 4.8 68.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human CSN4


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 Human CSN4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:40.2 occ:1.00 OG A:SER340 2.2 43.6 1.0 O A:HOH2324 2.3 36.2 1.0 O A:HOH2325 2.4 49.3 1.0 OG1 A:THR344 2.4 42.9 1.0 O A:SER340 2.5 36.9 1.0 C A:SER340 3.0 36.9 1.0 CB A:SER340 3.3 37.7 1.0 CA A:SER340 3.5 33.4 1.0 HA A:SER340 3.5 33.5 1.0 H A:THR344 3.5 38.0 1.0 HB A:THR344 3.6 38.2 1.0 CB A:THR344 3.6 41.0 1.0 HB3 A:SER340 3.7 36.5 1.0 HA A:GLN341 3.8 33.9 1.0 N A:GLN341 3.9 34.4 1.0 O A:HOH2329 3.9 58.7 1.0 HB2 A:SER340 4.1 36.5 1.0 N A:THR344 4.3 37.9 1.0 O A:HOH2326 4.3 42.3 1.0 HB A:ILE343 4.3 35.9 1.0 CA A:GLN341 4.3 34.9 1.0 HG22 A:THR344 4.4 42.7 1.0 CA A:THR344 4.5 37.5 1.0 H A:GLN341 4.6 35.2 1.0 CG2 A:THR344 4.6 41.9 1.0 HA A:THR344 4.8 37.1 1.0 O A:HOH2330 4.8 56.9 1.0 N A:SER340 4.9 32.8 1.0 HG21 A:THR344 5.0 43.4 1.0 HD11 A:ILE352 5.0 42.3 1.0

G.M.Lingaraju, R.D.Bunker, S.Cavadini, D.Hess, U.Hassiepen, M.Renatus, E.S.Fischer, N.H.Thoma. Crystal Structure of the COP9 Signalosome Nature V. 512 161 2014.
ISSN: ISSN 0028-0836
PubMed: 25043011
DOI: 10.1038/NATURE13566