Atomistry » Sodium » PDB 4coo-4ddo » 4d0p
Atomistry »
  Sodium »
    PDB 4coo-4ddo »
      4d0p »

Sodium in PDB 4d0p: Crystal Structure of Human CSN4

Protein crystallography data

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

Other elements in 4d0p:

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

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

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 4d0p

Go back to Sodium Binding Sites List in 4d0p
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 4d0p

Go back to Sodium Binding Sites List in 4d0p
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

Reference:

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
Page generated: Tue Dec 15 06:36:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy