Cadmium in PDB 4gsx: High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem

The structure of High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem, PDB code: 4gsx was solved by D.E.Klein, J.L.Choi, S.C.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.13 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	77.571, 77.571, 292.518, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 18.6

The structure of High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem (pdb code 4gsx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem, PDB code: 4gsx:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd502 b:43.7 occ:1.00 OE1 B:GLU311 2.4 28.1 1.0 OE2 B:GLU311 2.5 18.3 1.0 OD2 A:ASP98 2.5 18.1 1.0 O A:HOH710 2.7 25.1 1.0 CD B:GLU311 2.8 20.8 1.0 CG A:ASP98 3.3 16.3 1.0 CB A:ASP98 3.5 16.9 1.0 O A:HOH732 3.6 17.4 1.0 O B:HOH723 3.8 26.6 1.0 CG B:GLU311 4.2 21.1 1.0 OD1 A:ASP98 4.4 17.0 1.0 O B:HOH768 4.7 21.9 1.0 CB B:GLU311 5.0 19.2 1.0 O A:HOH628 5.0 14.9 1.0

Cadmium binding site 2 out of 4 in the High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd503 b:52.1 occ:1.00 OD1 A:ASP10 2.5 17.1 1.0 OD2 A:ASP10 2.6 16.9 1.0 O A:HOH623 2.6 14.8 1.0 O A:HOH932 2.6 50.6 1.0 O A:HOH777 2.7 22.1 1.0 CG A:ASP10 2.9 14.1 1.0 O A:HOH918 3.7 16.3 1.0 O A:HOH782 4.1 17.5 1.0 O A:HOH857 4.4 36.9 1.0 CB A:ASP10 4.4 10.7 1.0 O A:HOH671 4.9 12.6 1.0 O A:HOH894 4.9 52.9 1.0

Cadmium binding site 3 out of 4 in the High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd502 b:54.4 occ:1.00 OD1 B:ASP10 2.5 18.7 1.0 OD2 B:ASP10 2.6 16.6 1.0 CG B:ASP10 2.9 12.6 1.0 O B:HOH849 3.0 45.8 1.0 O B:HOH623 4.1 13.6 1.0 O B:HOH857 4.4 17.3 1.0 CB B:ASP10 4.4 9.0 1.0 O B:HOH793 4.4 29.8 1.0 O B:HOH631 4.7 14.8 1.0 O B:ASP22 4.8 10.5 1.0

Cadmium binding site 4 out of 4 in the High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of High Resolution Structure of Dengue Virus Serotype 1 Se Containing Stem within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd503 b:53.1 occ:1.00 CE1 B:HIS282 2.4 23.6 1.0 O B:HOH789 2.4 32.4 1.0 NE2 B:HIS282 2.4 22.4 1.0 NE2 B:HIS27 2.5 30.0 1.0 O B:HOH806 3.0 68.6 1.0 CE1 B:HIS27 3.3 31.2 1.0 OE1 B:GLU368 3.5 26.1 1.0 CD2 B:HIS27 3.6 26.5 1.0 ND1 B:HIS282 3.7 24.6 1.0 CD2 B:HIS282 3.8 23.3 1.0 O B:HOH764 4.2 59.1 1.0 CG B:HIS282 4.4 21.4 1.0 CD B:GLU368 4.4 16.8 1.0 ND1 B:HIS27 4.5 26.6 1.0 CB B:ALA280 4.5 28.3 1.0 O B:ALA280 4.6 20.4 1.0 CG B:HIS27 4.6 28.1 1.0 O B:HOH680 4.7 18.6 1.0 OE2 B:GLU368 4.9 15.5 1.0 OE1 B:GLU26 4.9 34.5 1.0

D.E.Klein, J.L.Choi, S.C.Harrison. Structure of A Dengue Virus Envelope Protein Late-Stage Fusion Intermediate. J.Virol. V. 87 2287 2013.
ISSN: ISSN 0022-538X
PubMed: 23236058
DOI: 10.1128/JVI.02957-12