Atomistry » Cadmium » PDB 4evc-4l1l » 4gsx
Atomistry »
  Cadmium »
    PDB 4evc-4l1l »
      4gsx »

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

Protein crystallography data

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

Other elements in 4gsx:

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

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

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 4gsx

Go back to Cadmium Binding Sites List in 4gsx
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 4gsx

Go back to Cadmium Binding Sites List in 4gsx
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 4gsx

Go back to Cadmium Binding Sites List in 4gsx
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 4gsx

Go back to Cadmium Binding Sites List in 4gsx
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

Reference:

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
Page generated: Sat Dec 12 08:24:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy