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Cadmium in PDB 4gt0: Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421

Protein crystallography data

The structure of Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421, PDB code: 4gt0 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) 28.48 / 2.57
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 77.893, 77.893, 292.291, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 21

Other elements in 4gt0:

The structure of Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421 (pdb code 4gt0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421, PDB code: 4gt0:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 4gt0

Go back to Cadmium Binding Sites List in 4gt0
Cadmium binding site 1 out of 4 in the Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:53.9
occ:1.00
OE2 B:GLU311 2.5 18.6 1.0
OE1 B:GLU311 2.5 22.2 1.0
OD2 A:ASP98 2.5 10.3 1.0
CD B:GLU311 2.8 15.5 1.0
CG A:ASP98 3.1 12.4 1.0
CB A:ASP98 3.3 15.3 1.0
O A:HOH695 3.7 20.6 1.0
OD1 A:ASP98 4.1 15.2 1.0
CG B:GLU311 4.3 14.7 1.0
CA A:ASP98 4.8 6.1 1.0
O B:HOH663 4.9 30.9 1.0

Cadmium binding site 2 out of 4 in 4gt0

Go back to Cadmium Binding Sites List in 4gt0
Cadmium binding site 2 out of 4 in the Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:52.1
occ:1.00
OD1 A:ASP10 2.5 9.3 1.0
OD2 A:ASP10 2.5 5.7 1.0
O A:HOH637 2.6 14.6 1.0
O A:HOH713 2.6 8.0 1.0
O A:HOH620 2.6 15.9 1.0
CG A:ASP10 2.8 3.9 1.0
O A:HOH626 4.1 24.0 1.0
CB A:ASP10 4.4 5.3 1.0

Cadmium binding site 3 out of 4 in 4gt0

Go back to Cadmium Binding Sites List in 4gt0
Cadmium binding site 3 out of 4 in the Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:65.0
occ:1.00
OD1 B:ASP10 2.5 22.1 1.0
OD2 B:ASP10 2.5 11.9 1.0
O B:HOH641 2.6 6.1 1.0
CG B:ASP10 2.8 11.2 1.0
CB B:ASP10 4.4 7.5 1.0
O B:HOH650 4.5 11.2 1.0
O B:HOH623 4.8 13.6 1.0

Cadmium binding site 4 out of 4 in 4gt0

Go back to Cadmium Binding Sites List in 4gt0
Cadmium binding site 4 out of 4 in the Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Dengue Virus Serotype 1 Se Containing Stem to Residue 421 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd503

b:62.4
occ:1.00
CE1 B:HIS282 2.5 24.3 1.0
NE2 B:HIS27 2.5 25.0 1.0
NE2 B:HIS282 2.5 20.2 1.0
CE1 B:HIS27 3.2 24.9 1.0
OE1 B:GLU368 3.6 18.0 1.0
CD2 B:HIS27 3.7 22.8 1.0
ND1 B:HIS282 3.8 25.0 1.0
CD2 B:HIS282 3.9 22.1 1.0
O B:HOH699 4.1 31.3 1.0
CD B:GLU368 4.4 14.3 1.0
ND1 B:HIS27 4.4 31.2 1.0
CG B:HIS282 4.5 20.2 1.0
CB B:ALA280 4.5 22.7 1.0
O B:ALA280 4.5 21.8 1.0
O B:HOH676 4.6 18.3 1.0
OE1 B:GLU26 4.6 27.8 1.0
CG B:HIS27 4.7 25.6 1.0
OE2 B:GLU368 4.9 12.0 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 08:24:39 2020

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