Magnesium in PDB 5zqk: Dengue Virus Non Structural Protein 5

Protein crystallography data

The structure of Dengue Virus Non Structural Protein 5, PDB code: 5zqk was solved by A.El Sahili, T.S.Soh, J.Schiltz, A.Gharbi-Ayachi, B.C.Goh, C.C.Seh, P.C.Dedon, P.Y.Shi, S.P.Lim, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.680, 146.100, 97.240, 90.00, 105.45, 90.00
R / Rfree (%) 19.6 / 23.5

Other elements in 5zqk:

The structure of Dengue Virus Non Structural Protein 5 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dengue Virus Non Structural Protein 5 (pdb code 5zqk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dengue Virus Non Structural Protein 5, PDB code: 5zqk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5zqk

Go back to Magnesium Binding Sites List in 5zqk
Magnesium binding site 1 out of 2 in the Dengue Virus Non Structural Protein 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dengue Virus Non Structural Protein 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:80.2
occ:1.00
OD1 B:ASP664 2.2 66.9 1.0
OD1 B:ASP534 2.2 60.1 1.0
MG B:MG1004 2.5 75.7 1.0
CG B:ASP664 3.3 63.5 1.0
CG B:ASP534 3.3 59.9 1.0
O B:CYS665 3.8 47.9 1.0
OD2 B:ASP664 3.9 73.6 1.0
OD2 B:ASP534 3.9 63.2 1.0
O B:ALA532 4.0 50.9 1.0
O B:HOH1372 4.0 73.6 1.0
N B:CYS665 4.1 45.2 1.0
C B:ALA532 4.2 50.8 1.0
O B:PRO707 4.3 47.3 1.0
O B:ASP533 4.3 54.4 1.0
CA B:ASP664 4.3 47.0 1.0
CB B:ASP664 4.4 48.8 1.0
C B:ASP533 4.4 53.8 1.0
N B:ASP534 4.5 50.1 1.0
CB B:ASP534 4.5 50.5 1.0
CA B:ASP534 4.5 49.2 1.0
CB B:ALA532 4.5 47.2 1.0
C B:ASP664 4.7 46.1 1.0
CA B:ALA532 4.7 46.6 1.0
C B:CYS665 4.7 47.9 1.0
N B:ASP533 4.8 49.1 1.0

Magnesium binding site 2 out of 2 in 5zqk

Go back to Magnesium Binding Sites List in 5zqk
Magnesium binding site 2 out of 2 in the Dengue Virus Non Structural Protein 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dengue Virus Non Structural Protein 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:75.7
occ:1.00
MG B:MG1003 2.5 80.2 1.0
OD1 B:ASP534 2.9 60.1 1.0
OD2 B:ASP534 3.0 63.2 1.0
CG B:ASP534 3.1 59.9 1.0
O B:ALA532 3.2 50.9 1.0
CG B:PRO707 3.7 48.5 1.0
O B:HOH1372 3.8 73.6 1.0
CB B:PRO707 3.9 45.3 1.0
O B:PRO707 3.9 47.3 1.0
C B:ALA532 4.1 50.8 1.0
CB B:ALA532 4.2 47.2 1.0
OD1 B:ASP664 4.4 66.9 1.0
CB B:ASP534 4.5 50.5 1.0
C B:PRO707 4.5 47.8 1.0
N B:ASP534 4.7 50.1 1.0
CA B:ALA532 4.8 46.6 1.0
CA B:PRO707 4.8 43.8 1.0
CD B:PRO707 4.9 45.0 1.0
CA B:ASP534 5.0 49.2 1.0

Reference:

A.El Sahili, T.S.Soh, J.Schiltz, A.Gharbi-Ayachi, B.C.Goh, C.C.Seh, P.C.Dedon, P.Y.Shi, S.P.Lim, J.Lescar. A Conformation of Dengue Virus Serotype 2 NS5 Akin to Its Zikv and Jev Homologues. To Be Published.
Page generated: Mon Dec 14 22:18:05 2020

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