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

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

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Dengue Virus Non Structural Protein 5 (pdb code 5zqk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dengue Virus Non Structural Protein 5, PDB code: 5zqk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Dengue Virus Non Structural Protein 5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue Virus Non Structural Protein 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:55.8 occ:1.00 CE1 A:HIS712 2.1 51.8 1.0 NE2 A:HIS714 2.2 50.6 1.0 SG A:CYS847 2.2 51.2 1.0 SG A:CYS728 2.3 51.4 1.0 NE2 A:HIS712 2.9 52.0 1.0 CD2 A:HIS714 3.1 51.4 1.0 ND1 A:HIS712 3.1 52.5 1.0 CB A:CYS728 3.2 47.6 1.0 CB A:CYS847 3.2 48.0 1.0 CE1 A:HIS714 3.3 50.5 1.0 CD2 A:HIS712 4.1 52.0 1.0 CG A:HIS712 4.2 50.4 1.0 O A:HOH1151 4.2 55.0 1.0 CG A:HIS714 4.3 50.5 1.0 ND1 A:HIS714 4.4 51.2 1.0 CA A:CYS728 4.4 47.8 1.0 N A:ARG729 4.5 49.4 1.0 C A:CYS728 4.5 52.4 1.0 CD1 A:LEU839 4.6 54.9 1.0 O A:ARG729 4.6 51.9 1.0 CA A:CYS847 4.6 48.8 1.0 O A:HOH1521 5.0 54.9 1.0

Zinc binding site 2 out of 4 in the Dengue Virus Non Structural Protein 5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue Virus Non Structural Protein 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:53.1 occ:1.00 NE2 A:HIS442 2.0 58.7 1.0 OE2 A:GLU438 2.1 66.0 1.0 SG A:CYS450 2.3 52.5 1.0 SG A:CYS447 2.3 55.7 1.0 CE1 A:HIS442 2.9 58.1 1.0 CD2 A:HIS442 3.1 58.9 1.0 CD A:GLU438 3.1 66.4 1.0 CB A:CYS450 3.1 49.5 1.0 CB A:CYS447 3.4 51.6 1.0 CG A:GLU438 3.5 57.2 1.0 N A:CYS450 3.8 52.0 1.0 CA A:CYS447 3.8 51.7 1.0 CA A:CYS450 4.1 50.5 1.0 ND1 A:HIS442 4.1 58.4 1.0 N A:GLU448 4.1 50.7 1.0 CG A:HIS442 4.2 56.9 1.0 CG2 A:THR572 4.2 57.7 1.0 OE1 A:GLU438 4.2 68.6 1.0 N A:THR449 4.3 48.2 1.0 OG1 A:THR449 4.4 51.0 1.0 C A:CYS447 4.4 54.4 1.0 O A:HOH1265 4.6 48.9 1.0 C A:THR449 4.8 55.3 1.0 O A:LYS446 4.8 53.9 1.0 CA A:THR449 5.0 48.1 1.0

Zinc binding site 3 out of 4 in the Dengue Virus Non Structural Protein 5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dengue Virus Non Structural Protein 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1005 b:52.5 occ:1.00 NE2 B:HIS442 2.1 59.6 1.0 OE2 B:GLU438 2.1 62.4 1.0 SG B:CYS450 2.2 58.9 1.0 SG B:CYS447 2.3 52.6 1.0 CE1 B:HIS442 3.0 59.1 1.0 CD B:GLU438 3.1 68.3 1.0 CB B:CYS450 3.1 54.1 1.0 CD2 B:HIS442 3.1 60.3 1.0 CB B:CYS447 3.4 50.1 1.0 CG B:GLU438 3.5 54.5 1.0 N B:CYS450 3.7 53.1 1.0 CA B:CYS447 3.8 51.1 1.0 CA B:CYS450 4.0 52.9 1.0 N B:GLU448 4.1 51.6 1.0 ND1 B:HIS442 4.2 60.1 1.0 OE1 B:GLU438 4.2 72.7 1.0 CG2 B:THR572 4.2 37.3 1.0 CG B:HIS442 4.2 59.1 1.0 N B:THR449 4.3 53.7 1.0 OG1 B:THR449 4.3 60.2 1.0 C B:CYS447 4.4 52.0 1.0 C B:THR449 4.7 56.5 1.0 O B:HOH1173 4.7 45.5 1.0 O B:LYS446 4.9 56.8 1.0 CA B:THR449 4.9 53.6 1.0

Zinc binding site 4 out of 4 in the Dengue Virus Non Structural Protein 5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dengue Virus Non Structural Protein 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:57.9 occ:1.00 CE1 B:HIS712 2.2 55.6 1.0 NE2 B:HIS714 2.2 54.9 1.0 SG B:CYS847 2.2 57.8 1.0 SG B:CYS728 2.3 58.4 1.0 NE2 B:HIS712 3.0 55.9 1.0 CD2 B:HIS714 3.1 55.0 1.0 CB B:CYS728 3.1 53.5 1.0 ND1 B:HIS712 3.2 56.3 1.0 CB B:CYS847 3.3 54.5 1.0 CE1 B:HIS714 3.3 54.4 1.0 CD2 B:HIS712 4.2 56.4 1.0 CG B:HIS714 4.3 53.2 1.0 CG B:HIS712 4.3 54.6 1.0 ND1 B:HIS714 4.4 54.7 1.0 CA B:CYS728 4.4 52.0 1.0 CD1 B:LEU839 4.4 60.2 1.0 N B:ARG729 4.5 54.2 1.0 C B:CYS728 4.5 56.3 1.0 O B:ARG729 4.7 60.5 1.0 CA B:CYS847 4.7 55.2 1.0 O B:HOH1481 4.7 63.7 1.0

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.