Zinc in PDB 6qsn: Crystal Structure of Yellow Fever Virus Polymerase NS5A

All present enzymatic activity of Crystal Structure of Yellow Fever Virus Polymerase NS5A:
2.1.1.56; 2.1.1.57; 2.7.7.48; 3.4.21.91; 3.6.1.15; 3.6.4.13;

The structure of Crystal Structure of Yellow Fever Virus Polymerase NS5A, PDB code: 6qsn was solved by E.Boura, A.Dubankova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.01 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.285, 142.114, 152.177, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27.1

The binding sites of Zinc atom in the Crystal Structure of Yellow Fever Virus Polymerase NS5A (pdb code 6qsn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Yellow Fever Virus Polymerase NS5A, PDB code: 6qsn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Yellow Fever Virus Polymerase NS5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Yellow Fever Virus Polymerase NS5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:43.6 occ:1.00 NE2 A:HIS443 2.0 51.8 1.0 OE2 A:GLU439 2.0 62.1 1.0 SG A:CYS448 2.3 60.0 1.0 SG A:CYS451 2.4 67.5 1.0 CE1 A:HIS443 2.8 47.4 1.0 CB A:CYS451 2.9 51.7 1.0 CD2 A:HIS443 3.1 59.2 1.0 CD A:GLU439 3.2 56.8 1.0 N A:CYS451 3.5 47.6 1.0 CB A:CYS448 3.5 52.7 1.0 OE1 A:GLU439 3.6 58.3 1.0 CA A:CYS451 3.8 52.3 1.0 CA A:CYS448 3.9 56.1 1.0 ND1 A:HIS443 4.0 50.3 1.0 N A:ARG449 4.1 64.8 1.0 CG A:HIS443 4.1 56.2 1.0 N A:THR450 4.2 60.7 1.0 C A:CYS448 4.4 58.9 1.0 CG A:GLU439 4.4 61.3 1.0 C A:THR450 4.5 53.3 1.0 OG1 A:THR450 4.6 47.0 1.0 NH1 A:ARG281 4.7 63.2 1.0 CD1 A:LEU485 4.8 43.2 1.0 CA A:THR450 4.9 58.0 1.0 OG1 A:THR573 4.9 49.7 1.0 C A:CYS451 4.9 52.3 1.0 CB A:GLU439 5.0 57.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Yellow Fever Virus Polymerase NS5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Yellow Fever Virus Polymerase NS5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:57.8 occ:1.00 NE2 A:HIS716 2.0 62.1 1.0 NE2 A:HIS718 2.1 59.8 1.0 SG A:CYS851 2.3 59.9 1.0 SG A:CYS732 2.4 60.5 1.0 CB A:CYS732 2.9 54.7 1.0 CD2 A:HIS718 2.9 53.0 1.0 CE1 A:HIS716 2.9 57.6 1.0 CD2 A:HIS716 3.0 62.4 1.0 CE1 A:HIS718 3.2 60.5 1.0 CB A:CYS851 3.3 57.9 1.0 ND1 A:HIS716 4.0 54.4 1.0 CG A:HIS718 4.1 53.8 1.0 CG A:HIS716 4.1 60.6 1.0 ND1 A:HIS718 4.2 57.2 1.0 CA A:CYS732 4.2 61.6 1.0 C A:CYS732 4.4 64.7 1.0 CD1 A:LEU843 4.6 64.0 1.0 N A:ARG733 4.6 55.8 1.0 CA A:CYS851 4.7 56.5 1.0 CG A:GLN847 4.8 66.8 1.0 O A:CYS732 4.8 62.6 1.0 NZ A:LYS773 4.9 59.1 1.0 O A:GLN847 4.9 68.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Yellow Fever Virus Polymerase NS5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Yellow Fever Virus Polymerase NS5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:59.2 occ:1.00 OE2 B:GLU439 1.9 49.2 1.0 NE2 B:HIS443 2.1 56.5 1.0 SG B:CYS448 2.3 61.4 1.0 SG B:CYS451 2.4 57.8 1.0 CB B:CYS451 2.8 53.0 1.0 CE1 B:HIS443 2.9 50.8 1.0 CD B:GLU439 3.0 59.6 1.0 CD2 B:HIS443 3.2 59.2 1.0 N B:CYS451 3.4 56.9 1.0 CB B:CYS448 3.4 56.5 1.0 CA B:CYS451 3.7 57.0 1.0 CG B:GLU439 3.8 59.5 1.0 CA B:CYS448 3.8 65.3 1.0 OE1 B:GLU439 4.0 62.0 1.0 ND1 B:HIS443 4.1 45.5 1.0 N B:ARG449 4.1 60.7 1.0 CG B:HIS443 4.3 53.4 1.0 N B:THR450 4.3 57.9 1.0 C B:CYS448 4.3 66.0 1.0 C B:THR450 4.5 48.1 1.0 OG1 B:THR573 4.6 53.5 1.0 OG1 B:THR450 4.7 63.4 1.0 C B:CYS451 4.8 61.1 1.0 O B:CYS451 4.9 64.8 1.0 CA B:THR450 4.9 56.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Yellow Fever Virus Polymerase NS5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Yellow Fever Virus Polymerase NS5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1007 b:65.0 occ:1.00 NE2 B:HIS716 2.0 52.4 1.0 NE2 B:HIS718 2.1 63.0 1.0 SG B:CYS851 2.3 46.6 1.0 SG B:CYS732 2.4 53.2 1.0 CD2 B:HIS718 2.7 57.4 1.0 CB B:CYS732 2.9 51.8 1.0 CE1 B:HIS716 3.0 56.9 1.0 CD2 B:HIS716 3.0 55.8 1.0 CE1 B:HIS718 3.3 54.2 1.0 CB B:CYS851 3.3 58.6 1.0 CG B:HIS718 4.0 55.0 1.0 ND1 B:HIS716 4.1 51.2 1.0 CG B:HIS716 4.1 55.3 1.0 ND1 B:HIS718 4.2 60.2 1.0 CA B:CYS732 4.2 52.0 1.0 CD1 B:LEU843 4.4 57.0 1.0 C B:CYS732 4.4 54.3 1.0 N B:ARG733 4.7 54.2 1.0 CA B:CYS851 4.8 60.5 1.0 O B:CYS732 4.9 54.8 1.0 O B:GLN847 4.9 66.8 1.0 NZ B:LYS773 4.9 58.2 1.0

A.Dubankova, E.Boura. Structure of the Yellow Fever NS5 Protein Reveals Conserved Drug Targets Shared Among Flaviviruses. Antiviral Res. V. 169 04536 2019.
ISSN: ISSN 0166-3542
PubMed: 31202975
DOI: 10.1016/J.ANTIVIRAL.2019.104536