Zinc in PDB 5u0c: Structure of Zika Virus NS5 Rna Polymerase Domain

All present enzymatic activity of Structure of Zika Virus NS5 Rna Polymerase Domain:
2.1.1.56; 2.1.1.57; 2.7.7.48;

The structure of Structure of Zika Virus NS5 Rna Polymerase Domain, PDB code: 5u0c was solved by B.Zhao, F.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.14 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	121.520, 188.710, 192.539, 90.00, 91.99, 90.00
R / Rfree (%)	22.6 / 26

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of Zika Virus NS5 Rna Polymerase Domain (pdb code 5u0c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of Zika Virus NS5 Rna Polymerase Domain, PDB code: 5u0c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:58.1 occ:1.00 OE2 A:GLU439 1.9 65.6 1.0 NE2 A:HIS443 2.1 63.5 1.0 SG A:CYS451 2.4 59.8 1.0 SG A:CYS448 2.4 62.6 1.0 CD A:GLU439 2.9 67.1 1.0 CE1 A:HIS443 3.0 62.6 1.0 CD2 A:HIS443 3.0 65.6 1.0 CG A:GLU439 3.3 66.5 1.0 CB A:CYS451 3.3 58.5 1.0 CB A:CYS448 3.6 65.2 1.0 CA A:CYS448 3.8 67.7 1.0 N A:CYS451 3.9 61.5 1.0 OE1 A:GLU439 4.0 69.3 1.0 N A:HIS449 4.0 68.9 1.0 ND1 A:HIS443 4.1 64.1 1.0 CG A:HIS443 4.1 66.1 1.0 CA A:CYS451 4.2 59.2 1.0 N A:SER450 4.3 66.6 1.0 C A:CYS448 4.3 68.4 1.0 C A:SER450 4.7 62.9 1.0 CB A:GLU439 4.8 68.9 1.0 O A:GLU439 4.9 70.4 1.0 NE A:ARG281 4.9 60.0 1.0 OG A:SER450 5.0 66.9 1.0

Zinc binding site 2 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:42.1 occ:1.00 NE2 A:HIS714 2.0 35.0 1.0 SG A:CYS849 2.3 34.3 1.0 SG A:CYS730 2.3 32.9 1.0 CD2 A:HIS714 2.9 35.9 1.0 CE1 A:HIS714 3.0 35.2 1.0 CB A:CYS730 3.3 33.7 1.0 CB A:CYS849 3.6 31.9 1.0 OD1 A:ASN716 3.9 36.5 1.0 CG A:HIS714 4.1 36.6 1.0 ND1 A:HIS714 4.1 36.2 1.0 CD1 A:LEU841 4.5 33.0 1.0 C A:CYS730 4.5 33.6 1.0 CA A:CYS730 4.5 33.5 1.0 N A:ARG731 4.6 33.6 1.0 O A:GLU845 4.7 33.8 1.0 O A:ARG731 4.7 33.4 1.0 CG A:ASN716 4.8 36.8 1.0 NH1 A:ARG771 4.8 30.9 1.0 CA A:CYS849 4.9 31.6 1.0 O A:CYS730 5.0 34.4 1.0 C A:ARG731 5.0 34.1 1.0

Zinc binding site 3 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:54.8 occ:1.00 NE2 B:HIS443 2.1 43.6 1.0 OE1 B:GLU439 2.2 47.3 1.0 SG B:CYS448 2.3 43.2 1.0 SG B:CYS451 2.3 41.1 1.0 CE1 B:HIS443 3.0 42.9 1.0 CD B:GLU439 3.1 49.3 1.0 CD2 B:HIS443 3.2 45.8 1.0 CB B:CYS451 3.2 40.3 1.0 OE2 B:GLU439 3.4 51.7 1.0 CB B:CYS448 3.5 45.1 1.0 N B:CYS451 3.7 42.5 1.0 CA B:CYS448 3.8 46.4 1.0 N B:HIS449 4.0 45.4 1.0 CA B:CYS451 4.0 40.8 1.0 ND1 B:HIS443 4.2 44.4 1.0 CG B:HIS443 4.3 46.4 1.0 C B:CYS448 4.3 46.7 1.0 N B:SER450 4.3 47.4 1.0 CG B:GLU439 4.4 50.1 1.0 C B:SER450 4.7 44.3 1.0 OG B:SER450 5.0 47.1 1.0

Zinc binding site 4 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:47.8 occ:1.00 NE2 B:HIS714 2.0 28.1 1.0 SG B:CYS849 2.3 27.5 1.0 SG B:CYS730 2.3 27.2 1.0 CD2 B:HIS714 2.9 28.6 1.0 CE1 B:HIS714 3.1 28.0 1.0 CB B:CYS730 3.3 27.4 1.0 CB B:CYS849 3.6 26.8 1.0 ND2 B:ASN716 4.0 24.9 1.0 CG B:HIS714 4.0 28.5 1.0 ND1 B:HIS714 4.1 28.1 1.0 CD1 B:LEU841 4.3 22.4 1.0 C B:CYS730 4.5 26.8 1.0 CA B:CYS730 4.5 27.0 1.0 CG B:ASN716 4.6 25.4 1.0 N B:ARG731 4.7 30.1 1.0 NH1 B:ARG771 4.7 24.8 1.0 O B:GLU845 4.8 29.6 1.0 OD1 B:ASN716 4.8 25.7 1.0 O B:ARG731 4.8 30.6 1.0 O B:CYS730 4.9 26.9 1.0 CA B:CYS849 4.9 27.6 1.0

Zinc binding site 5 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:69.0 occ:1.00 OE1 C:GLU439 2.2 73.3 1.0 CE1 C:HIS443 2.3 72.2 1.0 SG C:CYS451 2.3 67.5 1.0 SG C:CYS448 2.4 69.0 1.0 NE2 C:HIS443 3.1 71.9 1.0 CD C:GLU439 3.2 74.9 1.0 CB C:CYS451 3.3 65.4 1.0 ND1 C:HIS443 3.4 74.2 1.0 OE2 C:GLU439 3.5 75.5 1.0 CB C:CYS448 3.5 71.1 1.0 CA C:CYS448 3.8 73.7 1.0 N C:HIS449 4.2 74.4 1.0 N C:CYS451 4.2 67.0 1.0 CD2 C:TYR572 4.3 70.4 1.0 C C:SER450 4.3 69.9 1.0 CA C:CYS451 4.3 65.1 1.0 CD2 C:HIS443 4.4 73.7 1.0 O C:SER450 4.4 70.5 1.0 C C:CYS448 4.4 73.7 1.0 N C:SER450 4.4 73.3 1.0 CG C:HIS443 4.5 75.2 1.0 CG C:GLU439 4.5 76.4 1.0 CB C:TYR572 4.8 65.5 1.0 O C:GLU447 4.9 77.2 1.0 CG C:TYR572 4.9 69.0 1.0

Zinc binding site 6 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:42.6 occ:1.00 NE2 C:HIS714 2.0 26.9 1.0 SG C:CYS730 2.3 28.4 1.0 SG C:CYS849 2.3 33.8 1.0 CE1 C:HIS714 2.9 26.5 1.0 CD2 C:HIS714 3.1 26.8 1.0 CB C:CYS730 3.2 29.2 1.0 CB C:CYS849 3.6 33.4 1.0 ND2 C:ASN716 3.7 30.1 1.0 ND1 C:HIS714 4.1 26.0 1.0 CG C:HIS714 4.1 26.2 1.0 CD1 C:LEU841 4.2 32.1 1.0 C C:CYS730 4.4 26.9 1.0 CA C:CYS730 4.4 28.3 1.0 N C:ARG731 4.6 28.5 1.0 CG C:ASN716 4.7 29.8 1.0 O C:ARG731 4.7 28.2 1.0 O C:CYS730 4.7 27.3 1.0 NH1 C:ARG771 4.9 29.3 1.0 OD1 C:ASN716 4.9 28.6 1.0 CA C:CYS849 4.9 33.4 1.0

Zinc binding site 7 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:48.2 occ:1.00 NE2 D:HIS443 2.1 43.1 1.0 OE2 D:GLU439 2.1 46.4 1.0 SG D:CYS451 2.3 41.0 1.0 SG D:CYS448 2.3 39.6 1.0 CE1 D:HIS443 3.0 42.3 1.0 CD2 D:HIS443 3.1 45.1 1.0 CB D:CYS451 3.2 40.5 1.0 CD D:GLU439 3.2 47.2 1.0 CB D:CYS448 3.5 41.6 1.0 CG D:GLU439 3.7 44.7 1.0 N D:CYS451 3.8 46.4 1.0 CA D:CYS448 3.9 45.0 1.0 CA D:CYS451 4.1 42.5 1.0 ND1 D:HIS443 4.1 42.6 1.0 N D:HIS449 4.2 45.9 1.0 CG D:HIS443 4.2 44.1 1.0 OE1 D:GLU439 4.3 49.3 1.0 C D:CYS448 4.4 46.5 1.0 N D:SER450 4.5 50.1 1.0 CB D:TYR572 4.6 38.3 1.0 CD2 D:TYR572 4.7 41.6 1.0 CG D:TYR572 4.8 39.8 1.0 C D:SER450 4.9 46.8 1.0

Zinc binding site 8 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:44.4 occ:1.00 NE2 D:HIS714 2.0 29.8 1.0 SG D:CYS730 2.3 31.1 1.0 SG D:CYS849 2.3 33.9 1.0 CE1 D:HIS714 2.9 29.1 1.0 CD2 D:HIS714 3.1 29.6 1.0 CB D:CYS730 3.2 30.5 1.0 CB D:CYS849 3.5 34.0 1.0 ND2 D:ASN716 3.8 33.8 1.0 ND1 D:HIS714 4.1 28.4 1.0 CG D:HIS714 4.2 28.7 1.0 CD1 D:LEU841 4.2 38.0 1.0 CA D:CYS730 4.5 29.8 1.0 C D:CYS730 4.5 29.7 1.0 N D:ARG731 4.6 32.4 1.0 CG D:ASN716 4.7 33.9 1.0 O D:ARG731 4.7 33.2 1.0 NH1 D:ARG771 4.8 34.7 1.0 O D:GLU845 4.8 43.0 1.0 CA D:CYS849 4.9 36.0 1.0 OD1 D:ASN716 4.9 34.1 1.0 O D:CYS730 5.0 29.3 1.0

Zinc binding site 9 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:65.2 occ:1.00 NE2 E:HIS443 2.0 71.2 1.0 OE2 E:GLU439 2.3 75.5 1.0 SG E:CYS451 2.4 69.2 1.0 SG E:CYS448 2.4 71.9 1.0 CD2 E:HIS443 3.0 72.9 1.0 CE1 E:HIS443 3.1 69.5 1.0 CD E:GLU439 3.2 77.2 1.0 CB E:CYS451 3.4 68.2 1.0 CB E:CYS448 3.5 73.8 1.0 CG E:GLU439 3.7 76.1 1.0 N E:CYS451 3.7 72.7 1.0 CA E:CYS448 3.7 76.7 1.0 N E:HIS449 4.0 79.3 1.0 ND1 E:HIS443 4.1 70.0 1.0 OE1 E:GLU439 4.2 80.0 1.0 CG E:HIS443 4.2 72.2 1.0 CA E:CYS451 4.2 70.0 1.0 N E:SER450 4.2 78.2 1.0 C E:CYS448 4.3 78.5 1.0 C E:SER450 4.7 74.8 1.0 CA E:SER450 4.9 77.7 1.0 O E:GLU447 4.9 77.7 1.0

Zinc binding site 10 out of 16 in the Structure of Zika Virus NS5 Rna Polymerase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Zika Virus NS5 Rna Polymerase Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1002 b:52.5 occ:1.00 NE2 E:HIS714 2.1 32.2 1.0 SG E:CYS849 2.3 32.2 1.0 SG E:CYS730 2.3 30.5 1.0 CD2 E:HIS714 2.9 32.0 1.0 CE1 E:HIS714 3.1 32.6 1.0 CB E:CYS730 3.3 29.8 1.0 CB E:CYS849 3.5 31.8 1.0 CG E:HIS714 4.1 32.2 1.0 ND2 E:ASN716 4.2 32.7 1.0 ND1 E:HIS714 4.2 32.5 1.0 CD1 E:LEU841 4.4 29.1 1.0 CA E:CYS730 4.5 29.5 1.0 C E:CYS730 4.5 30.1 1.0 OD1 E:ASN716 4.6 32.6 1.0 O E:ARG731 4.7 34.6 1.0 CG E:ASN716 4.7 32.4 1.0 NH1 E:ARG771 4.8 30.3 1.0 N E:ARG731 4.8 33.6 1.0 O E:CYS730 4.8 30.2 1.0 O E:GLU845 4.9 33.7 1.0 CA E:CYS849 4.9 33.0 1.0

B.Zhao, G.Yi, F.Du, Y.C.Chuang, R.C.Vaughan, B.Sankaran, C.C.Kao, P.Li. Structure and Function of the Zika Virus Full-Length NS5 Protein. Nat Commun V. 8 14762 2017.
ISSN: ESSN 2041-1723
PubMed: 28345656
DOI: 10.1038/NCOMMS14762