Zinc in PDB 5tfr: Crystal Structure of Zika Virus NS5 Protein

All present enzymatic activity of Crystal Structure of Zika Virus NS5 Protein:
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 Zika Virus NS5 Protein, PDB code: 5tfr was solved by K.L.Longenecker, A.K.Upadhyay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.66 / 3.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	136.013, 196.412, 94.983, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.7

The binding sites of Zinc atom in the Crystal Structure of Zika Virus NS5 Protein (pdb code 5tfr). 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 Zika Virus NS5 Protein, PDB code: 5tfr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Zika Virus NS5 Protein


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 Zika Virus NS5 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:46.0 occ:1.00 NE2 A:HIS443 2.2 57.1 1.0 SG A:CYS448 2.2 49.3 1.0 OE2 A:GLU439 2.2 46.9 1.0 SG A:CYS451 2.3 54.0 1.0 CD2 A:HIS443 3.1 57.2 1.0 CD A:GLU439 3.2 54.7 1.0 CE1 A:HIS443 3.2 57.1 1.0 CB A:CYS451 3.3 49.6 1.0 CB A:CYS448 3.4 45.8 1.0 CG A:GLU439 3.4 55.2 1.0 CA A:CYS448 3.6 46.4 1.0 N A:CYS451 3.8 48.3 1.0 N A:HIS449 4.0 48.6 1.0 CA A:CYS451 4.2 48.9 1.0 C A:CYS448 4.2 52.4 1.0 CG A:HIS443 4.3 56.1 1.0 N A:SER450 4.3 48.7 1.0 OE1 A:GLU439 4.3 48.9 1.0 ND1 A:HIS443 4.3 58.0 1.0 C A:SER450 4.7 51.8 1.0 OG1 A:THR573 4.7 54.1 1.0 OG A:SER450 4.7 55.2 1.0 O A:GLU447 4.8 51.2 1.0 N A:CYS448 4.9 47.3 1.0 CB A:GLU439 4.9 51.7 1.0 CA A:SER450 5.0 48.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Zika Virus NS5 Protein


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 Zika Virus NS5 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:85.0 occ:1.00 NE2 A:HIS714 2.2 64.3 1.0 SG A:CYS849 2.2 79.5 1.0 SG A:CYS730 2.2 53.8 1.0 CE1 A:HIS714 3.1 63.9 1.0 CD2 A:HIS714 3.2 64.1 1.0 CB A:CYS849 3.4 75.7 1.0 CB A:CYS730 3.4 49.3 1.0 OD1 A:ASN716 3.8 77.7 1.0 CD2 A:LEU841 4.1 82.6 1.0 ND1 A:HIS714 4.3 64.0 1.0 CG A:HIS714 4.3 61.6 1.0 O A:GLU845 4.5 87.7 1.0 C A:CYS730 4.6 55.5 1.0 CA A:CYS730 4.6 48.9 1.0 N A:ARG731 4.6 52.7 1.0 O A:HOH1182 4.7 34.2 1.0 O A:ARG731 4.7 58.0 1.0 CA A:CYS849 4.8 75.5 1.0 CG A:ASN716 4.8 78.6 1.0 NH1 A:ARG771 4.9 72.4 1.0 ND2 A:ASN716 5.0 69.5 1.0 O A:CYS730 5.0 56.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Zika Virus NS5 Protein


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 Zika Virus NS5 Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:57.2 occ:1.00 OE2 B:GLU439 2.1 59.2 1.0 SG B:CYS448 2.2 53.4 1.0 NE2 B:HIS443 2.2 49.3 1.0 SG B:CYS451 2.3 61.3 1.0 CD B:GLU439 3.1 73.6 1.0 CD2 B:HIS443 3.1 49.5 1.0 CE1 B:HIS443 3.3 49.5 1.0 CB B:CYS451 3.3 56.7 1.0 CG B:GLU439 3.4 64.4 1.0 CB B:CYS448 3.4 50.1 1.0 CA B:CYS448 3.6 50.7 1.0 N B:CYS451 3.7 55.4 1.0 N B:HIS449 4.0 51.8 1.0 CA B:CYS451 4.2 55.5 1.0 C B:CYS448 4.2 55.3 1.0 N B:SER450 4.3 57.8 1.0 OE1 B:GLU439 4.3 62.0 1.0 CG B:HIS443 4.3 48.2 1.0 ND1 B:HIS443 4.4 50.4 1.0 C B:SER450 4.7 59.4 1.0 OG B:SER450 4.7 74.0 1.0 O B:GLU447 4.8 55.9 1.0 OG1 B:THR573 4.8 41.1 1.0 N B:CYS448 4.9 52.6 1.0 CB B:GLU439 4.9 54.5 1.0 CA B:SER450 5.0 57.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Zika Virus NS5 Protein


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 Zika Virus NS5 Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:94.6 occ:1.00 SG B:CYS849 2.3 78.5 1.0 NE2 B:HIS714 2.4 66.0 1.0 SG B:CYS730 2.4 68.6 1.0 CD2 B:HIS714 3.4 66.0 1.0 CE1 B:HIS714 3.4 65.6 1.0 CB B:CYS849 3.5 74.7 1.0 OD1 B:ASN716 3.6 82.0 1.0 CB B:CYS730 3.6 64.0 1.0 CD2 B:LEU841 3.8 89.0 1.0 O B:GLU845 4.3 89.2 1.0 CG B:HIS714 4.5 63.5 1.0 CG B:ASN716 4.5 88.9 1.0 ND1 B:HIS714 4.6 65.7 1.0 ND2 B:ASN716 4.7 82.3 1.0 C B:GLU845 4.8 90.5 1.0 CA B:CYS849 4.8 74.5 1.0 CA B:CYS730 4.8 63.2 1.0 C B:CYS730 4.9 67.5 1.0 CB B:GLU845 4.9 90.9 1.0 CG B:LEU841 4.9 88.1 1.0 N B:ARG731 4.9 61.8 1.0 O B:ARG731 5.0 63.9 1.0

A.K.Upadhyay, M.Cyr, K.Longenecker, R.Tripathi, C.Sun, D.J.Kempf. Crystal Structure of Full-Length Zika Virus NS5 Protein Reveals A Conformation Similar to Japanese Encephalitis Virus NS5. Acta Crystallogr F Struct V. 73 116 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28291746
DOI: 10.1107/S2053230X17001601