Zinc in PDB 5m2x: Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)

The structure of Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033), PDB code: 5m2x was solved by D.S.Ferrero, V.M.Ruiz-Arroyo, N.Soler, I.Uson, N.Verdaguer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.52 / 4.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	191.060, 192.060, 407.230, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27.6

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) (pdb code 5m2x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033), PDB code: 5m2x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


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 the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:0.2 occ:1.00 SG A:CYS849 2.4 0.7 1.0 SG A:CYS730 2.5 0.4 1.0 NE2 A:HIS714 2.6 0.3 1.0 CD2 A:HIS714 3.2 0.7 1.0 OD1 A:ASN716 3.2 0.5 1.0 CB A:CYS730 3.3 0.9 1.0 CE1 A:HIS714 3.6 0.3 1.0 CB A:CYS849 3.8 0.2 1.0 CD2 A:LEU841 4.0 0.3 1.0 CG A:HIS714 4.4 0.5 1.0 CG A:ASN716 4.4 0.1 1.0 ND1 A:HIS714 4.5 0.8 1.0 O A:GLU845 4.7 0.4 1.0 CA A:CYS730 4.7 0.5 1.0 O A:HIS714 4.8 0.1 1.0 C A:CYS730 4.9 0.7 1.0 N A:ARG731 5.0 0.6 1.0

Zinc binding site 2 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


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 the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:0.5 occ:1.00 OE2 A:GLU439 2.1 0.9 1.0 NE2 A:HIS443 2.1 0.3 1.0 SG A:CYS451 2.4 0.4 1.0 SG A:CYS448 2.5 0.7 1.0 CD2 A:HIS443 3.0 0.5 1.0 CD A:GLU439 3.1 0.7 1.0 CB A:CYS451 3.1 0.3 1.0 CE1 A:HIS443 3.2 0.8 1.0 N A:CYS451 3.5 0.6 1.0 CB A:CYS448 3.5 0.9 1.0 CG A:GLU439 3.7 0.5 1.0 CA A:CYS448 3.7 0.9 1.0 CA A:CYS451 3.9 0.5 1.0 N A:GLN449 4.1 0.3 1.0 OE1 A:GLU439 4.2 0.1 1.0 CG A:HIS443 4.2 0.5 1.0 ND1 A:HIS443 4.2 0.4 1.0 N A:SER450 4.2 0.2 1.0 C A:CYS448 4.3 0.4 1.0 C A:SER450 4.6 0.7 1.0 OG A:SER450 4.6 0.7 1.0 CD1 A:LEU485 4.8 0.6 1.0 CA A:SER450 4.9 0.8 1.0

Zinc binding site 3 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


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 the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:0.9 occ:1.00 SG B:CYS849 2.3 0.2 1.0 NE2 B:HIS714 2.5 0.2 1.0 SG B:CYS730 2.6 0.6 1.0 CD2 B:HIS714 3.2 0.2 1.0 OD1 B:ASN716 3.3 0.8 1.0 CB B:CYS730 3.5 0.6 1.0 CE1 B:HIS714 3.6 0.8 1.0 CB B:CYS849 3.8 0.5 1.0 CD2 B:LEU841 4.0 0.6 1.0 CG B:HIS714 4.4 0.8 1.0 CG B:ASN716 4.4 0.0 1.0 ND1 B:HIS714 4.5 0.2 1.0 O B:GLU845 4.6 0.7 1.0 CA B:CYS730 4.9 0.8 1.0 O B:HIS714 4.9 0.5 1.0

Zinc binding site 4 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


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 the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:0.1 occ:1.00 SG C:CYS849 2.4 0.3 1.0 SG C:CYS730 2.7 0.8 1.0 NE2 C:HIS714 2.8 0.7 1.0 OD1 C:ASN716 3.2 0.7 1.0 CD2 C:HIS714 3.4 0.2 1.0 CB C:CYS730 3.6 0.3 1.0 CD2 C:LEU841 3.8 0.3 1.0 CB C:CYS849 3.8 0.3 1.0 CE1 C:HIS714 3.9 0.7 1.0 CG C:ASN716 4.4 0.8 1.0 O C:GLU845 4.5 0.6 1.0 CG C:HIS714 4.6 0.3 1.0 ND1 C:HIS714 4.8 0.5 1.0 ND2 C:ASN716 5.0 0.8 1.0

Zinc binding site 5 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1004 b:0.3 occ:1.00 OE2 C:GLU439 2.0 0.1 1.0 NE2 C:HIS443 2.1 0.5 1.0 SG C:CYS448 2.4 0.1 1.0 SG C:CYS451 2.5 0.4 1.0 CD2 C:HIS443 2.9 0.3 1.0 CD C:GLU439 3.0 0.8 1.0 CE1 C:HIS443 3.1 0.1 1.0 CB C:CYS451 3.3 0.5 1.0 CB C:CYS448 3.4 0.9 1.0 CG C:GLU439 3.5 0.0 1.0 N C:CYS451 3.6 0.9 1.0 CA C:CYS448 3.6 0.2 1.0 N C:GLN449 4.0 0.0 1.0 CA C:CYS451 4.0 0.8 1.0 OE1 C:GLU439 4.0 0.5 1.0 CG C:HIS443 4.1 0.3 1.0 ND1 C:HIS443 4.1 0.5 1.0 N C:SER450 4.1 0.4 1.0 C C:CYS448 4.2 0.7 1.0 OG C:SER450 4.5 1.0 1.0 C C:SER450 4.6 0.1 1.0 CD1 C:LEU485 4.8 0.1 1.0 CA C:SER450 4.9 0.7 1.0 N C:CYS448 4.9 0.6 1.0 CB C:GLU439 5.0 0.1 1.0 O C:GLU439 5.0 0.3 1.0 C C:GLN449 5.0 0.9 1.0

Zinc binding site 6 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1006 b:0.1 occ:1.00 NE2 D:HIS714 2.0 0.4 1.0 SG D:CYS730 2.3 0.3 1.0 SG D:CYS849 2.4 0.3 1.0 CD2 D:HIS714 2.8 0.4 1.0 CE1 D:HIS714 3.0 0.1 1.0 CB D:CYS730 3.2 0.6 1.0 OD1 D:ASN716 3.6 0.4 1.0 CB D:CYS849 3.8 0.7 1.0 CG D:HIS714 3.9 0.8 1.0 ND1 D:HIS714 3.9 0.3 1.0 CA D:CYS730 4.5 0.4 1.0 C D:CYS730 4.5 0.1 1.0 N D:ARG731 4.5 0.6 1.0 O D:HIS714 4.6 0.7 1.0 CD2 D:LEU841 4.6 0.6 1.0 O D:ARG731 4.7 0.7 1.0 CG D:ASN716 4.8 0.4 1.0 O D:CYS730 5.0 0.6 1.0 CA D:ARG731 5.0 0.9 1.0

Zinc binding site 7 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1007 b:0.3 occ:1.00 OE2 D:GLU439 1.9 1.0 1.0 SG D:CYS451 2.3 77.1 1.0 SG D:CYS448 2.6 1.0 1.0 CD D:GLU439 2.6 0.6 1.0 NE2 D:HIS443 2.7 0.1 1.0 N D:CYS451 3.0 0.8 1.0 CG D:GLU439 3.1 0.1 1.0 CB D:CYS451 3.1 94.9 1.0 CD2 D:HIS443 3.5 0.4 1.0 N D:SER450 3.6 0.6 1.0 CA D:CYS451 3.6 0.1 1.0 OE1 D:GLU439 3.7 0.6 1.0 CE1 D:HIS443 3.7 0.5 1.0 CB D:CYS448 3.8 0.8 1.0 N D:GLN449 3.8 0.5 1.0 OG D:SER450 3.8 98.5 1.0 CA D:CYS448 3.9 0.8 1.0 C D:SER450 4.0 0.2 1.0 CA D:SER450 4.2 0.5 1.0 C D:CYS448 4.2 0.3 1.0 C D:GLN449 4.5 0.1 1.0 CB D:GLU439 4.6 0.0 1.0 CG D:HIS443 4.6 1.0 1.0 CB D:SER450 4.6 0.8 1.0 ND1 D:HIS443 4.7 0.8 1.0 CD1 D:LEU485 4.7 0.7 1.0 CA D:GLN449 4.8 0.6 1.0 C D:CYS451 4.8 0.8 1.0

Zinc binding site 8 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1004 b:0.8 occ:1.00 NE2 E:HIS714 2.1 0.6 1.0 SG E:CYS730 2.3 1.0 1.0 SG E:CYS849 2.4 0.9 1.0 CD2 E:HIS714 2.9 0.3 1.0 CE1 E:HIS714 3.1 0.9 1.0 CB E:CYS730 3.2 0.4 1.0 OD1 E:ASN716 3.5 0.1 1.0 CB E:CYS849 3.8 0.8 1.0 CG E:HIS714 4.0 0.9 1.0 ND1 E:HIS714 4.1 0.5 1.0 CD2 E:LEU841 4.5 0.8 1.0 CA E:CYS730 4.5 0.8 1.0 C E:CYS730 4.6 0.3 1.0 O E:HIS714 4.6 0.6 1.0 N E:ARG731 4.6 0.1 1.0 CG E:ASN716 4.7 0.2 1.0 O E:ARG731 4.8 0.3 1.0 O E:GLU845 5.0 0.4 1.0

Zinc binding site 9 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1005 b:0.3 occ:1.00 OE2 E:GLU439 2.0 0.2 1.0 NE2 E:HIS443 2.1 0.6 1.0 SG E:CYS451 2.4 0.4 1.0 SG E:CYS448 2.4 0.4 1.0 CD2 E:HIS443 3.0 0.4 1.0 CD E:GLU439 3.0 0.8 1.0 CE1 E:HIS443 3.2 0.2 1.0 CB E:CYS451 3.2 0.8 1.0 N E:CYS451 3.5 0.3 1.0 CB E:CYS448 3.5 0.7 1.0 CG E:GLU439 3.5 0.1 1.0 CA E:CYS448 3.7 0.4 1.0 CA E:CYS451 3.9 0.6 1.0 N E:GLN449 4.0 0.0 1.0 OE1 E:GLU439 4.1 0.7 1.0 N E:SER450 4.1 0.7 1.0 CG E:HIS443 4.2 1.0 1.0 ND1 E:HIS443 4.2 0.8 1.0 C E:CYS448 4.2 0.8 1.0 OG E:SER450 4.5 0.1 1.0 C E:SER450 4.6 0.4 1.0 CD1 E:LEU485 4.7 0.7 1.0 CA E:SER450 4.8 0.5 1.0 C E:GLN449 5.0 0.8 1.0 N E:CYS448 5.0 0.4 1.0

Zinc binding site 10 out of 11 in the Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Full-Length Zika Virus NS5 Protein (Human Isolate Z1106033) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1006 b:89.3 occ:1.00 SG F:CYS849 2.4 0.5 1.0 NE2 F:HIS714 2.8 98.5 1.0 OD1 F:ASN716 3.2 0.5 1.0 SG F:CYS730 3.2 0.5 1.0 CD2 F:HIS714 3.4 0.0 1.0 CD2 F:LEU841 3.9 0.9 1.0 CB F:CYS849 3.9 0.8 1.0 CE1 F:HIS714 4.0 97.4 1.0 CB F:CYS730 4.0 0.8 1.0 CG F:ASN716 4.3 0.4 1.0 O F:GLU845 4.3 0.3 1.0 CB F:GLU845 4.6 0.4 1.0 CG F:HIS714 4.6 0.9 1.0 ND2 F:ASN716 4.8 1.0 1.0 ND1 F:HIS714 4.9 0.1 1.0 C F:GLU845 4.9 0.9 1.0

D.S.Ferrero, V.M.Ruiz-Arroyo, N.Soler, I.Uson, A.Guarne, N.Verdaguer. Supramolecular Arrangement of the Full-Length Zika Virus NS5. Plos Pathog. V. 15 07656 2019.
ISSN: ESSN 1553-7374
PubMed: 30951555
DOI: 10.1371/JOURNAL.PPAT.1007656