Zinc in PDB 8gzr: Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex

The structure of Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex (pdb code 8gzr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex, PDB code: 8gzr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:54.2 occ:1.00 NE2 A:HIS714 2.0 34.1 1.0 NE2 A:HIS712 2.0 31.6 1.0 SG A:CYS728 2.3 32.8 1.0 SG A:CYS847 2.3 41.3 1.0 CD2 A:HIS714 2.9 34.1 1.0 CD2 A:HIS712 3.0 31.6 1.0 CE1 A:HIS712 3.0 31.6 1.0 CB A:CYS728 3.1 32.8 1.0 CE1 A:HIS714 3.1 34.1 1.0 CB A:CYS847 3.4 41.3 1.0 ND1 A:HIS712 4.1 31.6 1.0 CG A:HIS714 4.1 34.1 1.0 CG A:HIS712 4.1 31.6 1.0 ND1 A:HIS714 4.2 34.1 1.0 CA A:CYS728 4.3 32.8 1.0 C A:CYS728 4.4 32.8 1.0 CD1 A:LEU839 4.4 37.1 1.0 N A:ARG729 4.7 33.5 1.0 O A:CYS728 4.8 32.8 1.0 CA A:CYS847 4.8 41.3 1.0 NH1 A:ARG769 4.8 35.6 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:70.5 occ:1.00 OE2 A:GLU437 2.0 51.5 1.0 NE2 A:HIS441 2.3 49.0 1.0 SG A:CYS446 2.3 49.2 1.0 SG A:CYS449 2.3 47.3 1.0 CD A:GLU437 3.0 51.5 1.0 CE1 A:HIS441 3.2 49.0 1.0 CD2 A:HIS441 3.3 49.0 1.0 CB A:CYS449 3.3 47.3 1.0 CB A:CYS446 3.6 49.2 1.0 CG A:GLU437 3.6 51.5 1.0 CA A:CYS446 3.9 49.2 1.0 N A:CYS449 3.9 47.3 1.0 OE1 A:GLU437 4.1 51.5 1.0 CA A:CYS449 4.2 47.3 1.0 N A:GLY447 4.2 50.0 1.0 ND1 A:HIS441 4.3 49.0 1.0 CG A:HIS441 4.3 49.0 1.0 CG2 A:THR571 4.4 41.8 1.0 N A:SER448 4.4 50.5 1.0 C A:CYS446 4.6 49.2 1.0 C A:SER448 4.7 50.5 1.0 OG A:SER448 4.8 50.5 1.0

T.Osawa, M.Aoki, H.Ehara, S.I.Sekine. Structures of Dengue Virus Rna Replicase Complexes. Mol.Cell 2023.
ISSN: ISSN 1097-2765
PubMed: 37478848
DOI: 10.1016/J.MOLCEL.2023.06.023