Manganese 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:

Zinc

(Zn)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 3 binding sites of Manganese where determined in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex, PDB code: 8gzr:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1001 b:45.4 occ:1.00 O2B A:CDP1006 1.7 37.1 1.0 OD1 A:ASP533 1.8 41.1 1.0 OD2 A:ASP663 1.9 37.2 1.0 O A:THR534 2.1 37.7 1.0 O2A A:CDP1006 2.7 37.1 1.0 CG A:ASP533 2.9 41.1 1.0 CG A:ASP663 3.0 37.2 1.0 PB A:CDP1006 3.2 37.1 1.0 C A:THR534 3.3 37.7 1.0 OD2 A:ASP533 3.4 41.1 1.0 N A:THR534 3.6 37.7 1.0 OD1 A:ASP663 3.7 37.2 1.0 PA A:CDP1006 3.7 37.1 1.0 MN A:MN1002 3.8 50.8 1.0 O3A A:CDP1006 3.8 37.1 1.0 CA A:THR534 3.9 37.7 1.0 O3B A:CDP1006 4.0 37.1 1.0 CB A:ASP533 4.1 41.1 1.0 O1B A:CDP1006 4.1 37.1 1.0 CB A:ASP663 4.2 37.2 1.0 C5' A:CDP1006 4.2 37.1 1.0 C A:ASP533 4.2 41.1 1.0 CB A:TRP537 4.3 33.1 1.0 N A:TRP537 4.3 33.1 1.0 N A:ALA535 4.4 37.4 1.0 CB A:THR534 4.4 37.7 1.0 N A:GLY536 4.4 35.1 1.0 O5' A:CDP1006 4.5 37.1 1.0 CA A:ASP533 4.5 41.1 1.0 CA A:ALA535 4.7 37.4 1.0 CA A:TRP537 4.9 33.1 1.0 C A:ALA535 4.9 37.4 1.0 O1A A:CDP1006 5.0 37.1 1.0 O A:ASP533 5.0 41.1 1.0

Manganese binding site 2 out of 3 in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn1002 b:50.8 occ:1.00 OD2 A:ASP533 1.8 41.1 1.0 OD1 A:ASP663 2.3 37.2 1.0 OD1 A:ASP664 2.4 37.6 1.0 O2A A:CDP1006 2.5 37.1 1.0 CG A:ASP533 2.9 41.1 1.0 CG A:ASP664 3.1 37.6 1.0 O3' C:U40 3.1 36.3 1.0 CG A:ASP663 3.1 37.2 1.0 OD1 A:ASP533 3.4 41.1 1.0 OD2 A:ASP663 3.4 37.2 1.0 OD2 A:ASP664 3.5 37.6 1.0 PA A:CDP1006 3.7 37.1 1.0 MN A:MN1001 3.8 45.4 1.0 N A:ASP664 3.9 37.6 1.0 O1A A:CDP1006 4.0 37.1 1.0 CB A:ASP533 4.2 41.1 1.0 O5' A:CDP1006 4.2 37.1 1.0 CB A:ASP664 4.2 37.6 1.0 C A:ASP663 4.2 37.2 1.0 CA A:ASP664 4.3 37.6 1.0 C3' C:U40 4.4 36.3 1.0 CB A:ASP663 4.4 37.2 1.0 C5' A:CDP1006 4.6 37.1 1.0 O A:ASP663 4.7 37.2 1.0 CA A:ASP663 4.8 37.2 1.0 O2B A:CDP1006 4.8 37.1 1.0 N A:ASP663 4.9 37.2 1.0 C4' C:U40 5.0 36.3 1.0 C5' C:U40 5.0 36.3 1.0 CA A:ASP533 5.0 41.1 1.0

Manganese binding site 3 out of 3 in the Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo-Em Structure of the the NS5-NS3 Rna-Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:77.9 occ:1.00 O1B B:CDP702 1.8 75.6 1.0 OG1 B:THR201 2.0 71.5 1.0 PB B:CDP702 3.2 75.6 1.0 CB B:THR201 3.2 71.5 1.0 O3B B:CDP702 3.6 75.6 1.0 OE1 B:GLU286 3.8 57.8 1.0 N B:THR201 4.0 71.5 1.0 O1A B:CDP702 4.1 75.6 1.0 CA B:GLY415 4.1 66.0 1.0 O3A B:CDP702 4.1 75.6 1.0 CG2 B:THR201 4.2 71.5 1.0 CA B:THR201 4.2 71.5 1.0 O2B B:CDP702 4.2 75.6 1.0 OD1 B:ASP285 4.3 57.1 1.0 OD2 B:ASP285 4.4 57.1 1.0 PA B:CDP702 4.6 75.6 1.0 CE B:LYS200 4.6 71.3 1.0 O2A B:CDP702 4.7 75.6 1.0 CG B:ASP285 4.8 57.1 1.0 CB B:LYS200 4.8 71.3 1.0 O B:GLY415 4.9 66.0 1.0 C B:LYS200 4.9 71.3 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