Zinc in PDB 9dj8: Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket

All present enzymatic activity of Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket:
2.7.7.48;

The binding sites of Zinc atom in the Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket (pdb code 9dj8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket, PDB code: 9dj8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:25.8 occ:1.00 ND1 A:HIS295 2.3 0.9 1.0 SG A:CYS301 2.3 1.3 1.0 SG A:CYS310 2.4 2.0 1.0 SG A:CYS306 2.4 6.1 1.0 HB2 A:HIS295 3.1 0.5 1.0 CE1 A:HIS295 3.2 0.7 1.0 HE1 A:HIS295 3.3 0.7 1.0 CG A:HIS295 3.4 0.6 1.0 HA A:CYS301 3.4 1.6 1.0 O A:CYS306 3.4 1.4 1.0 HB2 A:CYS310 3.5 1.0 1.0 CB A:CYS301 3.5 1.8 1.0 HB3 A:CYS301 3.6 2.0 1.0 CB A:CYS310 3.6 0.9 1.0 H A:HIS295 3.6 0.5 1.0 CB A:HIS295 3.7 0.6 1.0 CB A:CYS306 3.8 1.9 1.0 C A:CYS306 3.9 1.2 1.0 HB3 A:CYS306 3.9 2.3 1.0 CA A:CYS301 4.0 1.6 1.0 HD1 A:HIS309 4.0 0.3 1.0 HB3 A:CYS310 4.1 0.7 1.0 N A:HIS295 4.2 0.5 1.0 CA A:CYS306 4.3 1.4 1.0 HA A:ILE307 4.3 1.3 1.0 H A:CYS310 4.3 0.8 1.0 HA A:CYS306 4.3 1.6 1.0 HB2 A:CYS301 4.3 1.8 1.0 NE2 A:HIS295 4.4 0.7 1.0 H A:LEU302 4.4 2.9 1.0 HB3 A:HIS295 4.4 0.5 1.0 CD2 A:HIS295 4.5 0.5 1.0 HB2 A:CYS306 4.6 2.3 1.0 O A:THR293 4.6 1.2 1.0 CA A:HIS295 4.6 0.5 1.0 N A:ILE307 4.6 1.4 1.0 HA A:TYR294 4.7 0.6 1.0 HG23 A:THR293 4.8 1.7 1.0 HB3 A:HIS309 4.8 0.7 1.0 N A:CYS301 4.8 1.6 1.0 N A:CYS310 4.8 0.8 1.0 CA A:CYS310 4.8 0.6 1.0 HA A:CYS298 4.9 0.9 1.0 ND1 A:HIS309 4.9 0.5 1.0 CA A:ILE307 5.0 1.1 1.0

Zinc binding site 2 out of 2 in the Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna-NSP9 Bound to the Niran Domain of the E-Rtc with An Empty G-Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:23.4 occ:1.00 ND1 A:HIS642 2.1 3.9 1.0 SG A:CYS645 2.2 7.1 1.0 SG A:CYS646 2.4 6.8 1.0 SG A:CYS487 2.4 8.4 1.0 CE1 A:HIS642 3.0 3.8 1.0 HB3 A:HIS642 3.1 4.0 1.0 HE1 A:HIS642 3.1 3.7 1.0 CG A:HIS642 3.2 3.4 1.0 HB2 A:CYS645 3.4 7.1 1.0 HE1 A:PHE571 3.5 2.9 1.0 CB A:CYS645 3.5 6.7 1.0 HB2 A:CYS646 3.5 5.9 1.0 H A:CYS487 3.6 6.7 1.0 CB A:CYS646 3.6 5.7 1.0 CB A:HIS642 3.6 4.1 1.0 CB A:CYS487 3.7 5.8 1.0 HB2 A:CYS487 3.7 6.3 1.0 HZ3 A:LYS532 3.9 3.8 1.0 C A:CYS645 4.0 7.3 1.0 N A:CYS487 4.0 6.6 1.0 N A:CYS646 4.0 6.9 1.0 HA A:HIS642 4.0 4.5 1.0 CE1 A:PHE571 4.1 2.8 1.0 NE2 A:HIS642 4.1 3.4 1.0 HA2 A:GLY486 4.2 4.1 1.0 HB3 A:CYS645 4.2 7.2 1.0 O A:CYS645 4.2 8.7 1.0 CD2 A:HIS642 4.3 3.1 1.0 H A:CYS646 4.3 7.0 1.0 CA A:CYS645 4.3 6.1 1.0 CA A:CYS646 4.3 5.2 1.0 HB3 A:CYS646 4.4 6.1 1.0 HB2 A:HIS642 4.4 4.0 1.0 HD1 A:PHE571 4.4 3.3 1.0 CA A:CYS487 4.4 5.4 1.0 HZ1 A:LYS532 4.4 3.8 1.0 CA A:HIS642 4.4 4.5 1.0 HB3 A:CYS487 4.5 6.3 1.0 CD1 A:PHE571 4.6 3.3 1.0 HA A:CYS646 4.6 5.8 1.0 NZ A:LYS532 4.6 3.9 1.0 HA A:CYS487 4.6 5.9 1.0 H A:CYS645 4.6 8.2 1.0 C A:GLY486 4.8 4.5 1.0 CZ A:PHE571 4.9 2.8 1.0 O A:HIS642 4.9 7.3 1.0 CA A:GLY486 4.9 3.8 1.0 HZ A:PHE571 4.9 2.8 1.0 HE2 A:HIS642 4.9 3.4 1.0 N A:CYS645 5.0 7.7 1.0

G.I.Small, S.A.Darst, E.A.Campbell. Matters Arising: There Is No Structure of the Catalytic Intermediate of Gtp-Mediated Mrna Capping By the Sars-Cov-2 Niran Domain, and Thus the Mechanism Remains Unknown To Be Published.