Fluorine in PDB 9ikz: Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3-

All present enzymatic activity of Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3-:
2.7.7.48; 2.7.7.50; 3.6.4.12; 3.6.4.13;

The structure of Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3- also contains other interesting chemical elements:

Zinc	(Zn)	8 atoms
Magnesium	(Mg)	1 atom

The binding sites of Fluorine atom in the Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3- (pdb code 9ikz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3-, PDB code: 9ikz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ A:F1004 b:26.7 occ:1.00 F1 A:BEF1004 0.0 26.7 1.0 BE A:BEF1004 1.7 23.1 1.0 OD2 A:ASP218 1.9 54.7 1.0 OD1 A:ASP218 2.1 62.4 1.0 CG A:ASP218 2.2 56.1 1.0 F3 A:BEF1004 2.8 26.6 1.0 F2 A:BEF1004 2.9 23.8 1.0 O1B A:GDP1003 2.9 297.8 1.0 CB A:ASP218 3.7 45.8 1.0 O3A A:GDP1003 3.7 290.8 1.0 NZ A:LYS73 3.8 51.2 1.0 PB A:GDP1003 4.0 316.0 1.0 OE2 A:GLU83 4.3 40.7 1.0 CA A:GLY220 4.3 40.2 1.0 N A:GLY220 4.3 41.3 1.0 CA A:ASP218 4.5 40.3 1.0 O2B A:GDP1003 4.6 303.9 1.0 OE1 A:GLU83 4.7 42.3 1.0 O1A A:GDP1003 4.8 265.3 1.0 C A:ASP218 4.8 40.2 1.0 N A:PHE219 4.8 39.7 1.0 CD A:GLU83 4.9 42.0 1.0 C A:GLY220 4.9 41.0 1.0 PA A:GDP1003 4.9 290.0 1.0 MG A:MG1005 5.0 30.0 1.0 OD1 G:ASN1 5.0 43.9 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ A:F1004 b:23.8 occ:1.00 F2 A:BEF1004 0.0 23.8 1.0 BE A:BEF1004 1.7 23.1 1.0 OD1 G:ASN1 2.3 43.9 1.0 F3 A:BEF1004 2.7 26.6 1.0 O1B A:GDP1003 2.8 297.8 1.0 F1 A:BEF1004 2.9 26.7 1.0 CG G:ASN1 3.0 43.0 1.0 ND2 G:ASN1 3.3 40.6 1.0 OD2 A:ASP218 3.5 54.7 1.0 CB G:ASN1 4.2 43.9 1.0 PB A:GDP1003 4.3 316.0 1.0 CA G:ASN1 4.4 42.1 1.0 OD2 A:ASP221 4.4 42.9 1.0 CG A:ASP218 4.6 56.1 1.0 N G:ASN1 4.8 42.4 1.0 OD1 A:ASP218 4.9 62.4 1.0 CG A:ASP221 4.9 42.0 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3-


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 E-Rtc Bound to Prna-NSP9 and Gdp-BEF3- within 5.0Å range: probe atom residue distance (Å) B Occ A:F1004 b:26.6 occ:1.00 F3 A:BEF1004 0.0 26.6 1.0 OD2 A:ASP218 1.7 54.7 1.0 BE A:BEF1004 1.7 23.1 1.0 F2 A:BEF1004 2.7 23.8 1.0 F1 A:BEF1004 2.8 26.7 1.0 CG A:ASP218 2.9 56.1 1.0 O1B A:GDP1003 3.0 297.8 1.0 MG A:MG1005 3.4 30.0 1.0 OD1 G:ASN1 3.6 43.9 1.0 CB A:ASP218 3.8 45.8 1.0 OD1 A:ASP218 3.8 62.4 1.0 O3A A:GDP1003 4.0 290.8 1.0 PB A:GDP1003 4.1 316.0 1.0 CA G:ASN1 4.4 42.1 1.0 N G:ASN1 4.4 42.4 1.0 CG G:ASN1 4.5 43.0 1.0 ND2 A:ASN209 4.6 41.2 1.0 O3B A:GDP1003 4.6 308.2 1.0 OD2 A:ASP221 4.9 42.9 1.0 OD1 A:ASN209 4.9 47.8 1.0

Y.C.Huang, L.P.Tan, H.S.Zhao, Y.X.Liu, J.B.Wang, J.Ge, S.H.Ye, Z.Y.Liu, W.Q.Lan, B.Huang, H.B.Zhang, Y.Gao, Z.H.Rao, L.M.Yan, Z.Y.Lou. Substrate Selection and Transition Reveal the Mechanism For Rna Capping Catalyzed By Sars-Cov-2 Niran To Be Published.