Zinc in PDB 9uht: Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp

All present enzymatic activity of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp:
2.7.7.48; 2.7.7.50; 3.6.4.12; 3.6.4.13;

The binding sites of Zinc atom in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp (pdb code 9uht). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp, PDB code: 9uht:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:128.0 occ:1.00 ND1 A:HIS295 2.1 84.1 1.0 SG A:CYS310 2.3 84.8 1.0 SG A:CYS301 2.3 87.0 1.0 SG A:CYS306 2.3 84.9 1.0 CE1 A:HIS295 2.9 71.8 1.0 CG A:HIS295 3.2 70.8 1.0 O A:CYS306 3.3 88.6 1.0 CB A:CYS301 3.4 87.7 1.0 CB A:CYS306 3.6 72.0 1.0 CB A:HIS295 3.6 58.8 1.0 CB A:CYS310 3.7 71.2 1.0 C A:CYS306 3.8 74.6 1.0 CA A:CYS301 3.8 81.2 1.0 NE2 A:HIS295 4.1 58.4 1.0 CA A:CYS306 4.2 71.9 1.0 CD2 A:HIS295 4.3 66.6 1.0 N A:HIS295 4.3 63.5 1.0 N A:ILE307 4.6 70.0 1.0 N A:CYS301 4.6 81.3 1.0 CA A:HIS295 4.6 52.9 1.0 O A:THR293 4.9 77.3 1.0 N A:CYS310 4.9 69.1 1.0 CA A:CYS310 4.9 55.8 1.0 N A:LEU302 5.0 93.1 1.0 CA A:ILE307 5.0 73.3 1.0 C A:CYS301 5.0 88.8 1.0

Zinc binding site 2 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:141.5 occ:1.00 ND1 A:HIS642 2.1 91.1 1.0 SG A:CYS487 2.3 95.9 1.0 SG A:CYS645 2.3 97.8 1.0 SG A:CYS646 2.3 89.0 1.0 CE1 A:HIS642 3.0 87.8 1.0 CG A:HIS642 3.1 77.6 1.0 CB A:HIS642 3.4 76.6 1.0 CB A:CYS645 3.5 92.4 1.0 CB A:CYS487 3.7 94.1 1.0 CB A:CYS646 3.7 84.0 1.0 C A:CYS645 4.1 98.8 1.0 N A:CYS487 4.1 88.2 1.0 NE2 A:HIS642 4.1 81.8 1.0 N A:CYS646 4.1 93.5 1.0 CD2 A:HIS642 4.2 77.7 1.0 CE1 A:PHE571 4.2 71.7 1.0 CA A:HIS642 4.3 74.9 1.0 O A:CYS645 4.3 101.0 1.0 CA A:CYS645 4.4 89.7 1.0 CA A:CYS487 4.4 90.7 1.0 CA A:CYS646 4.4 86.6 1.0 C A:GLY486 4.7 84.6 1.0 CD1 A:PHE571 4.7 83.5 1.0 O A:HIS642 4.8 97.3 1.0 CA A:GLY486 4.9 82.0 1.0 NZ A:LYS532 4.9 74.1 1.0 CZ A:PHE571 4.9 68.8 1.0 N A:CYS645 5.0 93.9 1.0

Zinc binding site 3 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:211.9 occ:1.00 NE2 E:HIS33 2.0 180.6 1.0 ND1 E:HIS39 2.0 185.1 1.0 SG E:CYS19 2.3 179.2 1.0 SG E:CYS16 2.3 165.6 1.0 CE1 E:HIS33 2.9 179.2 1.0 CG E:HIS39 3.0 185.0 1.0 CE1 E:HIS39 3.0 184.1 1.0 CD2 E:HIS33 3.1 180.7 1.0 CB E:HIS39 3.3 184.3 1.0 N E:CYS19 3.7 176.5 1.0 CB E:CYS16 3.7 158.2 1.0 CB E:CYS19 3.7 174.0 1.0 C E:ALA18 4.0 165.3 1.0 ND1 E:HIS33 4.1 179.2 1.0 NE2 E:HIS39 4.1 183.1 1.0 CB E:ALA18 4.1 163.2 1.0 CD2 E:HIS39 4.2 183.9 1.0 CA E:CYS19 4.2 175.9 1.0 CG E:HIS33 4.2 179.8 1.0 CA E:ALA18 4.4 164.4 1.0 N E:ALA18 4.4 163.0 1.0 O E:ALA18 4.6 163.9 1.0 CA E:HIS39 4.7 184.6 1.0 CA E:CYS16 4.9 158.5 1.0

Zinc binding site 4 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn702 b:250.9 occ:1.00 CB E:CYS26 1.8 186.5 1.0 SG E:CYS8 2.3 197.1 1.0 SG E:CYS29 2.3 167.6 1.0 SG E:CYS26 2.3 186.4 1.0 SG E:CYS5 2.3 188.7 1.0 CB E:CYS8 3.2 192.3 1.0 CA E:CYS26 3.3 184.4 1.0 CB E:CYS5 3.7 185.1 1.0 N E:CYS26 3.8 184.1 1.0 N E:CYS8 3.8 192.5 1.0 CB E:CYS29 3.9 167.8 1.0 CA E:CYS8 4.1 192.2 1.0 C E:CYS26 4.2 185.1 1.0 N E:CYS29 4.7 168.8 1.0 O E:CYS26 4.8 185.3 1.0 CB E:LEU7 4.9 181.8 1.0 N E:CYS27 4.9 178.2 1.0 C E:LEU7 4.9 183.4 1.0 CA E:GLY99 4.9 182.4 1.0 C E:CYS8 5.0 192.2 1.0 N E:GLY99 5.0 183.3 1.0 CA E:CYS29 5.0 167.9 1.0

Zinc binding site 5 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn703 b:238.1 occ:1.00 ND1 E:HIS75 2.1 182.7 1.0 CE1 E:HIS75 2.2 182.8 1.0 SG E:CYS55 2.3 192.5 1.0 SG E:CYS72 2.3 187.7 1.0 SG E:CYS50 2.3 176.1 1.0 CB E:CYS55 3.1 188.9 1.0 CG E:HIS75 3.3 180.3 1.0 NE2 E:HIS75 3.4 180.7 1.0 CB E:CYS72 3.4 183.8 1.0 CB E:ALA52 3.6 187.3 1.0 CB E:CYS50 3.7 172.6 1.0 CD2 E:HIS75 3.9 180.1 1.0 N E:CYS72 4.1 183.4 1.0 OG E:SER74 4.1 179.7 1.0 CB E:HIS75 4.2 178.6 1.0 CA E:CYS72 4.3 183.5 1.0 CG2 E:VAL57 4.5 174.6 1.0 CA E:CYS55 4.6 189.3 1.0 CA E:ALA52 4.8 189.4 1.0 N E:HIS75 4.8 178.9 1.0 N E:ALA52 4.8 188.7 1.0

Zinc binding site 6 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn701 b:254.8 occ:1.00 CE1 F:HIS33 2.1 185.9 1.0 ND1 F:HIS39 2.1 181.9 1.0 NE2 F:HIS33 2.1 188.1 1.0 SG F:CYS19 2.3 198.1 1.0 SG F:CYS16 2.3 183.4 1.0 CE1 F:HIS39 2.4 182.1 1.0 CB F:CYS19 3.0 193.2 1.0 CG F:HIS39 3.2 180.3 1.0 CB F:CYS16 3.2 178.1 1.0 ND1 F:HIS33 3.4 183.8 1.0 CD2 F:HIS33 3.5 186.4 1.0 NE2 F:HIS39 3.5 182.8 1.0 O F:ALA18 3.7 181.8 1.0 CD2 F:HIS39 3.9 182.4 1.0 CB F:HIS39 4.0 180.1 1.0 CG F:HIS33 4.0 186.3 1.0 CA F:CYS19 4.1 193.4 1.0 C F:ALA18 4.4 182.1 1.0 CG F:PRO23 4.6 165.5 1.0 N F:CYS19 4.6 193.9 1.0 CA F:CYS16 4.7 175.7 1.0

Zinc binding site 7 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn702 b:239.8 occ:1.00 CB F:CYS29 2.2 167.7 1.0 SG F:CYS8 2.3 185.1 1.0 SG F:CYS26 2.3 172.3 1.0 SG F:CYS5 2.3 183.0 1.0 SG F:CYS29 2.3 175.2 1.0 CB F:CYS8 3.3 187.9 1.0 N F:CYS26 3.5 162.7 1.0 CB F:CYS26 3.7 165.0 1.0 CA F:CYS29 3.8 165.3 1.0 CB F:CYS5 3.8 182.1 1.0 CA F:CYS26 4.2 164.1 1.0 N F:CYS8 4.3 188.2 1.0 CA F:CYS8 4.4 188.8 1.0 N F:CYS29 4.4 166.2 1.0 C F:LEU25 4.5 157.2 1.0 CA F:LEU25 4.5 158.7 1.0 CD1 F:LEU7 4.6 187.5 1.0 C F:CYS29 4.7 165.1 1.0 CG F:LEU7 4.7 188.1 1.0 C F:CYS26 4.9 164.9 1.0 O F:CYS26 4.9 166.6 1.0

Zinc binding site 8 out of 8 in the Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sars-Cov-2 E-Rtc in Complex with Rna-NSP9 and Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn703 b:243.0 occ:1.00 ND1 F:HIS75 2.1 179.1 1.0 SG F:CYS72 2.3 168.2 1.0 SG F:CYS55 2.3 165.0 1.0 SG F:CYS50 2.3 158.7 1.0 CG F:HIS75 2.7 177.0 1.0 CB F:HIS75 2.8 177.8 1.0 O F:HIS75 3.1 179.3 1.0 CB F:CYS50 3.2 152.4 1.0 CE1 F:HIS75 3.2 177.2 1.0 CB F:CYS55 3.5 160.6 1.0 CB F:CYS72 3.6 164.6 1.0 CA F:HIS75 3.7 179.3 1.0 C F:HIS75 3.8 179.0 1.0 CD2 F:HIS75 3.9 174.9 1.0 N F:HIS75 4.1 178.8 1.0 NE2 F:HIS75 4.1 175.3 1.0 N F:CYS72 4.1 157.3 1.0 CA F:CYS72 4.4 162.6 1.0 CA F:CYS50 4.6 152.8 1.0 C F:CYS72 4.8 161.5 1.0 CA F:CYS55 4.9 159.5 1.0

Y.Huang, L.Tan, Y.Liu, L.Yan, Z.Rao, Z.Lou. Response to Matter Arising: Substrate Selection and Transition State Support the Mechanism For Gtp-Mediate Rna Capping Catalyzed By Sars-Cov-2 Niran To Be Published.