Zinc in PDB 6nmi: Cryo-Em Structure of the Human Tfiih Core Complex

All present enzymatic activity of Cryo-Em Structure of the Human Tfiih Core Complex:
3.6.4.12;

The structure of Cryo-Em Structure of the Human Tfiih Core Complex also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Human Tfiih Core Complex (pdb code 6nmi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of the Human Tfiih Core Complex, PDB code: 6nmi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Human Tfiih Core 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 Human Tfiih Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:86.2 occ:1.00 SG E:CYS371 2.4 71.3 1.0 SG E:CYS345 2.4 75.7 1.0 SG E:CYS368 2.5 71.7 1.0 SG E:CYS348 2.9 64.8 1.0 CB E:CYS345 3.4 75.7 1.0 CB E:CYS371 3.7 71.3 1.0 CB E:CYS368 3.9 71.7 1.0 N E:CYS348 4.0 64.8 1.0 CB E:CYS348 4.2 64.8 1.0 N E:CYS368 4.2 71.7 1.0 N E:CYS371 4.2 71.3 1.0 CA E:CYS371 4.5 71.3 1.0 CA E:CYS368 4.6 71.7 1.0 CA E:CYS348 4.6 64.8 1.0 CA E:GLY347 4.6 67.9 1.0 C E:GLY347 4.8 67.9 1.0 CA E:CYS345 4.8 75.7 1.0 N E:GLY347 4.9 67.9 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Human Tfiih Core 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 Human Tfiih Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:98.2 occ:1.00 SG E:CYS363 2.4 87.9 1.0 SG E:CYS385 2.4 74.1 1.0 SG E:CYS382 2.7 71.6 1.0 SG E:CYS360 2.7 84.9 1.0 CB E:CYS360 3.4 84.9 1.0 CB E:CYS363 3.5 87.9 1.0 CB E:CYS382 3.5 71.6 1.0 N E:CYS363 3.6 87.9 1.0 N E:CYS385 3.7 74.1 1.0 CB E:CYS385 3.8 74.1 1.0 CA E:CYS363 4.2 87.9 1.0 CA E:CYS385 4.2 74.1 1.0 C E:GLY384 4.3 71.1 1.0 CA E:GLY384 4.4 71.1 1.0 N E:GLY384 4.6 71.1 1.0 N E:VAL362 4.6 85.9 1.0 CB E:VAL362 4.7 85.9 1.0 N E:GLN364 4.7 87.4 1.0 C E:VAL362 4.7 85.9 1.0 CA E:CYS382 4.9 71.6 1.0 C E:CYS363 4.9 87.9 1.0 CA E:CYS360 4.9 84.9 1.0 CA E:VAL362 4.9 85.9 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Human Tfiih Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Human Tfiih Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn403 b:0.5 occ:1.00 SG E:CYS308 2.4 86.6 1.0 SG E:CYS305 2.4 82.0 1.0 SG E:CYS294 2.5 89.5 1.0 CB E:CYS308 2.8 86.6 1.0 SG E:CYS291 2.9 79.0 1.0 CB E:CYS294 3.0 89.5 1.0 N E:CYS294 3.2 89.5 1.0 CB E:GLN293 3.6 83.7 1.0 CA E:CYS294 3.7 89.5 1.0 CB E:CYS305 3.8 82.0 1.0 CB E:CYS291 3.9 79.0 1.0 CA E:CYS308 4.1 86.6 1.0 C E:GLN293 4.1 83.7 1.0 N E:CYS308 4.2 86.6 1.0 CG E:GLN293 4.2 83.7 1.0 CA E:GLN293 4.3 83.7 1.0 N E:GLN293 4.5 83.7 1.0 CG1 E:ILE307 4.6 91.0 1.0 C E:CYS294 4.7 89.5 1.0 C E:ILE307 4.8 91.0 1.0 N E:ARG295 4.9 89.6 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Human Tfiih Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Human Tfiih Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:81.4 occ:1.00 SG F:CYS271 2.4 64.0 1.0 SG F:CYS268 2.4 66.0 1.0 SG F:CYS282 2.4 77.3 1.0 SG F:CYS285 2.4 82.6 1.0 CB F:CYS271 2.8 64.0 1.0 CB F:CYS268 3.0 66.0 1.0 N F:CYS271 3.2 64.0 1.0 CA F:CYS271 3.6 64.0 1.0 OG1 F:THR287 3.7 77.5 1.0 CB F:CYS282 3.7 77.3 1.0 CB F:CYS285 4.0 82.6 1.0 CB F:VAL270 4.2 61.4 1.0 C F:VAL270 4.3 61.4 1.0 N F:CYS285 4.4 82.6 1.0 CB F:THR287 4.5 77.5 1.0 CA F:CYS268 4.5 66.0 1.0 N F:VAL270 4.6 61.4 1.0 CA F:VAL270 4.6 61.4 1.0 C F:CYS271 4.6 64.0 1.0 CG1 F:VAL270 4.8 61.4 1.0 OG F:SER273 4.8 63.6 1.0 N F:LEU272 4.8 59.8 1.0 CA F:CYS285 4.8 82.6 1.0 CB F:THR284 4.9 77.3 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Human Tfiih Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Human Tfiih Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn400 b:0.3 occ:1.00 SG H:CYS34 2.4 0.3 1.0 SG H:CYS6 2.4 0.7 1.0 SG H:CYS31 2.4 0.1 1.0 SG H:CYS9 2.4 0.2 1.0 N H:CYS34 3.0 0.3 1.0 CB H:CYS34 3.3 0.3 1.0 CA H:CYS34 3.4 0.3 1.0 O H:CYS9 3.7 0.2 1.0 C H:SER33 3.8 0.5 1.0 CB H:CYS6 3.8 0.7 1.0 CB H:SER33 3.9 0.5 1.0 CB H:CYS9 4.0 0.2 1.0 CB H:CYS31 4.0 0.1 1.0 N H:CYS9 4.1 0.2 1.0 C H:CYS9 4.2 0.2 1.0 CA H:CYS9 4.3 0.2 1.0 CA H:SER33 4.3 0.5 1.0 O H:SER33 4.5 0.5 1.0 N H:SER33 4.6 0.5 1.0 N H:CYS31 4.7 0.1 1.0 CA H:CYS31 4.8 0.1 1.0 C H:CYS31 4.9 0.1 1.0 C H:CYS34 4.9 0.3 1.0 O H:CYS31 5.0 0.1 1.0 CA H:CYS6 5.0 0.7 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Human Tfiih Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the Human Tfiih Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn401 b:0.6 occ:1.00 ND1 H:HIS28 2.0 0.9 1.0 CE1 H:HIS28 2.3 0.9 1.0 SG H:CYS46 2.3 0.3 1.0 SG H:CYS26 2.3 0.1 1.0 SG H:CYS49 2.3 0.2 1.0 CG H:HIS28 3.3 0.9 1.0 CB H:CYS26 3.5 0.1 1.0 NE2 H:HIS28 3.5 0.9 1.0 CB H:CYS49 3.6 0.2 1.0 CB H:CYS46 3.8 0.3 1.0 N H:CYS49 3.9 0.2 1.0 CD2 H:HIS28 4.0 0.9 1.0 CB H:HIS28 4.1 0.9 1.0 CA H:CYS49 4.2 0.2 1.0 CA H:CYS26 4.6 0.1 1.0 C H:CYS26 4.6 0.1 1.0 N H:HIS28 4.7 0.9 1.0 C H:CYS49 4.7 0.2 1.0 N H:GLY27 4.7 0.4 1.0 N H:GLY50 5.0 0.4 1.0

B.J.Greber, D.B.Toso, J.Fang, E.Nogales. The Complete Structure of the Human Tfiih Core Complex. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30860024
DOI: 10.7554/ELIFE.44771