Zinc in PDB 7nvx: Tfiih in A Post-Translocated State (with Adp-BEF3)

Enzymatic activity of Tfiih in A Post-Translocated State (with Adp-BEF3)

All present enzymatic activity of Tfiih in A Post-Translocated State (with Adp-BEF3):
3.6.4.12;

Other elements in 7nvx:

The structure of Tfiih in A Post-Translocated State (with Adp-BEF3) also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 1 atom
Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tfiih in A Post-Translocated State (with Adp-BEF3) (pdb code 7nvx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Tfiih in A Post-Translocated State (with Adp-BEF3), PDB code: 7nvx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7nvx

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Zinc binding site 1 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn400

b:93.1
occ:1.00
 CB 3:CYS34 2.2 72.9 1.0
SG 3:CYS6 2.3 69.7 1.0
SG 3:CYS9 2.4 70.5 1.0
SG 3:CYS31 2.4 69.7 1.0
SG 3:CYS34 2.6 72.9 1.0
CB 3:CYS6 3.2 69.7 1.0
CA 3:CYS34 3.5 72.9 1.0
N 3:CYS34 3.9 72.9 1.0
CB 3:CYS9 4.0 70.5 1.0
CB 3:CYS31 4.1 69.7 1.0
N 3:CYS9 4.2 70.5 1.0
O 3:CYS9 4.2 70.5 1.0
N 3:CYS31 4.5 69.7 1.0
CA 3:CYS9 4.5 70.5 1.0
O 3:CYS31 4.6 69.7 1.0
NZ 3:LYS13 4.6 66.1 1.0
CA 3:CYS6 4.7 69.7 1.0
C 3:CYS34 4.7 72.9 1.0
CA 3:CYS31 4.7 69.7 1.0
C 3:CYS9 4.7 70.5 1.0
CB 3:ARG8 5.0 64.9 1.0

Zinc binding site 2 out of 7 in 7nvx

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Zinc binding site 2 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn401

b:119.2
occ:1.00
 NE2 3:HIS28 2.1 73.2 1.0
CE1 3:HIS28 2.1 73.2 1.0
CD2 3:HIS28 2.2 73.2 1.0
SG 3:CYS49 2.3 76.9 1.0
ND1 3:HIS28 2.3 73.2 1.0
SG 3:CYS46 2.3 78.2 1.0
CG 3:HIS28 2.4 73.2 1.0
SG 3:CYS26 2.5 63.5 1.0
CB 3:CYS49 3.3 76.9 1.0
CB 3:HIS28 3.5 73.2 1.0
CB 3:CYS46 3.8 78.2 1.0
CB 3:CYS26 3.9 63.5 1.0
N 3:CYS49 4.3 76.9 1.0
CA 3:CYS49 4.4 76.9 1.0
CA 3:HIS28 4.9 73.2 1.0

Zinc binding site 3 out of 7 in 7nvx

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Zinc binding site 3 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:101.6
occ:1.00
 CB 4:CYS285 2.1 50.8 1.0
SG 4:CYS268 2.3 40.3 1.0
SG 4:CYS271 2.4 42.7 1.0
SG 4:CYS285 2.5 50.8 1.0
SG 4:CYS282 2.5 55.8 1.0
CB 4:CYS271 3.1 42.7 1.0
CA 4:CYS285 3.3 50.8 1.0
N 4:CYS271 3.5 42.7 1.0
CB 4:CYS268 3.6 40.3 1.0
N 4:CYS285 3.7 50.8 1.0
CA 4:CYS271 3.9 42.7 1.0
CB 4:CYS282 4.2 55.8 1.0
CB 4:VAL270 4.4 41.0 1.0
OG1 4:THR284 4.4 49.4 1.0
C 4:CYS285 4.5 50.8 1.0
CG2 4:THR287 4.6 49.5 1.0
C 4:THR284 4.6 49.4 1.0
C 4:VAL270 4.6 41.0 1.0
O 4:CYS282 4.7 55.8 1.0
CA 4:VAL270 4.9 41.0 1.0
N 4:VAL270 5.0 41.0 1.0
CA 4:CYS268 5.0 40.3 1.0

Zinc binding site 4 out of 7 in 7nvx

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Zinc binding site 4 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn402

b:74.8
occ:1.00
 CD2 4:HIS258 1.8 59.0 1.0
NE2 4:HIS258 2.1 59.0 1.0
CB 4:CYS276 2.4 53.0 1.0
SG 4:CYS276 2.4 53.0 1.0
CB 4:CYS257 2.5 53.7 1.0
SG 4:CYS255 2.6 50.6 1.0
SG 4:CYS257 2.7 53.7 1.0
CG 4:HIS258 3.0 59.0 1.0
CE1 4:HIS258 3.3 59.0 1.0
ND1 4:HIS258 3.7 59.0 1.0
CB 4:CYS255 3.7 50.6 1.0
CA 4:CYS257 3.7 53.7 1.0
CA 4:CYS276 3.8 53.0 1.0
N 4:HIS258 3.9 59.0 1.0
CB 4:HIS258 4.0 59.0 1.0
N 4:CYS257 4.0 53.7 1.0
C 4:CYS257 4.1 53.7 1.0
N 4:CYS276 4.4 53.0 1.0
CA 4:HIS258 4.6 59.0 1.0
C 4:CYS276 4.8 53.0 1.0
OD1 4:ASN260 4.9 56.4 1.0

Zinc binding site 5 out of 7 in 7nvx

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Zinc binding site 5 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn401

b:106.8
occ:1.00
 SG 6:CYS345 2.3 33.6 1.0
SG 6:CYS348 2.3 23.0 1.0
SG 6:CYS371 2.3 23.7 1.0
SG 6:CYS368 2.3 31.6 1.0
CB 6:CYS345 3.1 33.6 1.0
CB 6:CYS348 3.3 23.0 1.0
CB 6:CYS371 3.3 23.7 1.0
CB 6:CYS368 3.5 31.6 1.0
N 6:CYS348 3.5 23.0 1.0
N 6:CYS368 3.7 31.6 1.0
CA 6:CYS348 4.0 23.0 1.0
N 6:CYS371 4.0 23.7 1.0
CA 6:CYS368 4.2 31.6 1.0
CA 6:CYS371 4.2 23.7 1.0
C 6:GLY347 4.4 27.5 1.0
CA 6:CYS345 4.5 33.6 1.0
CA 6:GLY347 4.6 27.5 1.0
N 6:GLY347 4.6 27.5 1.0
C 6:CYS348 4.8 23.0 1.0
C 6:PHE367 4.8 34.2 1.0
C 6:CYS368 4.8 31.6 1.0
C 6:CYS345 4.9 33.6 1.0

Zinc binding site 6 out of 7 in 7nvx

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Zinc binding site 6 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn402

b:71.3
occ:1.00
 CB 6:CYS385 2.0 55.5 1.0
SG 6:CYS360 2.3 49.3 1.0
SG 6:CYS363 2.4 64.0 1.0
SG 6:CYS382 2.5 38.3 1.0
SG 6:CYS385 2.7 55.5 1.0
CB 6:CYS360 3.1 49.3 1.0
CA 6:CYS385 3.2 55.5 1.0
CB 6:CYS363 3.3 64.0 1.0
CB 6:CYS382 3.4 38.3 1.0
N 6:CYS385 3.6 55.5 1.0
N 6:CYS363 4.3 64.0 1.0
CA 6:CYS363 4.4 64.0 1.0
CE2 6:PHE367 4.4 34.2 1.0
C 6:CYS385 4.5 55.5 1.0
CA 6:CYS360 4.6 49.3 1.0
C 6:GLY384 4.8 40.6 1.0
CA 6:CYS382 4.8 38.3 1.0
CZ 6:PHE367 4.8 34.2 1.0
N 6:CYS360 5.0 49.3 1.0
CZ 6:PHE331 5.0 43.8 1.0
N 6:GLN364 5.0 57.2 1.0

Zinc binding site 7 out of 7 in 7nvx

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Zinc binding site 7 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn403

b:78.2
occ:1.00
 SG 6:CYS294 2.2 37.4 1.0
SG 6:CYS308 2.3 38.8 1.0
SG 6:CYS305 2.3 45.1 1.0
SG 6:CYS291 2.4 33.6 1.0
CB 6:CYS305 3.1 45.1 1.0
CB 6:CYS294 3.1 37.4 1.0
N 6:CYS294 3.1 37.4 1.0
CB 6:CYS308 3.3 38.8 1.0
CA 6:CYS294 3.6 37.4 1.0
CB 6:CYS291 3.7 33.6 1.0
N 6:CYS308 4.0 38.8 1.0
CB 6:GLN293 4.2 37.5 1.0
C 6:GLN293 4.2 37.5 1.0
CA 6:CYS305 4.3 45.1 1.0
CA 6:CYS308 4.3 38.8 1.0
CA 6:GLN293 4.5 37.5 1.0
N 6:GLN293 4.5 37.5 1.0
CD1 6:LEU312 4.6 39.9 1.0
CD2 6:LEU312 4.8 39.9 1.0
OH 6:TYR298 5.0 37.1 1.0
CG 6:LEU312 5.0 39.9 1.0

Reference:

S.Aibara, S.Schilbach, P.Cramer. Structures of Mammalian Rna Polymerase II Pre-Initiation Complexes. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33902107
DOI: 10.1038/S41586-021-03554-8
Page generated: Mon Jul 12 17:29:24 2021

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