Zinc in PDB 7nvw: Tfiih in A Pre-Translocated State (Without Adp-BEF3)

Enzymatic activity of Tfiih in A Pre-Translocated State (Without Adp-BEF3)

All present enzymatic activity of Tfiih in A Pre-Translocated State (Without Adp-BEF3):
3.6.4.12;

Other elements in 7nvw:

The structure of Tfiih in A Pre-Translocated State (Without Adp-BEF3) also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tfiih in A Pre-Translocated State (Without Adp-BEF3) (pdb code 7nvw). 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 Pre-Translocated State (Without Adp-BEF3), PDB code: 7nvw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7nvw

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Zinc binding site 1 out of 7 in the Tfiih in A Pre-Translocated State (Without 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 Pre-Translocated State (Without Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn400

b:102.5
occ:1.00
 CB 3:CYS34 2.2 76.8 1.0
SG 3:CYS6 2.3 78.9 1.0
SG 3:CYS9 2.4 83.3 1.0
SG 3:CYS31 2.4 78.7 1.0
SG 3:CYS34 2.6 76.8 1.0
CB 3:CYS6 3.1 78.9 1.0
CA 3:CYS34 3.6 76.8 1.0
CB 3:CYS9 4.0 83.3 1.0
N 3:CYS34 4.0 76.8 1.0
N 3:CYS9 4.1 83.3 1.0
CB 3:CYS31 4.1 78.7 1.0
O 3:CYS9 4.2 83.3 1.0
N 3:CYS31 4.5 78.7 1.0
CA 3:CYS9 4.5 83.3 1.0
CA 3:CYS6 4.5 78.9 1.0
NZ 3:LYS13 4.7 75.4 1.0
O 3:CYS31 4.7 78.7 1.0
C 3:CYS34 4.7 76.8 1.0
C 3:CYS9 4.7 83.3 1.0
CA 3:CYS31 4.8 78.7 1.0
CB 3:ARG8 5.0 80.2 1.0

Zinc binding site 2 out of 7 in 7nvw

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Zinc binding site 2 out of 7 in the Tfiih in A Pre-Translocated State (Without 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 Pre-Translocated State (Without Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn401

b:120.6
occ:1.00
 NE2 3:HIS28 2.1 74.9 1.0
CE1 3:HIS28 2.2 74.9 1.0
CD2 3:HIS28 2.2 74.9 1.0
SG 3:CYS49 2.3 73.5 1.0
SG 3:CYS46 2.3 76.8 1.0
ND1 3:HIS28 2.3 74.9 1.0
CG 3:HIS28 2.4 74.9 1.0
SG 3:CYS26 2.5 67.2 1.0
CB 3:CYS49 3.3 73.5 1.0
CB 3:HIS28 3.5 74.9 1.0
CB 3:CYS46 3.7 76.8 1.0
CB 3:CYS26 4.0 67.2 1.0
N 3:CYS49 4.2 73.5 1.0
CA 3:CYS49 4.4 73.5 1.0
CA 3:HIS28 4.8 74.9 1.0

Zinc binding site 3 out of 7 in 7nvw

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Zinc binding site 3 out of 7 in the Tfiih in A Pre-Translocated State (Without 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 Pre-Translocated State (Without Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:56.8
occ:1.00
 CB 4:CYS285 2.1 42.8 1.0
SG 4:CYS268 2.3 27.1 1.0
SG 4:CYS271 2.5 26.6 1.0
SG 4:CYS285 2.5 42.8 1.0
SG 4:CYS282 2.5 49.5 1.0
CB 4:CYS271 3.2 26.6 1.0
CA 4:CYS285 3.3 42.8 1.0
CB 4:CYS268 3.5 27.1 1.0
N 4:CYS271 3.6 26.6 1.0
N 4:CYS285 3.8 42.8 1.0
CA 4:CYS271 4.0 26.6 1.0
CB 4:CYS282 4.1 49.5 1.0
C 4:THR284 4.4 38.7 1.0
CB 4:VAL270 4.5 27.1 1.0
OG1 4:THR284 4.5 38.7 1.0
C 4:CYS285 4.5 42.8 1.0
CG2 4:THR287 4.6 51.7 1.0
C 4:VAL270 4.7 27.1 1.0
O 4:THR284 4.7 38.7 1.0
O 4:CYS282 4.8 49.5 1.0
N 4:VAL270 4.9 27.1 1.0
CA 4:CYS268 4.9 27.1 1.0
CA 4:VAL270 4.9 27.1 1.0

Zinc binding site 4 out of 7 in 7nvw

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Zinc binding site 4 out of 7 in the Tfiih in A Pre-Translocated State (Without 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 Pre-Translocated State (Without Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn402

b:73.0
occ:1.00
 NE2 4:HIS258 2.1 41.6 1.0
CD2 4:HIS258 2.3 41.6 1.0
CB 4:CYS276 2.4 44.0 1.0
SG 4:CYS276 2.4 44.0 1.0
SG 4:CYS255 2.5 36.2 1.0
CB 4:CYS257 2.5 44.8 1.0
SG 4:CYS257 2.6 44.8 1.0
CE1 4:HIS258 3.1 41.6 1.0
CG 4:HIS258 3.3 41.6 1.0
CB 4:CYS255 3.6 36.2 1.0
ND1 4:HIS258 3.7 41.6 1.0
CA 4:CYS276 3.7 44.0 1.0
CA 4:CYS257 3.8 44.8 1.0
N 4:CYS257 4.1 44.8 1.0
N 4:HIS258 4.2 41.6 1.0
C 4:CYS257 4.3 44.8 1.0
N 4:CYS276 4.4 44.0 1.0
CB 4:HIS258 4.5 41.6 1.0
C 4:CYS276 4.8 44.0 1.0
CA 4:CYS255 4.9 36.2 1.0
OD1 4:ASN260 5.0 31.3 1.0

Zinc binding site 5 out of 7 in 7nvw

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Zinc binding site 5 out of 7 in the Tfiih in A Pre-Translocated State (Without 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 Pre-Translocated State (Without Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn401

b:98.0
occ:1.00
 SG 6:CYS368 2.3 33.0 1.0
SG 6:CYS371 2.3 27.1 1.0
SG 6:CYS348 2.3 18.1 1.0
SG 6:CYS345 2.4 29.8 1.0
CB 6:CYS345 3.2 29.8 1.0
CB 6:CYS368 3.3 33.0 1.0
CB 6:CYS348 3.3 18.1 1.0
CB 6:CYS371 3.4 27.1 1.0
N 6:CYS348 3.4 18.1 1.0
N 6:CYS368 3.5 33.0 1.0
CA 6:CYS368 4.0 33.0 1.0
CA 6:CYS348 4.0 18.1 1.0
C 6:GLY347 4.2 26.4 1.0
N 6:CYS371 4.3 27.1 1.0
CA 6:GLY347 4.4 26.4 1.0
CA 6:CYS371 4.4 27.1 1.0
N 6:GLY347 4.5 26.4 1.0
CA 6:CYS345 4.6 29.8 1.0
C 6:CYS368 4.6 33.0 1.0
C 6:PHE367 4.7 34.1 1.0
C 6:CYS348 4.8 18.1 1.0
C 6:CYS345 4.8 29.8 1.0
O 6:CYS368 4.9 33.0 1.0
CA 6:PHE367 4.9 34.1 1.0
O 6:CYS345 4.9 29.8 1.0

Zinc binding site 6 out of 7 in 7nvw

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Zinc binding site 6 out of 7 in the Tfiih in A Pre-Translocated State (Without 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 Pre-Translocated State (Without Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn402

b:117.7
occ:1.00
 CB 6:CYS385 2.1 35.8 1.0
SG 6:CYS360 2.3 43.1 1.0
SG 6:CYS363 2.4 45.5 1.0
SG 6:CYS382 2.5 25.7 1.0
SG 6:CYS385 2.7 35.8 1.0
CB 6:CYS360 3.1 43.1 1.0
CB 6:CYS363 3.2 45.5 1.0
CA 6:CYS385 3.3 35.8 1.0
CB 6:CYS382 3.4 25.7 1.0
N 6:CYS385 3.6 35.8 1.0
N 6:CYS363 4.2 45.5 1.0
CA 6:CYS363 4.3 45.5 1.0
CA 6:CYS360 4.6 43.1 1.0
C 6:CYS385 4.6 35.8 1.0
CE2 6:PHE367 4.7 34.1 1.0
CA 6:CYS382 4.8 25.7 1.0
C 6:GLY384 4.8 29.4 1.0
CZ 6:PHE331 4.9 32.9 1.0
CZ 6:PHE367 4.9 34.1 1.0
N 6:CYS360 5.0 43.1 1.0

Zinc binding site 7 out of 7 in 7nvw

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Zinc binding site 7 out of 7 in the Tfiih in A Pre-Translocated State (Without 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 Pre-Translocated State (Without Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn403

b:80.3
occ:1.00
 SG 6:CYS294 2.2 36.9 1.0
SG 6:CYS308 2.3 38.4 1.0
SG 6:CYS305 2.3 34.1 1.0
SG 6:CYS291 2.4 34.4 1.0
CB 6:CYS294 3.0 36.9 1.0
N 6:CYS294 3.1 36.9 1.0
CB 6:CYS308 3.2 38.4 1.0
CB 6:CYS305 3.4 34.1 1.0
CA 6:CYS294 3.5 36.9 1.0
CB 6:CYS291 3.8 34.4 1.0
N 6:CYS308 3.9 38.4 1.0
CA 6:CYS308 4.2 38.4 1.0
C 6:GLN293 4.2 37.5 1.0
CB 6:GLN293 4.3 37.5 1.0
CA 6:CYS305 4.5 34.1 1.0
N 6:GLN293 4.6 37.5 1.0
CA 6:GLN293 4.6 37.5 1.0
CD2 6:LEU312 4.6 27.5 1.0
CD1 6:LEU312 4.7 27.5 1.0
C 6:CYS294 4.9 36.9 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: Wed Oct 30 07:58:21 2024

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