Zinc in PDB 7ml3: General Transcription Factor Tfiih (Weak Binding)

Enzymatic activity of General Transcription Factor Tfiih (Weak Binding)

All present enzymatic activity of General Transcription Factor Tfiih (Weak Binding):
3.6.4.12;

Other elements in 7ml3:

The structure of General Transcription Factor Tfiih (Weak Binding) also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the General Transcription Factor Tfiih (Weak Binding) (pdb code 7ml3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the General Transcription Factor Tfiih (Weak Binding), PDB code: 7ml3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7ml3

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Zinc binding site 1 out of 7 in the General Transcription Factor Tfiih (Weak Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of General Transcription Factor Tfiih (Weak Binding) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn401

b:0.0
occ:1.00
 SG 3:CYS39 2.3 0.0 1.0
SG 3:CYS42 2.3 0.0 1.0
SG 3:CYS16 2.4 0.0 1.0
SG 3:CYS13 2.4 0.0 1.0
CB 3:CYS16 2.9 0.0 1.0
CB 3:CYS42 3.2 0.0 1.0
N 3:CYS16 3.3 0.0 1.0
CB 3:CYS39 3.4 0.0 1.0
CB 3:CYS13 3.6 0.0 1.0
CA 3:CYS16 3.7 0.0 1.0
CB 3:ILE15 3.8 0.0 1.0
N 3:CYS39 3.9 0.0 1.0
OG 3:SER41 4.1 0.0 1.0
CA 3:CYS39 4.2 0.0 1.0
C 3:ILE15 4.2 0.0 1.0
N 3:CYS42 4.3 0.0 1.0
CA 3:CYS42 4.4 0.0 1.0
CG2 3:ILE15 4.5 0.0 1.0
CA 3:ILE15 4.5 0.0 1.0
CG1 3:ILE38 4.5 0.0 1.0
O 3:CYS39 4.6 0.0 1.0
CG1 3:ILE15 4.6 0.0 1.0
C 3:CYS16 4.7 0.0 1.0
C 3:CYS39 4.7 0.0 1.0
N 3:ILE15 4.8 0.0 1.0
O 3:CYS16 4.8 0.0 1.0
CD1 3:ILE15 4.8 0.0 1.0
CA 3:CYS13 4.9 0.0 1.0

Zinc binding site 2 out of 7 in 7ml3

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Zinc binding site 2 out of 7 in the General Transcription Factor Tfiih (Weak Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of General Transcription Factor Tfiih (Weak Binding) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn402

b:0.0
occ:1.00
 ND1 3:HIS36 2.0 0.0 1.0
CE1 3:HIS36 2.2 0.0 1.0
SG 3:CYS54 2.2 0.0 1.0
CB 3:CYS34 2.7 0.0 1.0
SG 3:CYS59 2.7 0.0 1.0
CG 3:HIS36 3.3 0.0 1.0
CE 3:LYS61 3.3 0.0 1.0
SG 3:CYS34 3.3 0.0 1.0
CA 3:CYS34 3.4 0.0 1.0
NE2 3:HIS36 3.5 0.0 1.0
O 3:CYS34 3.5 0.0 1.0
NZ 3:LYS61 3.7 0.0 1.0
C 3:CYS34 3.9 0.0 1.0
CB 3:CYS54 3.9 0.0 1.0
CB 3:CYS59 3.9 0.0 1.0
CD2 3:HIS36 4.0 0.0 1.0
O 3:LYS61 4.0 0.0 1.0
CB 3:HIS36 4.1 0.0 1.0
O 3:CYS54 4.3 0.0 1.0
CB 3:LYS61 4.3 0.0 1.0
CD 3:LYS61 4.3 0.0 1.0
N 3:CYS54 4.5 0.0 1.0
CA 3:CYS54 4.6 0.0 1.0
CB 3:TYR56 4.8 0.0 1.0
C 3:CYS54 4.8 0.0 1.0
N 3:CYS34 4.8 0.0 1.0
C 3:LYS61 4.9 0.0 1.0
CG 3:LYS61 4.9 0.0 1.0

Zinc binding site 3 out of 7 in 7ml3

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Zinc binding site 3 out of 7 in the General Transcription Factor Tfiih (Weak Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of General Transcription Factor Tfiih (Weak Binding) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:0.0
occ:1.00
 CB 4:CYS292 2.2 0.0 1.0
SG 4:CYS305 2.3 0.0 1.0
SG 4:CYS292 2.3 0.0 1.0
SG 4:CYS308 2.4 0.0 1.0
SG 4:CYS289 2.4 0.0 1.0
CB 4:CYS308 3.3 0.0 1.0
CB 4:CYS294 3.4 0.0 1.0
CB 4:CYS289 3.5 0.0 1.0
CA 4:CYS292 3.6 0.0 1.0
CB 4:CYS305 3.8 0.0 1.0
N 4:CYS308 3.8 0.0 1.0
N 4:CYS294 3.9 0.0 1.0
C 4:CYS292 4.1 0.0 1.0
CA 4:CYS308 4.1 0.0 1.0
CA 4:CYS294 4.3 0.0 1.0
N 4:LEU293 4.3 0.0 1.0
N 4:CYS292 4.3 0.0 1.0
CB 4:ALA307 4.5 0.0 1.0
C 4:ALA307 4.6 0.0 1.0
O 4:CYS308 4.6 0.0 1.0
N 4:SER290 4.7 0.0 1.0
CB 4:SER290 4.8 0.0 1.0
O 4:CYS292 4.8 0.0 1.0
C 4:CYS308 4.9 0.0 1.0
CA 4:CYS289 4.9 0.0 1.0
CA 4:ALA307 4.9 0.0 1.0
CZ 4:PHE312 4.9 0.0 1.0

Zinc binding site 4 out of 7 in 7ml3

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Zinc binding site 4 out of 7 in the General Transcription Factor Tfiih (Weak Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of General Transcription Factor Tfiih (Weak Binding) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn501

b:0.0
occ:1.00
 SG 6:CYS406 2.0 0.0 1.0
SG 6:CYS403 2.2 0.0 1.0
SG 6:CYS440 2.2 0.0 1.0
SG 6:CYS437 2.2 0.0 1.0
CB 6:CYS403 3.0 0.0 1.0
N 6:CYS437 3.0 0.0 1.0
CB 6:CYS406 3.0 0.0 1.0
CB 6:CYS440 3.1 0.0 1.0
CB 6:CYS437 3.2 0.0 1.0
N 6:CYS406 3.4 0.0 1.0
CA 6:CYS406 3.6 0.0 1.0
CA 6:CYS437 3.6 0.0 1.0
C 6:CYS406 3.9 0.0 1.0
C 6:PHE436 4.0 0.0 1.0
CA 6:PHE436 4.2 0.0 1.0
CB 6:SER408 4.3 0.0 1.0
O 6:CYS406 4.3 0.0 1.0
CA 6:CYS440 4.3 0.0 1.0
CA 6:CYS403 4.4 0.0 1.0
N 6:GLN407 4.4 0.0 1.0
N 6:CYS440 4.5 0.0 1.0
C 6:CYS437 4.5 0.0 1.0
C 6:SER405 4.6 0.0 1.0
O 6:CYS437 4.7 0.0 1.0
N 6:SER408 4.8 0.0 1.0
CB 6:SER405 4.9 0.0 1.0
CB 6:PHE436 4.9 0.0 1.0
N 6:SER405 4.9 0.0 1.0

Zinc binding site 5 out of 7 in 7ml3

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Zinc binding site 5 out of 7 in the General Transcription Factor Tfiih (Weak Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of General Transcription Factor Tfiih (Weak Binding) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn502

b:0.0
occ:1.00
 SG 6:CYS454 2.2 0.0 1.0
SG 6:CYS432 2.3 0.0 1.0
SG 6:CYS429 2.3 0.0 1.0
SG 6:CYS451 2.3 0.0 1.0
CB 6:CYS429 2.6 0.0 1.0
CB 6:CYS432 3.0 0.0 1.0
CB 6:CYS454 3.3 0.0 1.0
N 6:CYS454 3.5 0.0 1.0
N 6:CYS432 3.7 0.0 1.0
CA 6:CYS454 3.8 0.0 1.0
CB 6:CYS451 3.9 0.0 1.0
CA 6:CYS432 3.9 0.0 1.0
CA 6:CYS429 4.1 0.0 1.0
C 6:GLY453 4.2 0.0 1.0
CA 6:GLY453 4.7 0.0 1.0
C 6:CYS432 4.7 0.0 1.0
N 6:GLU430 4.7 0.0 1.0
N 6:LYS433 4.8 0.0 1.0
C 6:CYS429 4.8 0.0 1.0
C 6:ASP431 4.8 0.0 1.0
N 6:ASP431 4.9 0.0 1.0
O 6:GLY453 5.0 0.0 1.0

Zinc binding site 6 out of 7 in 7ml3

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Zinc binding site 6 out of 7 in the General Transcription Factor Tfiih (Weak Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of General Transcription Factor Tfiih (Weak Binding) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn503

b:0.0
occ:1.00
 SG 6:CYS363 2.4 0.0 1.0
SG 6:CYS352 2.5 0.0 1.0
SG 6:CYS349 2.5 0.0 1.0
CB 6:CYS352 2.6 0.0 1.0
CB 6:CYS366 2.8 0.0 1.0
N 6:CYS366 3.1 0.0 1.0
SG 6:CYS366 3.5 0.0 1.0
CB 6:CYS363 3.5 0.0 1.0
CA 6:CYS366 3.5 0.0 1.0
CA 6:CYS352 3.8 0.0 1.0
N 6:CYS352 3.9 0.0 1.0
CB 6:CYS349 4.0 0.0 1.0
C 6:CYS366 4.1 0.0 1.0
C 6:CYS365 4.2 0.0 1.0
N 6:ASP367 4.3 0.0 1.0
CB 6:CYS365 4.3 0.0 1.0
CA 6:CYS365 4.6 0.0 1.0
N 6:CYS365 4.7 0.0 1.0
C 6:CYS352 4.8 0.0 1.0
CA 6:CYS363 4.9 0.0 1.0
O 6:CYS366 4.9 0.0 1.0

Zinc binding site 7 out of 7 in 7ml3

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Zinc binding site 7 out of 7 in the General Transcription Factor Tfiih (Weak Binding)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of General Transcription Factor Tfiih (Weak Binding) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn504

b:0.0
occ:1.00
 SG 6:CYS338 2.2 30.0 1.0
SG 6:CYS336 2.2 30.0 1.0
SG 6:CYS357 2.3 30.0 1.0
ND1 6:HIS339 2.8 30.0 1.0
N 6:HIS339 2.9 0.0 1.0
CB 6:CYS357 3.2 30.0 1.0
CB 6:CYS338 3.5 30.0 1.0
CB 6:HIS339 3.5 30.0 1.0
C 6:CYS338 3.5 0.0 1.0
CG 6:HIS339 3.5 30.0 1.0
CB 6:CYS336 3.6 30.0 1.0
N 6:CYS338 3.7 0.0 1.0
CA 6:CYS338 3.7 0.0 1.0
CA 6:HIS339 3.8 0.0 1.0
N 6:CYS357 3.8 0.0 1.0
CE1 6:HIS339 3.9 30.0 1.0
CA 6:CYS357 4.1 0.0 1.0
O 6:CYS338 4.5 0.0 1.0
C 6:HIS339 4.6 0.0 1.0
N 6:SER340 4.7 0.0 1.0
N 6:SER337 4.7 0.0 1.0
CA 6:CYS336 4.7 0.0 1.0
CD2 6:HIS339 4.8 30.0 1.0
NE2 6:HIS339 4.9 30.0 1.0
C 6:SER337 4.9 0.0 1.0
C 6:VAL356 5.0 0.0 1.0

Reference:

C.Yang, R.Fujiwara, H.J.Kim, P.Basnet, Y.Zhu, J.J.Gorbea Colon, S.Steimle, B.A.Garcia, C.D.Kaplan, K.Murakami. Structural Visualization of De Novo Transcription Initiation By Saccharomyces Cerevisiae Rna Polymerase II. Mol.Cell V. 82 660 2022.
ISSN: ISSN 1097-2765
PubMed: 35051353
DOI: 10.1016/J.MOLCEL.2021.12.020
Page generated: Tue Oct 29 23:32:26 2024

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