Zinc in PDB 7o4k: Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex

Enzymatic activity of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex

All present enzymatic activity of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex:
2.7.7.6; 3.6.4.12;

Other elements in 7o4k:

The structure of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex (pdb code 7o4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex, PDB code: 7o4k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7o4k

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Zinc binding site 1 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn401

b:138.7
occ:1.00
 SG 3:CYS39 2.3 104.9 1.0
SG 3:CYS42 2.3 106.0 1.0
SG 3:CYS16 2.3 104.7 1.0
SG 3:CYS13 2.3 106.2 1.0
CB 3:CYS13 3.0 106.2 1.0
CB 3:CYS42 3.3 106.0 1.0
CB 3:CYS16 3.3 104.7 1.0
CB 3:CYS39 3.7 104.9 1.0
N 3:CYS16 3.8 104.7 1.0
CA 3:CYS16 4.1 104.7 1.0
OG 3:SER41 4.2 104.5 1.0
N 3:CYS39 4.2 104.9 1.0
N 3:CYS42 4.2 106.0 1.0
CA 3:CYS42 4.3 106.0 1.0
CG2 3:THR18 4.3 104.5 1.0
CA 3:CYS13 4.5 106.2 1.0
CA 3:CYS39 4.5 104.9 1.0
CB 3:ILE15 4.7 105.2 1.0
O 3:CYS39 4.8 104.9 1.0
C 3:CYS16 4.8 104.7 1.0
CG1 3:ILE38 4.9 102.7 1.0
C 3:ILE15 4.9 105.2 1.0
C 3:CYS13 4.9 106.2 1.0
C 3:CYS39 5.0 104.9 1.0
N 3:LYS17 5.0 104.0 1.0
O 3:CYS13 5.0 106.2 1.0

Zinc binding site 2 out of 10 in 7o4k

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Zinc binding site 2 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn402

b:170.0
occ:1.00
 ND1 3:HIS36 2.1 104.0 1.0
SG 3:CYS54 2.3 107.2 1.0
SG 3:CYS34 2.3 105.0 1.0
SG 3:CYS59 2.3 117.7 1.0
CE1 3:HIS36 2.6 104.0 1.0
CB 3:CYS54 3.0 107.2 1.0
CB 3:CYS34 3.1 105.0 1.0
CG 3:HIS36 3.2 104.0 1.0
CB 3:CYS59 3.3 117.7 1.0
NE2 3:HIS36 3.7 104.0 1.0
CB 3:HIS36 3.9 104.0 1.0
CD2 3:HIS36 4.0 104.0 1.0
CB 3:TYR56 4.4 108.2 1.0
CA 3:CYS54 4.5 107.2 1.0
CA 3:CYS34 4.6 105.0 1.0
CG 3:TYR56 4.7 108.2 1.0
CA 3:CYS59 4.7 117.7 1.0
C 3:CYS34 4.9 105.0 1.0
CD1 3:TYR56 4.9 108.2 1.0

Zinc binding site 3 out of 10 in 7o4k

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Zinc binding site 3 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:109.9
occ:1.00
 SG 4:CYS305 2.3 101.5 1.0
SG 4:CYS308 2.3 100.2 1.0
SG 4:CYS292 2.3 81.8 1.0
SG 4:CYS289 2.3 82.9 1.0
CB 4:CYS289 2.9 82.9 1.0
CB 4:CYS305 3.3 101.5 1.0
CB 4:CYS292 3.5 81.8 1.0
CB 4:CYS308 3.7 100.2 1.0
N 4:CYS292 3.8 81.8 1.0
N 4:CYS308 4.1 100.2 1.0
SG 4:CYS294 4.2 85.5 1.0
CA 4:CYS292 4.2 81.8 1.0
CA 4:CYS289 4.4 82.9 1.0
CA 4:CYS308 4.6 100.2 1.0
CB 4:VAL291 4.6 79.8 1.0
CB 4:ALA307 4.7 97.7 1.0
CA 4:CYS305 4.7 101.5 1.0
CZ 4:PHE312 4.8 97.8 1.0
C 4:VAL291 4.9 79.8 1.0
C 4:CYS289 4.9 82.9 1.0
CB 4:SER310 4.9 99.2 1.0
C 4:CYS292 4.9 81.8 1.0
N 4:VAL291 4.9 79.8 1.0
C 4:ALA307 4.9 97.7 1.0
N 4:LEU293 5.0 75.3 1.0

Zinc binding site 4 out of 10 in 7o4k

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Zinc binding site 4 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn501

b:144.9
occ:1.00
 SG 6:CYS349 2.3 87.9 1.0
SG 6:CYS352 2.3 101.9 1.0
SG 6:CYS363 2.3 85.9 1.0
SG 6:CYS366 2.3 94.5 1.0
CB 6:CYS349 3.1 87.9 1.0
CB 6:CYS363 3.2 85.9 1.0
OG 6:SER354 3.7 98.0 1.0
CB 6:CYS366 3.7 94.5 1.0
CB 6:CYS352 3.8 101.9 1.0
N 6:CYS352 3.9 101.9 1.0
N 6:CYS366 4.1 94.5 1.0
CB 6:ASN351 4.3 94.9 1.0
CA 6:CYS352 4.4 101.9 1.0
CA 6:CYS366 4.5 94.5 1.0
CA 6:CYS349 4.6 87.9 1.0
CA 6:CYS363 4.6 85.9 1.0
CB 6:CYS365 4.7 98.0 1.0
C 6:ASN351 4.7 94.9 1.0
N 6:ASN351 4.8 94.9 1.0
CA 6:ASN351 4.8 94.9 1.0

Zinc binding site 5 out of 10 in 7o4k

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Zinc binding site 5 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn502

b:133.3
occ:1.00
 SG 6:CYS406 2.3 84.0 1.0
SG 6:CYS440 2.3 85.3 1.0
SG 6:CYS437 2.3 94.1 1.0
SG 6:CYS403 2.3 95.7 1.0
CB 6:CYS403 3.2 95.7 1.0
CB 6:CYS440 3.2 85.3 1.0
CB 6:CYS437 3.2 94.1 1.0
CB 6:CYS406 3.3 84.0 1.0
OG 6:SER405 3.8 81.2 1.0
N 6:CYS437 3.8 94.1 1.0
N 6:CYS406 3.9 84.0 1.0
N 6:CYS440 4.0 85.3 1.0
CA 6:CYS437 4.0 94.1 1.0
CA 6:CYS440 4.2 85.3 1.0
CA 6:CYS406 4.2 84.0 1.0
CA 6:CYS403 4.6 95.7 1.0
C 6:CYS437 4.6 94.1 1.0
O 6:CYS437 4.7 94.1 1.0
CB 6:SER408 4.7 94.3 1.0
C 6:CYS406 4.8 84.0 1.0

Zinc binding site 6 out of 10 in 7o4k

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Zinc binding site 6 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn503

b:150.7
occ:1.00
 SG 6:CYS432 2.3 98.9 1.0
SG 6:CYS454 2.3 86.0 1.0
SG 6:CYS429 2.3 100.9 1.0
SG 6:CYS451 2.3 80.8 1.0
CB 6:CYS429 3.0 100.9 1.0
CB 6:CYS451 3.2 80.8 1.0
CB 6:CYS432 3.5 98.9 1.0
N 6:CYS454 3.6 86.0 1.0
CB 6:CYS454 3.7 86.0 1.0
N 6:CYS432 3.8 98.9 1.0
CA 6:CYS454 4.1 86.0 1.0
CA 6:CYS432 4.3 98.9 1.0
CB 6:ASP431 4.3 101.4 1.0
CA 6:CYS429 4.4 100.9 1.0
C 6:GLY453 4.4 85.2 1.0
CA 6:CYS451 4.6 80.8 1.0
CA 6:GLY453 4.6 85.2 1.0
O 6:CYS429 4.7 100.9 1.0
C 6:ASP431 4.7 101.4 1.0
C 6:CYS429 4.7 100.9 1.0
N 6:GLY453 4.8 85.2 1.0
N 6:ASP431 4.9 101.4 1.0
CA 6:ASP431 4.9 101.4 1.0
O 6:CYS451 4.9 80.8 1.0
C 6:CYS451 4.9 80.8 1.0
CE1 6:PHE436 5.0 94.3 1.0

Zinc binding site 7 out of 10 in 7o4k

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Zinc binding site 7 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn504

b:150.1
occ:1.00
 ND1 6:HIS339 2.1 105.0 1.0
SG 6:CYS357 2.3 87.5 1.0
SG 6:CYS338 2.3 100.8 1.0
SG 6:CYS336 2.3 107.6 1.0
CG 6:HIS339 2.8 105.0 1.0
CE1 6:HIS339 2.9 105.0 1.0
CB 6:CYS336 2.9 107.6 1.0
N 6:HIS339 3.2 105.0 1.0
CB 6:HIS339 3.2 105.0 1.0
CB 6:CYS357 3.5 87.5 1.0
CD2 6:HIS339 3.7 105.0 1.0
NE2 6:HIS339 3.8 105.0 1.0
CA 6:HIS339 3.8 105.0 1.0
CB 6:CYS338 3.9 100.8 1.0
C 6:CYS338 4.2 100.8 1.0
N 6:CYS338 4.3 100.8 1.0
CA 6:CYS338 4.3 100.8 1.0
CA 6:CYS336 4.4 107.6 1.0
N 6:CYS357 4.4 87.5 1.0
CG 6:LYS341 4.5 110.2 1.0
C 6:HIS339 4.6 105.0 1.0
CA 6:CYS357 4.6 87.5 1.0
N 6:SER340 4.7 110.1 1.0
C 6:CYS336 4.7 107.6 1.0
CD 6:LYS341 4.9 110.2 1.0
CG2 6:VAL343 5.0 107.5 1.0

Zinc binding site 8 out of 10 in 7o4k

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Zinc binding site 8 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:116.7
occ:1.00
 SG A:CYS107 2.3 81.9 1.0
SG A:CYS110 2.3 78.0 1.0
SG A:CYS167 2.3 92.2 1.0
SG A:CYS148 2.3 93.1 1.0
CB A:CYS107 3.1 81.9 1.0
CB A:CYS148 3.4 93.1 1.0
CB A:CYS110 3.5 78.0 1.0
N A:CYS167 3.8 92.2 1.0
CB A:CYS167 3.9 92.2 1.0
N A:CYS110 4.0 78.0 1.0
CA A:CYS167 4.3 92.2 1.0
CA A:CYS110 4.4 78.0 1.0
CA A:CYS107 4.5 81.9 1.0
CA A:CYS148 4.6 93.1 1.0
C A:GLY166 4.7 92.8 1.0
CA A:GLY166 4.7 92.8 1.0
NE2 A:GLN171 4.7 84.1 1.0
CB A:HIS109 4.8 80.0 1.0
N A:GLY168 4.8 93.3 1.0
C A:CYS167 4.8 92.2 1.0
C A:HIS109 4.9 80.0 1.0

Zinc binding site 9 out of 10 in 7o4k

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Zinc binding site 9 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:58.6
occ:1.00
 SG B:CYS1185 2.3 55.2 1.0
SG B:CYS1182 2.3 45.9 1.0
SG B:CYS1166 2.3 51.5 1.0
SG B:CYS1163 2.3 52.5 1.0
CB B:CYS1163 2.8 52.5 1.0
CB B:CYS1185 3.1 55.2 1.0
CB B:CYS1166 3.5 51.5 1.0
CB B:CYS1182 3.5 45.9 1.0
N B:CYS1166 3.9 51.5 1.0
O B:CYS1166 4.1 51.5 1.0
CA B:CYS1166 4.2 51.5 1.0
CA B:CYS1163 4.3 52.5 1.0
CA B:CYS1185 4.5 55.2 1.0
OG1 B:THR1170 4.6 53.6 1.0
C B:CYS1166 4.6 51.5 1.0
OD1 B:ASN1187 4.6 48.5 1.0
O B:CYS1182 4.7 45.9 1.0
N B:CYS1185 4.7 55.2 1.0
CA B:CYS1182 4.8 45.9 1.0
C B:CYS1163 4.9 52.5 1.0
ND2 B:ASN1187 4.9 48.5 1.0
CB B:ILE1165 4.9 50.1 1.0
C B:ILE1165 5.0 50.1 1.0

Zinc binding site 10 out of 10 in 7o4k

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Zinc binding site 10 out of 10 in the Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Yeast Tfiih in the Contracted State Within the Pre-Initiation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn501

b:121.4
occ:1.00
 SG W:CYS124 2.3 99.7 1.0
SG W:CYS127 2.3 100.4 1.0
SG W:CYS152 2.3 96.5 1.0
SG W:CYS149 2.3 90.8 1.0
CB W:CYS149 3.2 90.8 1.0
CB W:CYS127 3.3 100.4 1.0
CB W:CYS152 3.3 96.5 1.0
CB W:CYS124 3.3 99.7 1.0
N W:CYS127 3.8 100.4 1.0
N W:CYS152 3.9 96.5 1.0
CA W:CYS127 4.1 100.4 1.0
OG1 W:THR129 4.2 99.6 1.0
CA W:CYS152 4.2 96.5 1.0
CA W:CYS124 4.7 99.7 1.0
CA W:CYS149 4.7 90.8 1.0
CB W:LEU151 4.7 90.1 1.0
CB W:ILE126 4.8 97.4 1.0
C W:CYS127 4.9 100.4 1.0
C W:ILE126 4.9 97.4 1.0
C W:LEU151 5.0 90.1 1.0

Reference:

S.Schilbach, S.Aibara, C.Dienemann, F.Grabbe, P.Cramer. Structure of Rna Polymerase II Pre-Initiation Complex at 2.9 Angstrom Defines Initial Dna Opening Cell(Cambridge,Mass.) 2021.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2021.05.012
Page generated: Wed Oct 30 08:17:08 2024

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