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Zinc in PDB 7o75: Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna

Enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna

All present enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna:
3.6.4.12;

Other elements in 7o75:

The structure of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Fluorine (F) 3 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna (pdb code 7o75). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna, PDB code: 7o75:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 7o75

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Zinc binding site 1 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn401

b:157.4
occ:1.00
 SG 3:CYS39 2.3 90.1 1.0
SG 3:CYS42 2.3 91.5 1.0
SG 3:CYS16 2.3 91.6 1.0
SG 3:CYS13 2.3 94.0 1.0
CB 3:CYS13 3.1 94.0 1.0
CB 3:CYS16 3.2 91.6 1.0
CB 3:CYS39 3.4 90.1 1.0
CB 3:CYS42 3.5 91.5 1.0
N 3:CYS16 3.8 91.6 1.0
CA 3:CYS16 4.1 91.6 1.0
N 3:CYS42 4.1 91.5 1.0
N 3:CYS39 4.2 90.1 1.0
CA 3:CYS39 4.3 90.1 1.0
CA 3:CYS42 4.4 91.5 1.0
CA 3:CYS13 4.5 94.0 1.0
O 3:CYS39 4.7 90.1 1.0
OG1 3:THR18 4.7 88.0 1.0
C 3:CYS16 4.8 91.6 1.0
C 3:CYS39 4.8 90.1 1.0
N 3:LYS17 4.9 89.7 1.0
CB 3:ILE15 5.0 92.5 1.0

Zinc binding site 2 out of 17 in 7o75

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Zinc binding site 2 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn402

b:125.8
occ:1.00
 ND1 3:HIS36 2.1 86.3 1.0
SG 3:CYS54 2.3 87.1 1.0
SG 3:CYS59 2.3 90.1 1.0
SG 3:CYS34 2.3 86.0 1.0
CE1 3:HIS36 2.6 86.3 1.0
CB 3:CYS54 3.2 87.1 1.0
CB 3:CYS34 3.3 86.0 1.0
CG 3:HIS36 3.3 86.3 1.0
CB 3:CYS59 3.3 90.1 1.0
NE2 3:HIS36 3.9 86.3 1.0
CB 3:HIS36 4.0 86.3 1.0
CD2 3:HIS36 4.2 86.3 1.0
CD1 3:TYR56 4.4 90.5 1.0
CB 3:TYR56 4.4 90.5 1.0
CG 3:TYR56 4.6 90.5 1.0
CA 3:CYS54 4.7 87.1 1.0
CA 3:CYS34 4.7 86.0 1.0
CA 3:CYS59 4.8 90.1 1.0
CE 3:LYS61 5.0 85.8 1.0

Zinc binding site 3 out of 17 in 7o75

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Zinc binding site 3 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:88.9
occ:1.00
 SG 4:CYS305 2.3 83.6 1.0
SG 4:CYS292 2.3 60.0 1.0
SG 4:CYS289 2.3 62.8 1.0
SG 4:CYS308 2.3 76.6 1.0
CB 4:CYS289 2.9 62.8 1.0
CB 4:CYS305 3.3 83.6 1.0
CB 4:CYS292 3.4 60.0 1.0
CB 4:CYS308 3.5 76.6 1.0
N 4:CYS292 4.0 60.0 1.0
N 4:CYS308 4.0 76.6 1.0
CA 4:CYS292 4.3 60.0 1.0
CA 4:CYS308 4.3 76.6 1.0
CA 4:CYS289 4.4 62.8 1.0
CB 4:SER310 4.7 80.8 1.0
CA 4:CYS305 4.7 83.6 1.0
OG 4:SER310 4.8 80.8 1.0
CB 4:CYS294 4.9 63.5 1.0
CB 4:ALA307 4.9 76.4 1.0
C 4:CYS292 5.0 60.0 1.0
CB 4:VAL291 5.0 59.9 1.0
CZ 4:PHE312 5.0 82.4 1.0
C 4:ALA307 5.0 76.4 1.0
C 4:CYS308 5.0 76.6 1.0

Zinc binding site 4 out of 17 in 7o75

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Zinc binding site 4 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn501

b:127.1
occ:1.00
 SG 6:CYS366 2.3 67.3 1.0
SG 6:CYS363 2.3 59.9 1.0
SG 6:CYS352 2.3 72.9 1.0
SG 6:CYS349 2.3 58.7 1.0
CB 6:CYS349 3.1 58.7 1.0
CB 6:CYS363 3.3 59.9 1.0
CB 6:CYS366 3.6 67.3 1.0
OG 6:SER354 3.7 65.5 1.0
CB 6:CYS352 3.8 72.9 1.0
N 6:CYS352 3.9 72.9 1.0
N 6:CYS366 4.0 67.3 1.0
CA 6:CYS352 4.4 72.9 1.0
CA 6:CYS366 4.4 67.3 1.0
CB 6:ASN351 4.4 67.2 1.0
CA 6:CYS349 4.6 58.7 1.0
CA 6:CYS363 4.7 59.9 1.0
C 6:ASN351 4.7 67.2 1.0
CB 6:CYS365 4.8 71.0 1.0
N 6:ASN351 4.9 67.2 1.0
CA 6:ASN351 4.9 67.2 1.0
CB 6:SER354 5.0 65.5 1.0
C 6:CYS352 5.0 72.9 1.0

Zinc binding site 5 out of 17 in 7o75

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Zinc binding site 5 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn502

b:125.7
occ:1.00
 SG 6:CYS440 2.3 67.0 1.0
SG 6:CYS437 2.3 76.2 1.0
SG 6:CYS406 2.3 63.7 1.0
SG 6:CYS403 2.3 77.4 1.0
CB 6:CYS403 3.1 77.4 1.0
CB 6:CYS437 3.2 76.2 1.0
CB 6:CYS440 3.4 67.0 1.0
CB 6:CYS406 3.4 63.7 1.0
OG 6:SER405 3.7 60.2 1.0
N 6:CYS437 3.8 76.2 1.0
N 6:CYS406 4.0 63.7 1.0
N 6:CYS440 4.0 67.0 1.0
CA 6:CYS437 4.0 76.2 1.0
CA 6:CYS406 4.2 63.7 1.0
CA 6:CYS440 4.3 67.0 1.0
CA 6:CYS403 4.6 77.4 1.0
C 6:CYS437 4.7 76.2 1.0
CB 6:SER408 4.7 75.6 1.0
O 6:CYS437 4.8 76.2 1.0
C 6:CYS406 4.8 63.7 1.0
N 6:GLN407 4.9 68.7 1.0
N 6:SER408 5.0 75.6 1.0
C 6:PHE436 5.0 76.1 1.0
CB 6:SER405 5.0 60.2 1.0
C 6:SER405 5.0 60.2 1.0

Zinc binding site 6 out of 17 in 7o75

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Zinc binding site 6 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn503

b:86.6
occ:1.00
 SG 6:CYS451 2.3 59.4 1.0
SG 6:CYS454 2.3 66.6 1.0
SG 6:CYS432 2.3 81.4 1.0
SG 6:CYS429 2.3 83.8 1.0
CB 6:CYS429 3.0 83.8 1.0
CB 6:CYS451 3.2 59.4 1.0
CB 6:CYS432 3.5 81.4 1.0
CB 6:CYS454 3.7 66.6 1.0
N 6:CYS454 3.7 66.6 1.0
N 6:CYS432 3.9 81.4 1.0
CA 6:CYS454 4.1 66.6 1.0
CA 6:CYS432 4.3 81.4 1.0
CB 6:ASP431 4.3 83.2 1.0
CA 6:CYS429 4.4 83.8 1.0
CE2 6:PHE436 4.5 76.1 1.0
C 6:GLY453 4.5 66.7 1.0
CA 6:CYS451 4.6 59.4 1.0
O 6:CYS429 4.7 83.8 1.0
C 6:ASP431 4.7 83.2 1.0
CA 6:GLY453 4.7 66.7 1.0
C 6:CYS429 4.7 83.8 1.0
CZ 6:PHE389 4.8 75.4 1.0
CZ 6:PHE436 4.8 76.1 1.0
CE1 6:PHE389 4.8 75.4 1.0
N 6:GLY453 4.8 66.7 1.0
N 6:ASP431 4.9 83.2 1.0
CA 6:ASP431 4.9 83.2 1.0
C 6:CYS451 5.0 59.4 1.0

Zinc binding site 7 out of 17 in 7o75

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Zinc binding site 7 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn504

b:117.7
occ:1.00
 ND1 6:HIS339 2.1 82.1 1.0
SG 6:CYS357 2.3 55.6 1.0
SG 6:CYS338 2.3 75.8 1.0
SG 6:CYS336 2.3 85.3 1.0
CG 6:HIS339 2.8 82.1 1.0
CE1 6:HIS339 3.0 82.1 1.0
CB 6:CYS336 3.1 85.3 1.0
CB 6:HIS339 3.2 82.1 1.0
N 6:HIS339 3.4 82.1 1.0
CB 6:CYS357 3.8 55.6 1.0
CA 6:HIS339 3.9 82.1 1.0
CD2 6:HIS339 3.9 82.1 1.0
NE2 6:HIS339 3.9 82.1 1.0
CB 6:CYS338 4.0 75.8 1.0
C 6:CYS338 4.3 75.8 1.0
N 6:CYS357 4.4 55.6 1.0
N 6:CYS338 4.5 75.8 1.0
CA 6:CYS336 4.5 85.3 1.0
CA 6:CYS338 4.5 75.8 1.0
C 6:HIS339 4.7 82.1 1.0
CA 6:CYS357 4.7 55.6 1.0
C 6:CYS336 4.7 85.3 1.0
N 6:SER340 4.8 87.5 1.0
O 6:CYS336 4.9 85.3 1.0

Zinc binding site 8 out of 17 in 7o75

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Zinc binding site 8 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:115.5
occ:1.00
 SG A:CYS107 2.3 60.8 1.0
SG A:CYS167 2.3 89.8 1.0
SG A:CYS148 2.3 86.4 1.0
SG A:CYS110 2.3 64.2 1.0
CB A:CYS107 3.2 60.8 1.0
CB A:CYS148 3.3 86.4 1.0
CB A:CYS110 3.6 64.2 1.0
CB A:CYS167 3.8 89.8 1.0
N A:CYS167 3.8 89.8 1.0
N A:CYS110 3.9 64.2 1.0
CA A:CYS110 4.3 64.2 1.0
CA A:CYS167 4.4 89.8 1.0
CB A:HIS109 4.5 70.6 1.0
C A:GLY166 4.5 86.0 1.0
NE2 A:GLN171 4.5 69.6 1.0
CA A:GLY166 4.6 86.0 1.0
CA A:CYS107 4.6 60.8 1.0
CA A:CYS148 4.7 86.4 1.0
C A:HIS109 4.8 70.6 1.0
N A:HIS109 4.9 70.6 1.0
CA A:HIS109 5.0 70.6 1.0

Zinc binding site 9 out of 17 in 7o75

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Zinc binding site 9 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:29.1
occ:1.00
 NE2 A:HIS80 2.1 21.5 1.0
SG A:CYS67 2.3 35.2 1.0
SG A:CYS70 2.3 30.4 1.0
SG A:CYS77 2.3 24.6 1.0
CD2 A:HIS80 2.8 21.5 1.0
CB A:CYS67 2.9 35.2 1.0
CE1 A:HIS80 3.2 21.5 1.0
CB A:CYS77 3.5 24.6 1.0
CB A:CYS70 3.7 30.4 1.0
N A:CYS70 3.9 30.4 1.0
CG A:HIS80 4.0 21.5 1.0
ND1 A:HIS80 4.2 21.5 1.0
CA A:CYS77 4.3 24.6 1.0
CA A:CYS70 4.4 30.4 1.0
CA A:CYS67 4.4 35.2 1.0
CA A:GLY59 4.4 28.3 1.0
CB A:THR69 4.5 30.0 1.0
CD A:PRO78 4.9 18.7 1.0
C A:THR69 4.9 30.0 1.0
C A:CYS67 5.0 35.2 1.0
N A:THR69 5.0 30.0 1.0
N A:GLY79 5.0 22.0 1.0
C A:CYS77 5.0 24.6 1.0

Zinc binding site 10 out of 17 in 7o75

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Zinc binding site 10 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:28.6
occ:1.00
 SG B:CYS1185 2.3 27.1 1.0
SG B:CYS1166 2.3 19.6 1.0
SG B:CYS1182 2.3 15.1 1.0
SG B:CYS1163 2.3 16.5 1.0
CB B:CYS1163 2.9 16.5 1.0
CB B:CYS1185 3.2 27.1 1.0
CB B:CYS1166 3.6 19.6 1.0
CB B:CYS1182 3.6 15.1 1.0
N B:CYS1166 3.7 19.6 1.0
O B:CYS1166 4.1 19.6 1.0
CA B:CYS1166 4.2 19.6 1.0
CA B:CYS1163 4.4 16.5 1.0
CB B:ILE1165 4.4 21.3 1.0
OD1 B:ASN1187 4.5 24.1 1.0
CA B:CYS1185 4.6 27.1 1.0
C B:CYS1166 4.6 19.6 1.0
O B:CYS1182 4.7 15.1 1.0
C B:ILE1165 4.8 21.3 1.0
N B:CYS1185 4.8 27.1 1.0
ND2 B:ASN1187 4.9 24.1 1.0
N B:ILE1165 4.9 21.3 1.0
C B:CYS1163 4.9 16.5 1.0
CA B:CYS1182 4.9 15.1 1.0
CA B:ILE1165 4.9 21.3 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 08:17:10 2024

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