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Zinc in PDB 5oqm: Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator

Enzymatic activity of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator

All present enzymatic activity of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator:
2.7.7.6; 3.6.4.12;

Other elements in 5oqm:

The structure of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator (pdb code 5oqm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator, PDB code: 5oqm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 5oqm

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Zinc binding site 1 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.0
occ:1.00
 SG A:CYS107 2.4 0.0 1.0
SG A:CYS148 2.4 0.0 1.0
SG A:CYS110 2.4 0.0 1.0
SG A:CYS167 2.4 0.0 1.0
CB A:CYS167 2.6 0.0 1.0
CB A:CYS148 2.9 0.0 1.0
CB A:CYS107 3.2 0.0 1.0
CB A:CYS110 3.7 0.0 1.0
NE2 A:GLN171 3.8 0.0 1.0
CA A:CYS167 4.1 0.0 1.0
N A:CYS110 4.1 0.0 1.0
N A:GLY168 4.2 0.0 1.0
CA A:CYS148 4.4 0.0 1.0
CA A:CYS110 4.5 0.0 1.0
O A:GLY166 4.5 0.0 1.0
CA A:CYS107 4.6 0.0 1.0
C A:CYS167 4.7 0.0 1.0
N A:CYS167 4.8 0.0 1.0
C A:GLY166 5.0 0.0 1.0

Zinc binding site 2 out of 16 in 5oqm

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Zinc binding site 2 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.0
occ:1.00
 SG A:CYS67 2.4 0.0 1.0
NE2 A:HIS80 2.4 0.0 1.0
SG A:CYS77 2.4 0.0 1.0
SG A:CYS70 2.4 0.0 1.0
CD2 A:HIS80 2.5 0.0 1.0
CB A:CYS70 2.7 0.0 1.0
CB A:CYS77 3.6 0.0 1.0
CE1 A:HIS80 3.6 0.0 1.0
CG A:HIS80 3.7 0.0 1.0
N A:CYS70 3.7 0.0 1.0
CA A:CYS70 3.8 0.0 1.0
CB A:CYS67 3.9 0.0 1.0
N A:GLY79 4.2 0.0 1.0
ND1 A:HIS80 4.2 0.0 1.0
CA A:CYS77 4.3 0.0 1.0
C A:GLY79 4.3 0.0 1.0
O A:GLY79 4.3 0.0 1.0
CA A:GLY79 4.4 0.0 1.0
CA A:GLY59 4.6 0.0 1.0
O A:LEU58 4.6 0.0 1.0
CD A:PRO78 4.6 0.0 1.0
O A:CYS67 4.7 0.0 1.0
C A:CYS77 4.8 0.0 1.0
N A:HIS80 4.8 0.0 1.0
C A:THR69 4.8 0.0 1.0
CB A:HIS80 4.9 0.0 1.0
C A:CYS70 4.9 0.0 1.0
N A:PRO78 4.9 0.0 1.0
CG2 A:THR69 4.9 0.0 1.0

Zinc binding site 3 out of 16 in 5oqm

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Zinc binding site 3 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.0
occ:1.00
 SG B:CYS1185 2.3 0.0 1.0
SG B:CYS1182 2.4 0.0 1.0
SG B:CYS1166 2.4 0.0 1.0
SG B:CYS1163 2.4 0.0 1.0
CB B:CYS1163 2.5 0.0 1.0
CB B:CYS1182 3.2 0.0 1.0
O B:CYS1166 3.7 0.0 1.0
CB B:CYS1185 3.8 0.0 1.0
CB B:CYS1166 3.9 0.0 1.0
N B:CYS1166 3.9 0.0 1.0
CA B:CYS1163 4.0 0.0 1.0
CA B:CYS1166 4.3 0.0 1.0
C B:CYS1166 4.4 0.0 1.0
C B:CYS1163 4.6 0.0 1.0
CA B:CYS1182 4.6 0.0 1.0
N B:CYS1163 4.7 0.0 1.0
C B:CYS1182 4.9 0.0 1.0
N B:ILE1165 4.9 0.0 1.0
N B:GLY1164 5.0 0.0 1.0
O B:CYS1182 5.0 0.0 1.0
CA B:CYS1185 5.0 0.0 1.0

Zinc binding site 4 out of 16 in 5oqm

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Zinc binding site 4 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.0
occ:1.00
 SG C:CYS95 2.3 0.0 1.0
SG C:CYS86 2.3 0.0 1.0
SG C:CYS88 2.3 0.0 1.0
SG C:CYS92 2.4 0.0 1.0
CB C:CYS86 2.8 0.0 1.0
CB C:CYS92 3.5 0.0 1.0
CB C:CYS88 3.7 0.0 1.0
N C:CYS92 3.7 0.0 1.0
CB C:CYS95 4.0 0.0 1.0
C C:HIS91 4.1 0.0 1.0
CA C:CYS92 4.2 0.0 1.0
CA C:CYS86 4.2 0.0 1.0
CA C:HIS91 4.4 0.0 1.0
N C:CYS88 4.4 0.0 1.0
N C:CYS95 4.4 0.0 1.0
C C:CYS86 4.5 0.0 1.0
O C:CYS92 4.6 0.0 1.0
CB C:LYS94 4.6 0.0 1.0
CA C:CYS88 4.6 0.0 1.0
C C:CYS92 4.7 0.0 1.0
O C:HIS91 4.7 0.0 1.0
O C:CYS86 4.8 0.0 1.0
CA C:CYS95 4.9 0.0 1.0
O C:ASP90 5.0 0.0 1.0

Zinc binding site 5 out of 16 in 5oqm

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Zinc binding site 5 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.0
occ:1.00
 SG I:CYS32 2.3 0.0 1.0
SG I:CYS29 2.3 0.0 1.0
SG I:CYS7 2.4 0.0 1.0
SG I:CYS10 2.4 0.0 1.0
CB I:CYS10 2.4 0.0 1.0
CB I:CYS7 3.2 0.0 1.0
CB I:CYS29 3.3 0.0 1.0
OG1 I:THR31 3.4 0.0 1.0
CB I:CYS32 3.6 0.0 1.0
CA I:CYS10 3.8 0.0 1.0
N I:CYS10 4.2 0.0 1.0
O I:ARG8 4.2 0.0 1.0
N I:CYS32 4.2 0.0 1.0
CA I:CYS32 4.5 0.0 1.0
CB I:THR31 4.6 0.0 1.0
ND2 I:ASN12 4.6 0.0 1.0
CA I:CYS7 4.7 0.0 1.0
CB I:TYR34 4.7 0.0 1.0
C I:CYS10 4.7 0.0 1.0
CA I:CYS29 4.7 0.0 1.0
N I:ASN11 4.9 0.0 1.0

Zinc binding site 6 out of 16 in 5oqm

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Zinc binding site 6 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.0
occ:1.00
 SG I:CYS103 2.5 0.0 1.0
SG I:CYS78 2.5 0.0 1.0
SG I:CYS75 2.5 0.0 1.0
SG I:CYS106 2.5 0.0 1.0
CB I:CYS103 2.8 0.0 1.0
CB I:CYS75 3.0 0.0 1.0
OG I:SER105 3.6 0.0 1.0
CB I:CYS78 3.9 0.0 1.0
CB I:CYS106 4.0 0.0 1.0
N I:CYS78 4.1 0.0 1.0
N I:CYS106 4.3 0.0 1.0
CA I:CYS103 4.3 0.0 1.0
CB I:HIS108 4.4 0.0 1.0
CA I:CYS75 4.5 0.0 1.0
CA I:CYS78 4.6 0.0 1.0
CA I:CYS106 4.7 0.0 1.0
CE1 I:PHE110 4.7 0.0 1.0
CB I:LYS77 4.8 0.0 1.0
N I:HIS108 4.8 0.0 1.0
CB I:SER80 4.9 0.0 1.0
CB I:SER105 5.0 0.0 1.0

Zinc binding site 7 out of 16 in 5oqm

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Zinc binding site 7 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.0
occ:1.00
 SG J:CYS10 2.3 0.0 1.0
SG J:CYS45 2.3 0.0 1.0
SG J:CYS7 2.4 0.0 1.0
SG J:CYS46 2.4 0.0 1.0
N J:CYS46 2.6 0.0 1.0
C J:CYS45 3.0 0.0 1.0
CA J:CYS46 3.1 0.0 1.0
CB J:CYS45 3.2 0.0 1.0
CB J:CYS46 3.3 0.0 1.0
O J:CYS45 3.5 0.0 1.0
CB J:CYS7 3.6 0.0 1.0
CB J:CYS10 3.6 0.0 1.0
CA J:CYS45 3.7 0.0 1.0
N J:CYS10 3.8 0.0 1.0
CB J:SER9 4.3 0.0 1.0
CA J:CYS10 4.4 0.0 1.0
N J:CYS45 4.5 0.0 1.0
C J:CYS46 4.6 0.0 1.0
N J:SER9 4.8 0.0 1.0
C J:SER9 4.9 0.0 1.0
CA J:SER9 4.9 0.0 1.0
N J:GLY11 5.0 0.0 1.0
NE J:ARG43 5.0 0.0 1.0

Zinc binding site 8 out of 16 in 5oqm

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Zinc binding site 8 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.0
occ:1.00
 SG L:CYS31 2.3 0.0 1.0
SG L:CYS48 2.3 0.0 1.0
SG L:CYS51 2.3 0.0 1.0
SG L:CYS34 2.4 0.0 1.0
CB L:CYS31 3.0 0.0 1.0
CB L:CYS48 3.6 0.0 1.0
CB L:CYS34 3.7 0.0 1.0
OG L:SER36 3.7 0.0 1.0
CB L:CYS51 3.8 0.0 1.0
O L:LYS49 4.0 0.0 1.0
N L:CYS51 4.4 0.0 1.0
N L:CYS34 4.4 0.0 1.0
CA L:CYS31 4.5 0.0 1.0
CA L:CYS51 4.6 0.0 1.0
CA L:CYS34 4.6 0.0 1.0
O L:CYS51 4.8 0.0 1.0
CG L:GLU33 4.8 0.0 1.0
CB L:SER36 4.9 0.0 1.0
C L:LYS49 4.9 0.0 1.0
C L:CYS51 5.0 0.0 1.0
CA L:CYS48 5.0 0.0 1.0

Zinc binding site 9 out of 16 in 5oqm

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Zinc binding site 9 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:0.0
occ:1.00
 SG M:CYS27 2.3 0.0 1.0
SG M:CYS48 2.4 0.0 1.0
SG M:CYS45 2.4 0.0 1.0
SG M:CYS24 2.4 0.0 1.0
CB M:CYS45 2.7 0.0 1.0
CB M:CYS24 3.0 0.0 1.0
CB M:CYS27 3.7 0.0 1.0
CB M:CYS48 3.8 0.0 1.0
N M:CYS48 3.9 0.0 1.0
CA M:CYS45 4.2 0.0 1.0
CA M:CYS48 4.4 0.0 1.0
CA M:CYS24 4.5 0.0 1.0
CB M:LEU50 4.6 0.0 1.0
CB M:LEU47 4.6 0.0 1.0
N M:CYS27 4.6 0.0 1.0
C M:CYS45 4.7 0.0 1.0
N M:LEU50 4.7 0.0 1.0
O M:LEU50 4.8 0.0 1.0
O M:CYS45 4.8 0.0 1.0
CA M:CYS27 4.8 0.0 1.0
N M:GLY49 4.9 0.0 1.0
C M:CYS48 4.9 0.0 1.0
N M:LEU47 4.9 0.0 1.0
CD1 M:LEU52 4.9 0.0 1.0
C M:LEU47 5.0 0.0 1.0
N M:CYS45 5.0 0.0 1.0

Zinc binding site 10 out of 16 in 5oqm

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Zinc binding site 10 out of 16 in the Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Yeast Transcription Pre-Initiation Complex with Tfiih and Core Mediator within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn601

b:0.0
occ:1.00
 SG W:CYS124 2.4 0.0 1.0
SG W:CYS152 2.4 0.0 1.0
SG W:CYS149 2.4 0.0 1.0
SG W:CYS127 2.4 0.0 1.0
CB W:CYS152 3.1 0.0 1.0
CB W:CYS127 3.4 0.0 1.0
CB W:CYS149 3.5 0.0 1.0
CB W:CYS124 3.6 0.0 1.0
N W:CYS152 3.7 0.0 1.0
N W:CYS127 3.8 0.0 1.0
CA W:CYS152 4.0 0.0 1.0
CB W:LEU151 4.0 0.0 1.0
CA W:CYS127 4.2 0.0 1.0
C W:LEU151 4.4 0.0 1.0
OH W:TYR131 4.4 0.0 1.0
CE1 W:TYR131 4.6 0.0 1.0
CB W:ILE126 4.6 0.0 1.0
CA W:LEU151 4.6 0.0 1.0
C W:ILE126 4.8 0.0 1.0
CA W:CYS149 4.8 0.0 1.0
N W:LEU151 4.8 0.0 1.0
CZ W:TYR131 4.9 0.0 1.0
CA W:CYS124 5.0 0.0 1.0

Reference:

S.Schilbach, M.Hantsche, D.Tegunov, C.Dienemann, C.Wigge, H.Urlaub, P.Cramer. Structures of Transcription Pre-Initiation Complex with Tfiih and Mediator. Nature V. 551 204 2017.
ISSN: ESSN 1476-4687
PubMed: 29088706
DOI: 10.1038/NATURE24282
Page generated: Sun Oct 27 23:46:50 2024

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