Zinc in PDB 7zs9: Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)

Enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)

All present enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A):
2.7.7.6; 3.6.4.12;

Other elements in 7zs9:

The structure of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A) also contains other interesting chemical elements:

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

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 the +1 Nucleosome (Complex A) (pdb code 7zs9). 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 the +1 Nucleosome (Complex A), PDB code: 7zs9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 7zs9

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Zinc binding site 1 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:120.0
occ:1.00
 SG A:CYS110 2.3 105.6 1.0
SG A:CYS148 2.3 129.2 1.0
SG A:CYS107 2.3 101.5 1.0
SG A:CYS167 2.3 137.7 1.0
CB A:CYS107 3.2 101.5 1.0
CB A:CYS148 3.3 129.2 1.0
CB A:CYS110 3.6 105.6 1.0
N A:CYS110 3.7 105.6 1.0
CB A:CYS167 3.8 137.7 1.0
N A:CYS167 3.8 137.7 1.0
NE2 A:GLN171 4.1 126.0 1.0
CA A:CYS110 4.2 105.6 1.0
CB A:HIS109 4.3 130.1 1.0
CA A:CYS167 4.4 137.7 1.0
C A:HIS109 4.6 130.1 1.0
CA A:CYS148 4.6 129.2 1.0
CA A:CYS107 4.7 101.5 1.0
N A:HIS109 4.8 130.1 1.0
CA A:HIS109 4.8 130.1 1.0
N A:GLY168 4.8 139.6 1.0
C A:GLY166 4.9 131.5 1.0
C A:CYS110 4.9 105.6 1.0
ND1 A:HIS109 4.9 130.1 1.0
CA A:GLY166 4.9 131.5 1.0
N A:GLY111 5.0 94.0 1.0
C A:CYS167 5.0 137.7 1.0

Zinc binding site 2 out of 17 in 7zs9

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Zinc binding site 2 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:82.3
occ:1.00
 NE2 A:HIS80 2.1 59.1 1.0
SG A:CYS70 2.3 82.1 1.0
SG A:CYS77 2.3 68.6 1.0
SG A:CYS67 2.3 88.2 1.0
CB A:CYS67 2.8 88.2 1.0
CD2 A:HIS80 2.9 59.1 1.0
CE1 A:HIS80 3.2 59.1 1.0
CB A:CYS77 3.2 68.6 1.0
CB A:CYS70 3.3 82.1 1.0
N A:CYS70 3.7 82.1 1.0
CG A:HIS80 4.1 59.1 1.0
CA A:CYS70 4.1 82.1 1.0
CA A:CYS77 4.1 68.6 1.0
ND1 A:HIS80 4.2 59.1 1.0
CA A:CYS67 4.4 88.2 1.0
CA A:GLY59 4.5 74.1 1.0
CB A:THR69 4.7 77.2 1.0
CD A:PRO78 4.7 59.6 1.0
N A:GLY79 4.8 61.0 1.0
C A:CYS77 4.8 68.6 1.0
C A:CYS70 4.8 82.1 1.0
C A:THR69 4.9 77.2 1.0
C A:CYS67 4.9 88.2 1.0
N A:GLN71 4.9 97.5 1.0
N A:THR69 5.0 77.2 1.0
N A:PRO78 5.0 59.6 1.0

Zinc binding site 3 out of 17 in 7zs9

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Zinc binding site 3 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:96.5
occ:1.00
 SG B:CYS1163 2.3 68.0 1.0
SG B:CYS1185 2.3 92.4 1.0
SG B:CYS1166 2.3 73.3 1.0
SG B:CYS1182 2.3 78.6 1.0
CB B:CYS1166 3.4 73.3 1.0
CB B:CYS1185 3.4 92.4 1.0
CB B:CYS1182 3.6 78.6 1.0
N B:CYS1166 3.6 73.3 1.0
CB B:CYS1163 3.7 68.0 1.0
CA B:CYS1166 4.0 73.3 1.0
O B:CYS1166 4.0 73.3 1.0
C B:CYS1166 4.4 73.3 1.0
OD1 B:ASN1187 4.5 81.5 1.0
CB B:ILE1165 4.5 76.0 1.0
N B:CYS1185 4.6 92.4 1.0
CA B:CYS1185 4.6 92.4 1.0
C B:ILE1165 4.8 76.0 1.0
O B:LYS1183 4.8 79.4 1.0
OG1 B:THR1170 4.9 63.7 1.0
CA B:CYS1182 4.9 78.6 1.0
CA B:CYS1163 4.9 68.0 1.0
CG2 B:ILE1165 5.0 76.0 1.0

Zinc binding site 4 out of 17 in 7zs9

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Zinc binding site 4 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:101.5
occ:1.00
 SG C:CYS88 2.3 77.3 1.0
SG C:CYS86 2.3 68.2 1.0
SG C:CYS92 2.3 55.6 1.0
SG C:CYS95 2.3 53.8 1.0
CB C:CYS88 3.2 77.3 1.0
CB C:CYS86 3.2 68.2 1.0
CB C:CYS95 3.4 53.8 1.0
CB C:CYS92 3.6 55.6 1.0
N C:CYS92 3.6 55.6 1.0
N C:CYS95 4.1 53.8 1.0
CA C:CYS92 4.1 55.6 1.0
C C:HIS91 4.1 55.6 1.0
N C:CYS88 4.2 77.3 1.0
CA C:CYS88 4.3 77.3 1.0
CA C:CYS95 4.3 53.8 1.0
CA C:HIS91 4.4 55.6 1.0
CA C:CYS86 4.6 68.2 1.0
C C:CYS92 4.6 55.6 1.0
CB C:LYS94 4.6 52.6 1.0
O C:CYS92 4.7 55.6 1.0
C C:LYS94 4.8 52.6 1.0
C C:CYS86 4.8 68.2 1.0
O C:HIS91 4.9 55.6 1.0
N C:LYS94 4.9 52.6 1.0
N C:PHE87 5.0 75.0 1.0

Zinc binding site 5 out of 17 in 7zs9

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Zinc binding site 5 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:171.6
occ:1.00
 SG I:CYS32 2.3 151.2 1.0
SG I:CYS10 2.3 119.4 1.0
SG I:CYS7 2.3 119.7 1.0
SG I:CYS29 2.3 149.1 1.0
OG1 I:THR31 2.9 152.2 1.0
CB I:CYS7 3.0 119.7 1.0
CB I:CYS29 3.4 149.1 1.0
CB I:CYS10 3.7 119.4 1.0
CB I:CYS32 3.7 151.2 1.0
N I:CYS10 3.8 119.4 1.0
N I:CYS32 3.8 151.2 1.0
CA I:CYS10 4.3 119.4 1.0
CA I:CYS32 4.3 151.2 1.0
CB I:THR31 4.4 152.2 1.0
CB I:TYR34 4.4 134.8 1.0
CB I:ASP9 4.4 122.0 1.0
CA I:CYS7 4.5 119.7 1.0
C I:ASP9 4.8 122.0 1.0
C I:CYS32 4.8 151.2 1.0
CA I:CYS29 4.8 149.1 1.0
C I:THR31 4.8 152.2 1.0
N I:ASP9 4.8 122.0 1.0
C I:CYS10 4.8 119.4 1.0
N I:ASN11 4.9 106.1 1.0
CA I:ASP9 4.9 122.0 1.0
CA I:THR31 5.0 152.2 1.0
N I:THR31 5.0 152.2 1.0

Zinc binding site 6 out of 17 in 7zs9

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Zinc binding site 6 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:114.9
occ:1.00
 SG I:CYS106 2.3 74.0 1.0
SG I:CYS78 2.3 84.0 1.0
SG I:CYS103 2.3 70.7 1.0
SG I:CYS75 2.3 77.4 1.0
CB I:CYS103 3.0 70.7 1.0
CB I:CYS75 3.3 77.4 1.0
OG I:SER105 3.3 75.0 1.0
CB I:CYS78 3.5 84.0 1.0
CB I:CYS106 3.7 74.0 1.0
N I:CYS106 4.0 74.0 1.0
N I:CYS78 4.1 84.0 1.0
OG I:SER80 4.3 81.1 1.0
CA I:CYS78 4.3 84.0 1.0
CA I:CYS106 4.4 74.0 1.0
CB I:SER80 4.4 81.1 1.0
CA I:CYS103 4.5 70.7 1.0
CB I:SER105 4.7 75.0 1.0
CB I:HIS108 4.7 65.7 1.0
CA I:CYS75 4.7 77.4 1.0
C I:CYS78 4.7 84.0 1.0
N I:HIS79 4.9 82.6 1.0
N I:SER80 4.9 81.1 1.0
CB I:LYS77 4.9 78.1 1.0
C I:SER105 4.9 75.0 1.0
C I:CYS106 5.0 74.0 1.0
C I:LYS77 5.0 78.1 1.0
N I:SER105 5.0 75.0 1.0

Zinc binding site 7 out of 17 in 7zs9

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Zinc binding site 7 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:47.3
occ:1.00
 SG J:CYS46 2.3 27.1 1.0
SG J:CYS10 2.3 39.9 1.0
SG J:CYS45 2.3 27.4 1.0
SG J:CYS7 2.3 36.6 1.0
CB J:CYS7 3.2 36.6 1.0
N J:CYS46 3.2 27.1 1.0
CB J:CYS10 3.4 39.9 1.0
CB J:CYS46 3.5 27.1 1.0
CA J:CYS46 3.6 27.1 1.0
CB J:CYS45 3.6 27.4 1.0
C J:CYS45 3.6 27.4 1.0
N J:CYS10 3.8 39.9 1.0
NE J:ARG43 4.0 28.7 1.0
O J:CYS45 4.1 27.4 1.0
CA J:CYS10 4.2 39.9 1.0
NH2 J:ARG43 4.2 28.7 1.0
CA J:CYS45 4.2 27.4 1.0
CZ J:ARG43 4.6 28.7 1.0
CB J:LYS12 4.6 31.4 1.0
CA J:CYS7 4.6 36.6 1.0
N J:GLY11 4.7 39.0 1.0
N J:LYS12 4.8 31.4 1.0
CB J:SER9 4.8 40.7 1.0
C J:CYS10 4.8 39.9 1.0
CB J:ARG43 4.9 28.7 1.0
C J:SER9 5.0 40.7 1.0
CD J:ARG43 5.0 28.7 1.0

Zinc binding site 8 out of 17 in 7zs9

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Zinc binding site 8 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:95.8
occ:1.00
 SG L:CYS34 2.3 67.2 1.0
SG L:CYS31 2.3 66.1 1.0
SG L:CYS51 2.3 71.9 1.0
SG L:CYS48 2.3 67.3 1.0
CB L:CYS31 2.9 66.1 1.0
CB L:CYS48 3.1 67.3 1.0
CB L:CYS34 3.3 67.2 1.0
CB L:CYS51 3.4 71.9 1.0
N L:CYS51 3.7 71.9 1.0
CA L:CYS51 4.0 71.9 1.0
N L:CYS34 4.1 67.2 1.0
OG L:SER36 4.2 63.0 1.0
CA L:CYS34 4.2 67.2 1.0
N L:GLY52 4.3 63.5 1.0
C L:CYS51 4.3 71.9 1.0
CA L:CYS31 4.4 66.1 1.0
N L:HIS53 4.5 57.2 1.0
CB L:HIS53 4.5 57.2 1.0
CA L:CYS48 4.6 67.3 1.0
CG L:GLU33 4.7 69.8 1.0
C L:ASP50 4.8 70.4 1.0
CB L:ASP50 4.8 70.4 1.0
C L:CYS34 4.9 67.2 1.0
C L:CYS31 5.0 66.1 1.0

Zinc binding site 9 out of 17 in 7zs9

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Zinc binding site 9 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:155.4
occ:1.00
 SG M:CYS24 2.3 108.4 1.0
SG M:CYS48 2.3 88.8 1.0
SG M:CYS27 2.3 115.2 1.0
SG M:CYS45 2.3 94.0 1.0
CB M:CYS45 3.2 94.0 1.0
CB M:CYS24 3.2 108.4 1.0
CB M:CYS27 3.3 115.2 1.0
CB M:CYS48 3.5 88.8 1.0
N M:CYS48 3.8 88.8 1.0
N M:CYS27 3.9 115.2 1.0
CA M:CYS27 4.2 115.2 1.0
CA M:CYS48 4.2 88.8 1.0
CB M:LEU47 4.4 94.8 1.0
CA M:CYS45 4.6 94.0 1.0
CA M:CYS24 4.7 108.4 1.0
C M:LEU47 4.8 94.8 1.0
N M:LEU47 4.9 94.8 1.0
CA M:LEU47 4.9 94.8 1.0
C M:GLU26 5.0 105.2 1.0

Zinc binding site 10 out of 17 in 7zs9

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Zinc binding site 10 out of 17 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome (Complex A)


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 the +1 Nucleosome (Complex A) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn501

b:255.6
occ:1.00
 SG W:CYS127 2.3 198.8 1.0
SG W:CYS124 2.3 197.1 1.0
SG W:CYS152 2.3 190.1 1.0
SG W:CYS149 2.3 188.9 1.0
CB W:CYS152 3.2 190.1 1.0
CB W:CYS127 3.2 198.8 1.0
CB W:CYS124 3.2 197.1 1.0
CB W:CYS149 3.4 188.9 1.0
N W:CYS127 3.8 198.8 1.0
N W:CYS152 3.8 190.1 1.0
CA W:CYS152 4.1 190.1 1.0
CA W:CYS127 4.1 198.8 1.0
OG1 W:THR129 4.4 198.1 1.0
CA W:CYS124 4.6 197.1 1.0
CB W:ILE126 4.7 192.1 1.0
CA W:CYS149 4.8 188.9 1.0
C W:ILE126 4.8 192.1 1.0
C W:LEU151 4.9 170.3 1.0
CB W:LEU151 5.0 170.3 1.0
C W:CYS127 5.0 198.8 1.0

Reference:

H.Wang, S.Schilbach, M.Ninov, H.Urlaub, P.Cramer. Structures of Transcription Preinitiation Complex Engaged with the +1 Nucleosome. Nat.Struct.Mol.Biol. 2022.
ISSN: ESSN 1545-9985
PubMed: 36411341
DOI: 10.1038/S41594-022-00865-W
Page generated: Wed Oct 30 17:19:52 2024

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