Zinc in PDB 7zsa: Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B)

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

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

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

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 and Ntp (Complex B) (pdb code 7zsa). 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 and Ntp (Complex B), PDB code: 7zsa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

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


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 the +1 Nucleosome and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:123.9 occ:1.00 SG A:CYS107 2.3 111.9 1.0 SG A:CYS110 2.3 92.8 1.0 SG A:CYS148 2.3 110.4 1.0 SG A:CYS167 2.3 106.7 1.0 CB A:CYS107 3.2 111.9 1.0 N A:CYS167 3.4 106.7 1.0 CB A:CYS148 3.5 110.4 1.0 CB A:CYS110 3.6 92.8 1.0 CB A:CYS167 3.6 106.7 1.0 N A:CYS110 3.7 92.8 1.0 CA A:CYS167 4.0 106.7 1.0 CA A:CYS110 4.2 92.8 1.0 CB A:HIS109 4.3 110.7 1.0 C A:GLY166 4.4 98.7 1.0 NE2 A:GLN171 4.4 111.7 1.0 CA A:GLY166 4.4 98.7 1.0 N A:GLY168 4.5 108.4 1.0 ND1 A:HIS109 4.5 110.7 1.0 C A:HIS109 4.6 110.7 1.0 CA A:CYS107 4.7 111.9 1.0 C A:CYS167 4.7 106.7 1.0 N A:HIS109 4.7 110.7 1.0 CA A:CYS148 4.8 110.4 1.0 CA A:HIS109 4.8 110.7 1.0 C A:CYS110 4.9 92.8 1.0 CG A:HIS109 4.9 110.7 1.0 N A:GLY111 5.0 88.8 1.0

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


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 the +1 Nucleosome and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:189.9 occ:1.00 NE2 A:HIS80 2.1 70.1 1.0 SG A:CYS70 2.3 93.0 1.0 SG A:CYS67 2.3 92.2 1.0 SG A:CYS77 2.3 42.0 1.0 CB A:CYS67 2.8 92.2 1.0 CD2 A:HIS80 3.0 70.1 1.0 CE1 A:HIS80 3.1 70.1 1.0 CB A:CYS70 3.5 93.0 1.0 CB A:CYS77 3.6 42.0 1.0 N A:CYS70 4.0 93.0 1.0 CG A:HIS80 4.1 70.1 1.0 ND1 A:HIS80 4.1 70.1 1.0 CA A:CYS77 4.3 42.0 1.0 CA A:CYS67 4.3 92.2 1.0 CA A:CYS70 4.3 93.0 1.0 N A:GLY79 4.5 48.1 1.0 CD A:PRO78 4.6 33.5 1.0 CA A:GLY59 4.9 61.7 1.0 CA A:GLY79 4.9 48.1 1.0 C A:CYS77 4.9 42.0 1.0 N A:PRO78 4.9 33.5 1.0 C A:CYS67 5.0 92.2 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:109.5 occ:1.00 SG B:CYS1166 2.3 29.9 1.0 SG B:CYS1182 2.3 45.9 1.0 SG B:CYS1185 2.3 57.0 1.0 SG B:CYS1163 2.3 30.5 1.0 CB B:CYS1163 2.8 30.5 1.0 CB B:CYS1185 3.2 57.0 1.0 CB B:CYS1166 3.4 29.9 1.0 N B:CYS1166 3.6 29.9 1.0 CB B:CYS1182 3.7 45.9 1.0 CA B:CYS1166 4.0 29.9 1.0 OD1 B:ASN1187 4.1 39.4 1.0 O B:CYS1166 4.3 29.9 1.0 CA B:CYS1163 4.3 30.5 1.0 CB B:ILE1165 4.4 33.7 1.0 CA B:CYS1185 4.5 57.0 1.0 N B:CYS1185 4.5 57.0 1.0 C B:CYS1166 4.6 29.9 1.0 C B:ILE1165 4.7 33.7 1.0 N B:ILE1165 4.8 33.7 1.0 O B:LYS1183 4.8 67.5 1.0 CA B:ILE1165 4.9 33.7 1.0 CG B:ASN1187 4.9 39.4 1.0 CA B:CYS1182 5.0 45.9 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:137.0 occ:1.00 SG C:CYS92 2.3 61.9 1.0 SG C:CYS88 2.3 103.4 1.0 SG C:CYS95 2.3 59.9 1.0 SG C:CYS86 2.3 89.0 1.0 CB C:CYS95 3.0 59.9 1.0 CB C:CYS92 3.2 61.9 1.0 CB C:CYS86 3.4 89.0 1.0 CB C:CYS88 3.5 103.4 1.0 N C:CYS92 3.5 61.9 1.0 N C:CYS95 3.8 59.9 1.0 CA C:CYS92 3.9 61.9 1.0 CA C:CYS95 4.0 59.9 1.0 C C:HIS91 4.2 63.4 1.0 N C:CYS88 4.3 103.4 1.0 C C:CYS92 4.4 61.9 1.0 CA C:CYS88 4.5 103.4 1.0 O C:CYS92 4.5 61.9 1.0 CA C:HIS91 4.6 63.4 1.0 C C:LYS94 4.7 66.2 1.0 CA C:CYS86 4.8 89.0 1.0 CB C:LYS94 4.9 66.2 1.0 O C:HIS91 4.9 63.4 1.0 N C:PHE87 4.9 105.1 1.0 C C:CYS95 4.9 59.9 1.0 N C:LYS94 4.9 66.2 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:148.2 occ:1.00 SG I:CYS10 2.3 91.1 1.0 SG I:CYS32 2.3 94.5 1.0 SG I:CYS29 2.3 96.9 1.0 SG I:CYS7 2.3 87.8 1.0 OG1 I:THR31 3.0 93.1 1.0 CB I:CYS7 3.1 87.8 1.0 CB I:CYS29 3.3 96.9 1.0 N I:CYS10 3.9 91.1 1.0 CB I:CYS10 3.9 91.1 1.0 CB I:CYS32 3.9 94.5 1.0 N I:CYS32 4.0 94.5 1.0 CB I:ASP9 4.3 92.8 1.0 CB I:THR31 4.4 93.1 1.0 CB I:TYR34 4.4 102.5 1.0 CA I:CYS10 4.4 91.1 1.0 CA I:CYS32 4.5 94.5 1.0 CA I:CYS7 4.6 87.8 1.0 CA I:CYS29 4.7 96.9 1.0 N I:ASP9 4.8 92.8 1.0 C I:ASP9 4.8 92.8 1.0 CA I:ASP9 4.9 92.8 1.0 CB I:ASN12 4.9 80.1 1.0 C I:CYS10 5.0 91.1 1.0 C I:THR31 5.0 93.1 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:162.3 occ:1.00 SG I:CYS106 2.3 83.1 1.0 SG I:CYS78 2.3 87.8 1.0 SG I:CYS103 2.3 87.9 1.0 SG I:CYS75 2.3 84.5 1.0 CB I:CYS103 3.0 87.9 1.0 OG I:SER105 3.1 88.0 1.0 CB I:CYS75 3.5 84.5 1.0 CB I:CYS78 3.7 87.8 1.0 CB I:CYS106 3.7 83.1 1.0 N I:CYS106 3.8 83.1 1.0 OG I:SER80 3.9 76.9 1.0 N I:CYS78 4.1 87.8 1.0 CA I:CYS106 4.3 83.1 1.0 CB I:SER80 4.4 76.9 1.0 CA I:CYS78 4.5 87.8 1.0 CB I:SER105 4.5 88.0 1.0 CA I:CYS103 4.5 87.9 1.0 CB I:HIS108 4.6 76.9 1.0 CB I:LYS77 4.7 86.9 1.0 N I:SER105 4.7 88.0 1.0 C I:SER105 4.8 88.0 1.0 C I:CYS106 4.8 83.1 1.0 CA I:CYS75 4.9 84.5 1.0 C I:LYS77 4.9 86.9 1.0 N I:SER107 4.9 73.5 1.0 CA I:SER105 4.9 88.0 1.0 O I:CYS75 4.9 84.5 1.0 N I:HIS108 4.9 76.9 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:53.4 occ:1.00 SG J:CYS10 2.3 16.7 1.0 SG J:CYS46 2.3 23.2 1.0 SG J:CYS45 2.3 53.4 1.0 SG J:CYS7 2.3 25.0 1.0 N J:CYS46 2.9 23.2 1.0 CB J:CYS7 3.1 25.0 1.0 C J:CYS45 3.3 53.4 1.0 CA J:CYS46 3.3 23.2 1.0 CB J:CYS10 3.4 16.7 1.0 CB J:CYS46 3.4 23.2 1.0 CB J:CYS45 3.5 53.4 1.0 OG J:SER9 3.6 27.6 1.0 NH2 J:ARG43 3.7 32.9 1.0 O J:CYS45 3.8 53.4 1.0 N J:CYS10 3.9 16.7 1.0 CA J:CYS45 4.0 53.4 1.0 CA J:CYS10 4.2 16.7 1.0 NE J:ARG43 4.5 32.9 1.0 CZ J:ARG43 4.5 32.9 1.0 CA J:CYS7 4.6 25.0 1.0 N J:GLY11 4.7 22.3 1.0 N J:CYS45 4.8 53.4 1.0 C J:CYS46 4.8 23.2 1.0 CB J:SER9 4.9 27.6 1.0 C J:CYS10 4.9 16.7 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:148.2 occ:1.00 SG L:CYS31 2.3 40.6 1.0 SG L:CYS51 2.3 83.3 1.0 SG L:CYS34 2.3 58.9 1.0 SG L:CYS48 2.3 66.0 1.0 CB L:CYS31 2.9 40.6 1.0 CB L:CYS48 3.2 66.0 1.0 CB L:CYS34 3.7 58.9 1.0 CB L:CYS51 3.7 83.3 1.0 OG L:SER36 4.0 65.0 1.0 N L:CYS51 4.0 83.3 1.0 N L:CYS34 4.1 58.9 1.0 CA L:CYS51 4.4 83.3 1.0 CA L:CYS31 4.4 40.6 1.0 CA L:CYS34 4.5 58.9 1.0 N L:GLY52 4.6 62.5 1.0 O L:HIS53 4.7 53.6 1.0 N L:HIS53 4.7 53.6 1.0 CA L:CYS48 4.7 66.0 1.0 CB L:HIS53 4.7 53.6 1.0 C L:CYS51 4.8 83.3 1.0 CB L:ASP50 4.9 90.4 1.0 C L:CYS31 5.0 40.6 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn401 b:133.3 occ:1.00 SG M:CYS48 2.3 57.5 1.0 SG M:CYS27 2.3 80.8 1.0 SG M:CYS24 2.3 57.6 1.0 SG M:CYS45 2.3 65.4 1.0 CB M:CYS45 3.1 65.4 1.0 CB M:CYS24 3.3 57.6 1.0 CB M:CYS27 3.4 80.8 1.0 CB M:CYS48 3.5 57.5 1.0 N M:CYS48 3.9 57.5 1.0 N M:CYS27 4.1 80.8 1.0 CA M:CYS48 4.3 57.5 1.0 CA M:CYS27 4.4 80.8 1.0 CB M:LEU47 4.5 70.8 1.0 CA M:CYS45 4.6 65.4 1.0 CA M:CYS24 4.7 57.6 1.0 C M:LEU47 4.9 70.8 1.0 N M:LEU47 5.0 70.8 1.0 CB M:LEU50 5.0 44.2 1.0 C M:CYS45 5.0 65.4 1.0

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


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 and Ntp (Complex B) within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn501 b:172.1 occ:1.00 N W:CYS127 2.3 108.8 1.0 SG W:CYS124 2.3 101.8 1.0 SG W:CYS152 2.3 102.9 1.0 SG W:CYS127 2.3 108.8 1.0 CB W:CYS127 2.9 108.8 1.0 CB W:CYS152 3.1 102.9 1.0 CA W:CYS127 3.1 108.8 1.0 C W:ILE126 3.2 95.4 1.0 CB W:ILE126 3.2 95.4 1.0 CA W:ILE126 3.4 95.4 1.0 N W:ILE126 3.4 95.4 1.0 CG2 W:ILE126 3.7 95.4 1.0 CB W:CYS124 3.7 101.8 1.0 O W:CYS124 4.2 101.8 1.0 C W:CYS127 4.2 108.8 1.0 C W:CYS124 4.2 101.8 1.0 O W:ILE126 4.3 95.4 1.0 N W:LEU128 4.3 93.3 1.0 CG1 W:ILE126 4.5 95.4 1.0 C W:PRO125 4.5 106.9 1.0 CA W:CYS124 4.5 101.8 1.0 CA W:CYS152 4.5 102.9 1.0 OE1 W:GLU154 4.5 103.8 1.0 CB W:GLU154 4.6 103.8 1.0 N W:PRO125 4.6 106.9 1.0 SG W:CYS149 4.8 112.2 1.0 OG1 W:THR129 4.8 93.3 1.0 N W:CYS152 4.9 102.9 1.0

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