Zinc in PDB 7ml2: Rna Polymerase II Pre-Initiation Complex (PIC3)

All present enzymatic activity of Rna Polymerase II Pre-Initiation Complex (PIC3):
2.7.7.6; 3.6.4.12;

The structure of Rna Polymerase II Pre-Initiation Complex (PIC3) 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 Rna Polymerase II Pre-Initiation Complex (PIC3) (pdb code 7ml2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Rna Polymerase II Pre-Initiation Complex (PIC3), PDB code: 7ml2:
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 Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:0.0 occ:1.00 CB A:CYS107 2.2 0.0 1.0 SG A:CYS107 2.3 0.0 1.0 SG A:CYS167 2.3 0.0 1.0 SG A:CYS110 2.3 0.0 1.0 SG A:CYS148 2.3 0.0 1.0 CB A:CYS110 2.7 0.0 1.0 CB A:CYS148 3.2 0.0 1.0 N A:CYS110 3.3 0.0 1.0 CA A:CYS110 3.6 0.0 1.0 CA A:CYS107 3.7 0.0 1.0 O A:GLY166 3.8 0.0 1.0 CB A:CYS167 4.1 0.0 1.0 C A:CYS107 4.3 0.0 1.0 O A:CYS107 4.4 0.0 1.0 C A:HIS109 4.5 0.0 1.0 N A:CYS107 4.5 0.0 1.0 N A:GLY111 4.5 0.0 1.0 C A:CYS110 4.5 0.0 1.0 N A:HIS109 4.6 0.0 1.0 CA A:CYS148 4.6 0.0 1.0 NE2 A:GLN171 4.6 0.0 1.0 CG A:LYS112 4.6 0.0 1.0 CB A:HIS109 4.7 0.0 1.0 C A:CYS167 4.8 0.0 1.0 N A:GLY168 4.9 0.0 1.0 CA A:HIS109 4.9 0.0 1.0 C A:GLY166 4.9 0.0 1.0 O A:LYS112 4.9 0.0 1.0 CA A:CYS167 5.0 0.0 1.0

Zinc binding site 2 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:0.0 occ:1.00 CD2 A:HIS80 1.9 0.0 1.0 NE2 A:HIS80 2.0 0.0 1.0 SG A:CYS77 2.3 0.0 1.0 SG A:CYS67 2.3 0.0 1.0 SG A:CYS70 2.3 0.0 1.0 CG A:HIS80 2.9 0.0 1.0 CE1 A:HIS80 3.1 0.0 1.0 CB A:CYS77 3.4 0.0 1.0 ND1 A:HIS80 3.5 0.0 1.0 CB A:CYS67 3.7 0.0 1.0 CA A:GLY59 3.7 0.0 1.0 N A:HIS80 4.0 0.0 1.0 N A:GLY79 4.0 0.0 1.0 CB A:CYS70 4.0 0.0 1.0 C A:GLY79 4.0 0.0 1.0 CB A:HIS80 4.0 0.0 1.0 CA A:GLY79 4.1 0.0 1.0 OG1 A:THR69 4.1 0.0 1.0 O A:CYS70 4.1 0.0 1.0 CA A:CYS77 4.1 0.0 1.0 N A:GLY59 4.2 0.0 1.0 O A:LEU58 4.3 0.0 1.0 N A:CYS70 4.4 0.0 1.0 C A:LEU58 4.4 0.0 1.0 C A:CYS77 4.5 0.0 1.0 CD A:PRO78 4.5 0.0 1.0 O A:GLY79 4.5 0.0 1.0 CA A:CYS70 4.6 0.0 1.0 CA A:HIS80 4.6 0.0 1.0 N A:PRO78 4.6 0.0 1.0 C A:CYS70 4.8 0.0 1.0 O A:CYS67 4.8 0.0 1.0 CA A:CYS67 4.9 0.0 1.0 C A:GLY59 4.9 0.0 1.0 N A:SER60 5.0 0.0 1.0

Zinc binding site 3 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:0.0 occ:1.00 SG B:CYS1166 2.3 0.0 1.0 SG B:CYS1163 2.3 0.0 1.0 SG B:CYS1182 2.3 0.0 1.0 SG B:CYS1185 2.3 0.0 1.0 CB B:CYS1163 2.8 0.0 1.0 CB B:CYS1185 2.8 0.0 1.0 CB B:CYS1166 3.2 0.0 1.0 N B:CYS1166 3.5 0.0 1.0 CB B:CYS1182 3.6 0.0 1.0 CA B:CYS1166 3.9 0.0 1.0 CA B:CYS1185 4.1 0.0 1.0 N B:CYS1185 4.2 0.0 1.0 O B:CYS1166 4.2 0.0 1.0 CA B:CYS1163 4.3 0.0 1.0 OG1 B:THR1170 4.3 0.0 1.0 O B:LYS1183 4.4 0.0 1.0 C B:CYS1166 4.5 0.0 1.0 CB B:ILE1165 4.6 0.0 1.0 C B:ILE1165 4.7 0.0 1.0 C B:GLY1184 4.7 0.0 1.0 O B:CYS1182 4.8 0.0 1.0 CA B:CYS1182 4.9 0.0 1.0 O B:GLY1184 4.9 0.0 1.0 N B:ILE1165 5.0 0.0 1.0 CA B:ILE1165 5.0 0.0 1.0 C B:CYS1163 5.0 0.0 1.0

Zinc binding site 4 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Pre-Initiation Complex (PIC3) 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:CYS88 2.3 0.0 1.0 SG C:CYS92 2.3 0.0 1.0 SG C:CYS86 2.3 0.0 1.0 CB C:CYS95 2.4 0.0 1.0 CB C:CYS86 2.7 0.0 1.0 CB C:CYS88 3.3 0.0 1.0 N C:CYS95 3.3 0.0 1.0 CA C:CYS95 3.4 0.0 1.0 CB C:CYS92 3.6 0.0 1.0 N C:CYS92 3.7 0.0 1.0 CA C:HIS91 3.8 0.0 1.0 C C:HIS91 3.9 0.0 1.0 CA C:CYS92 4.1 0.0 1.0 CA C:CYS86 4.1 0.0 1.0 C C:LYS94 4.2 0.0 1.0 O C:CYS92 4.3 0.0 1.0 N C:HIS91 4.4 0.0 1.0 CB C:LYS94 4.4 0.0 1.0 C C:CYS92 4.5 0.0 1.0 C C:CYS95 4.5 0.0 1.0 CA C:CYS88 4.6 0.0 1.0 N C:SER96 4.7 0.0 1.0 CA C:LYS94 4.7 0.0 1.0 N C:CYS88 4.8 0.0 1.0 O C:HIS91 4.8 0.0 1.0 N C:LYS94 4.8 0.0 1.0 C C:CYS86 4.9 0.0 1.0 C C:ASP90 4.9 0.0 1.0 CB C:HIS91 4.9 0.0 1.0

Zinc binding site 5 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.0 occ:1.00 CB I:CYS10 1.8 0.0 1.0 SG I:CYS7 2.3 0.0 1.0 SG I:CYS10 2.3 0.0 1.0 SG I:CYS32 2.3 0.0 1.0 SG I:CYS29 2.3 0.0 1.0 CB I:CYS29 2.9 0.0 1.0 CB I:CYS7 3.1 0.0 1.0 OG1 I:THR31 3.1 0.0 1.0 CA I:CYS10 3.2 0.0 1.0 CB I:CYS32 3.3 0.0 1.0 N I:CYS10 3.7 0.0 1.0 OD1 I:ASN12 3.7 0.0 1.0 N I:CYS32 3.9 0.0 1.0 C I:CYS10 4.0 0.0 1.0 CA I:CYS32 4.1 0.0 1.0 CB I:TYR34 4.3 0.0 1.0 CA I:CYS29 4.4 0.0 1.0 N I:ASN11 4.4 0.0 1.0 O I:ARG8 4.5 0.0 1.0 CB I:THR31 4.6 0.0 1.0 CA I:CYS7 4.6 0.0 1.0 C I:ASP9 4.6 0.0 1.0 CG I:ASN12 4.6 0.0 1.0 O I:CYS10 4.7 0.0 1.0 C I:THR31 4.8 0.0 1.0 O I:CYS29 4.8 0.0 1.0 C I:CYS32 4.8 0.0 1.0 N I:TYR34 4.8 0.0 1.0 O I:ASP9 4.9 0.0 1.0 N I:ARG8 4.9 0.0 1.0 C I:CYS29 4.9 0.0 1.0 CB I:ASN12 4.9 0.0 1.0 N I:ASN12 5.0 0.0 1.0

Zinc binding site 6 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:0.0 occ:1.00 SG I:CYS106 2.3 0.0 1.0 SG I:CYS75 2.3 0.0 1.0 SG I:CYS78 2.4 0.0 1.0 SG I:CYS103 2.4 0.0 1.0 CB I:CYS75 2.6 0.0 1.0 OG I:SER80 2.7 0.0 1.0 CB I:CYS78 2.7 0.0 1.0 OG I:SER105 2.9 0.0 1.0 CB I:CYS103 3.5 0.0 1.0 CB I:HIS108 3.7 0.0 1.0 N I:CYS78 3.7 0.0 1.0 CB I:CYS106 3.8 0.0 1.0 CA I:CYS78 3.8 0.0 1.0 N I:CYS106 4.0 0.0 1.0 CB I:SER80 4.0 0.0 1.0 CA I:CYS75 4.0 0.0 1.0 CB I:SER105 4.4 0.0 1.0 CA I:CYS106 4.4 0.0 1.0 CG I:HIS108 4.5 0.0 1.0 N I:HIS108 4.7 0.0 1.0 N I:SER80 4.7 0.0 1.0 C I:CYS78 4.8 0.0 1.0 N I:CYS75 4.8 0.0 1.0 CA I:HIS108 4.8 0.0 1.0 C I:CYS106 4.9 0.0 1.0 C I:CYS75 4.9 0.0 1.0 CA I:SER80 4.9 0.0 1.0 O I:SER80 5.0 0.0 1.0 CA I:CYS103 5.0 0.0 1.0 C I:LYS77 5.0 0.0 1.0 C I:SER105 5.0 0.0 1.0

Zinc binding site 7 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:0.0 occ:1.00 N J:CYS46 2.2 0.0 1.0 SG J:CYS10 2.3 0.0 1.0 SG J:CYS45 2.3 0.0 1.0 SG J:CYS46 2.3 0.0 1.0 SG J:CYS7 2.3 0.0 1.0 C J:CYS45 2.7 0.0 1.0 CA J:CYS46 2.8 0.0 1.0 CB J:CYS46 3.1 0.0 1.0 CB J:CYS45 3.1 0.0 1.0 CB J:CYS7 3.1 0.0 1.0 O J:CYS45 3.2 0.0 1.0 CB J:CYS10 3.4 0.0 1.0 CA J:CYS45 3.4 0.0 1.0 N J:CYS10 3.7 0.0 1.0 CD J:ARG43 3.9 0.0 1.0 N J:CYS45 4.1 0.0 1.0 CA J:CYS10 4.2 0.0 1.0 C J:CYS46 4.2 0.0 1.0 N J:GLY11 4.6 0.0 1.0 CA J:CYS7 4.6 0.0 1.0 CG J:MET49 4.6 0.0 1.0 NH2 J:ARG48 4.7 0.0 1.0 CG J:ARG43 4.8 0.0 1.0 CB J:SER9 4.9 0.0 1.0 C J:SER9 4.9 0.0 1.0 C J:TYR44 4.9 0.0 1.0 N J:SER9 4.9 0.0 1.0 N J:ARG47 4.9 0.0 1.0 C J:CYS10 5.0 0.0 1.0 O J:CYS46 5.0 0.0 1.0 NE J:ARG43 5.0 0.0 1.0

Zinc binding site 8 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:0.0 occ:1.00 SG L:CYS31 2.4 30.0 1.0 CB L:CYS34 2.4 30.0 1.0 SG L:CYS51 2.6 0.0 1.0 O L:LYS49 2.8 0.0 1.0 SG L:CYS48 3.0 0.0 1.0 SG L:CYS34 3.0 30.0 1.0 CB L:CYS48 3.4 0.0 1.0 CA L:CYS34 3.6 0.0 1.0 N L:CYS34 3.6 0.0 1.0 CB L:CYS31 3.7 30.0 1.0 C L:LYS49 3.9 0.0 1.0 OG L:SER36 4.0 0.0 1.0 C L:GLU33 4.1 0.0 1.0 N L:LYS49 4.1 0.0 1.0 O L:CYS51 4.1 0.0 1.0 CB L:CYS51 4.2 0.0 1.0 CB L:HIS53 4.3 0.0 1.0 C L:CYS48 4.3 0.0 1.0 O L:GLU33 4.4 0.0 1.0 CA L:CYS48 4.5 0.0 1.0 C L:CYS34 4.5 0.0 1.0 N L:CYS51 4.5 0.0 1.0 CA L:LYS49 4.6 0.0 1.0 N L:SER35 4.7 0.0 1.0 CA L:GLU33 4.8 0.0 1.0 CB L:GLU33 4.8 0.0 1.0 CA L:CYS51 4.8 0.0 1.0 N L:GLU33 4.9 0.0 1.0 C L:CYS51 4.9 0.0 1.0 O L:CYS48 4.9 0.0 1.0 N L:ASP50 4.9 0.0 1.0 C L:ASP50 4.9 0.0 1.0 CA L:CYS31 5.0 0.0 1.0

Zinc binding site 9 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn401 b:0.0 occ:1.00 SG M:CYS45 2.3 0.0 1.0 SG M:CYS24 2.3 0.0 1.0 SG M:CYS27 2.3 0.0 1.0 SG M:CYS48 2.3 0.0 1.0 CB M:CYS48 2.8 0.0 1.0 CB M:CYS27 3.0 0.0 1.0 CB M:CYS45 3.4 0.0 1.0 CB M:CYS24 3.4 0.0 1.0 N M:CYS27 3.5 0.0 1.0 CA M:CYS27 3.8 0.0 1.0 C M:GLU26 4.0 0.0 1.0 CA M:CYS48 4.0 0.0 1.0 N M:CYS48 4.1 0.0 1.0 O M:GLU26 4.4 0.0 1.0 CB M:GLU26 4.6 0.0 1.0 CA M:GLU26 4.6 0.0 1.0 N M:GLU26 4.7 0.0 1.0 CA M:CYS24 4.8 0.0 1.0 CA M:CYS45 4.8 0.0 1.0 C M:CYS48 4.9 0.0 1.0

Zinc binding site 10 out of 17 in the Rna Polymerase II Pre-Initiation Complex (PIC3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Rna Polymerase II Pre-Initiation Complex (PIC3) within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn501 b:0.0 occ:1.00 SG W:CYS152 2.3 0.0 1.0 SG W:CYS124 2.3 0.0 1.0 SG W:CYS149 2.3 0.0 1.0 SG W:CYS127 2.3 0.0 1.0 CB W:CYS149 3.0 0.0 1.0 CB W:CYS124 3.2 0.0 1.0 CB W:CYS152 3.6 0.0 1.0 N W:CYS152 3.8 0.0 1.0 CB W:CYS127 3.9 0.0 1.0 OH W:TYR131 4.0 0.0 1.0 N W:CYS127 4.1 0.0 1.0 CB W:LEU151 4.2 0.0 1.0 CA W:CYS152 4.3 0.0 1.0 OG1 W:THR129 4.4 0.0 1.0 O W:GLU154 4.5 0.0 1.0 CA W:CYS149 4.5 0.0 1.0 CA W:CYS127 4.5 0.0 1.0 CA W:CYS124 4.6 0.0 1.0 CE2 W:TYR131 4.6 0.0 1.0 CZ W:TYR131 4.8 0.0 1.0 C W:LEU151 4.8 0.0 1.0 CD1 W:LEU151 4.8 0.0 1.0 CB W:ILE126 4.8 0.0 1.0 CD2 W:LEU156 4.9 0.0 1.0 N W:LEU151 4.9 0.0 1.0 CA W:LEU151 4.9 0.0 1.0

C.Yang, R.Fujiwara, H.J.Kim, P.Basnet, Y.Zhu, J.J.Gorbea Colon, S.Steimle, B.A.Garcia, C.D.Kaplan, K.Murakami. Structural Visualization of De Novo Transcription Initiation By Saccharomyces Cerevisiae Rna Polymerase II. Mol.Cell V. 82 660 2022.
ISSN: ISSN 1097-2765
PubMed: 35051353
DOI: 10.1016/J.MOLCEL.2021.12.020