Zinc in PDB 7ml4: Rna Polymerase II Initially Transcribing Complex (Itc)

Enzymatic activity of Rna Polymerase II Initially Transcribing Complex (Itc)

All present enzymatic activity of Rna Polymerase II Initially Transcribing Complex (Itc):
2.7.7.6; 3.6.4.12;

Other elements in 7ml4:

The structure of Rna Polymerase II Initially Transcribing Complex (Itc) 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 - 15;

Binding sites:

The binding sites of Zinc atom in the Rna Polymerase II Initially Transcribing Complex (Itc) (pdb code 7ml4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Rna Polymerase II Initially Transcribing Complex (Itc), PDB code: 7ml4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 7ml4

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Zinc binding site 1 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:111.9
occ:1.00
 SG M:CYS45 2.3 109.0 1.0
SG M:CYS48 2.3 92.6 1.0
SG M:CYS24 2.3 110.5 1.0
SG M:CYS27 2.3 115.0 1.0
CB M:CYS48 2.6 101.6 1.0
CB M:CYS27 2.8 135.3 1.0
CB M:CYS45 3.1 85.0 1.0
N M:CYS48 3.3 101.8 1.0
CB M:CYS24 3.3 132.9 1.0
N M:CYS27 3.3 133.0 1.0
CA M:CYS48 3.5 97.4 1.0
CA M:CYS27 3.6 137.4 1.0
CB M:GLU26 4.3 135.0 1.0
C M:CYS48 4.3 85.8 1.0
O M:CYS45 4.4 89.1 1.0
CB M:LEU47 4.5 100.0 1.0
C M:GLU26 4.5 127.7 1.0
C M:LEU47 4.5 99.0 1.0
CA M:CYS45 4.5 82.5 1.0
N M:GLY49 4.5 78.8 1.0
CA M:CYS24 4.7 133.8 1.0
CA M:GLU26 4.8 125.7 1.0
C M:CYS45 4.8 87.8 1.0
C M:CYS27 4.9 142.0 1.0
N M:LEU50 4.9 84.9 1.0
CA M:LEU47 4.9 97.7 1.0
OE1 M:GLU26 4.9 147.6 1.0
N M:GLU26 4.9 118.5 1.0
CB M:LEU50 4.9 80.7 1.0

Zinc binding site 2 out of 15 in 7ml4

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Zinc binding site 2 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:274.6
occ:1.00
 SG A:CYS107 2.3 23.2 1.0
SG A:CYS148 2.3 24.1 1.0
SG A:CYS110 2.3 23.4 1.0
SG A:CYS167 2.3 26.0 1.0
CB A:CYS110 2.5 23.0 1.0
CB A:CYS107 2.7 22.4 1.0
N A:CYS110 3.1 22.7 1.0
CA A:CYS110 3.4 22.8 1.0
CB A:CYS148 3.7 23.6 1.0
CB A:CYS167 3.9 25.9 1.0
N A:CYS167 3.9 26.0 1.0
O A:CYS167 4.0 26.1 1.0
CA A:CYS107 4.2 22.1 1.0
C A:CYS110 4.2 23.0 1.0
N A:GLY111 4.2 22.3 1.0
CA A:CYS167 4.3 26.0 1.0
C A:CYS167 4.4 26.4 1.0
C A:HIS109 4.4 23.1 1.0
NE2 A:GLN171 4.5 29.0 1.0
N A:HIS109 4.7 22.4 1.0
C A:CYS107 4.8 22.5 1.0
CB A:HIS109 4.8 23.0 1.0
CA A:HIS109 4.9 22.6 1.0
N A:LYS112 4.9 22.2 1.0
C A:GLY166 5.0 26.7 1.0
O A:CYS148 5.0 24.3 1.0
CA A:CYS148 5.0 23.6 1.0

Zinc binding site 3 out of 15 in 7ml4

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Zinc binding site 3 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:116.2
occ:1.00
 CE1 A:HIS80 1.2 19.0 1.0
NE2 A:HIS80 2.0 18.9 1.0
OE1 A:GLU72 2.1 23.0 1.0
SG A:CYS67 2.3 20.4 1.0
SG A:CYS77 2.3 18.8 1.0
SG A:CYS70 2.3 20.4 1.0
ND1 A:HIS80 2.4 19.1 1.0
OE2 A:GLU72 2.5 22.6 1.0
CD A:GLU72 2.7 23.5 1.0
NE2 A:GLN68 2.8 20.1 1.0
CB A:CYS67 3.1 20.1 1.0
CD2 A:HIS80 3.2 18.9 1.0
CG A:HIS80 3.4 18.7 1.0
CB A:CYS77 3.6 18.2 1.0
O A:CYS67 3.8 20.9 1.0
CB A:CYS70 3.8 20.2 1.0
CD A:GLN68 3.9 21.5 1.0
C A:CYS67 4.1 20.9 1.0
CG A:GLU72 4.1 20.7 1.0
CA A:CYS67 4.2 20.4 1.0
N A:GLN71 4.2 20.4 1.0
CG A:GLN68 4.4 20.4 1.0
CA A:CYS77 4.6 17.9 1.0
OE1 A:GLN68 4.8 20.6 1.0
CB A:HIS80 4.8 18.3 1.0
CA A:CYS70 4.8 20.5 1.0
N A:GLN68 4.9 20.6 1.0
CA A:GLY59 4.9 18.7 1.0
C A:CYS70 4.9 20.8 1.0
CB A:GLU72 5.0 19.3 1.0
N A:HIS80 5.0 17.9 1.0
CA A:GLN71 5.0 20.3 1.0

Zinc binding site 4 out of 15 in 7ml4

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Zinc binding site 4 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:146.6
occ:1.00
 SG B:CYS1166 2.3 15.4 1.0
SG B:CYS1163 2.3 15.4 1.0
SG B:CYS1185 2.3 18.1 1.0
SG B:CYS1182 2.3 18.6 1.0
CB B:CYS1166 2.4 14.9 1.0
CB B:CYS1163 2.8 14.8 1.0
CB B:CYS1185 3.2 17.9 1.0
N B:CYS1166 3.2 14.9 1.0
CA B:CYS1166 3.4 14.8 1.0
CB B:CYS1182 3.6 18.1 1.0
N B:CYS1185 4.2 18.1 1.0
CA B:CYS1163 4.3 14.6 1.0
CA B:CYS1185 4.3 18.1 1.0
C B:CYS1166 4.4 15.1 1.0
OG1 B:THR1170 4.4 16.9 1.0
C B:ILE1165 4.4 15.4 1.0
N B:GLY1167 4.5 14.7 1.0
O B:CYS1182 4.5 18.9 1.0
CB B:ILE1165 4.7 15.8 1.0
C B:CYS1163 4.9 15.1 1.0
N B:ILE1165 4.9 15.0 1.0
CA B:CYS1182 4.9 18.3 1.0
CA B:ILE1165 4.9 15.1 1.0
O B:LYS1183 5.0 18.5 1.0
C B:CYS1182 5.0 18.9 1.0

Zinc binding site 5 out of 15 in 7ml4

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Zinc binding site 5 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:64.5
occ:1.00
 SG C:CYS88 2.3 8.8 1.0
SG C:CYS86 2.3 9.5 1.0
SG C:CYS95 2.3 9.6 1.0
SG C:CYS92 2.3 10.5 1.0
CB C:CYS92 2.8 10.1 1.0
CB C:CYS86 3.0 8.8 1.0
N C:CYS92 3.1 9.8 1.0
CB C:CYS95 3.2 9.1 1.0
CA C:CYS92 3.4 10.0 1.0
C C:HIS91 3.6 10.3 1.0
CB C:CYS88 3.6 8.5 1.0
N C:CYS95 3.7 9.4 1.0
CA C:HIS91 3.9 9.7 1.0
C C:CYS92 4.0 10.5 1.0
CA C:CYS95 4.1 9.2 1.0
O C:HIS91 4.3 10.3 1.0
CA C:CYS86 4.4 8.7 1.0
O C:CYS92 4.4 10.3 1.0
N C:LYS94 4.4 9.7 1.0
C C:LYS94 4.4 10.1 1.0
N C:HIS91 4.6 9.7 1.0
CE C:LYS94 4.6 15.1 1.0
N C:CYS88 4.7 8.5 1.0
CB C:LYS94 4.7 10.0 1.0
N C:ASP93 4.7 10.2 1.0
CA C:CYS88 4.7 8.5 1.0
CA C:LYS94 4.7 9.6 1.0
C C:CYS95 4.8 9.7 1.0
C C:CYS86 4.8 9.2 1.0

Zinc binding site 6 out of 15 in 7ml4

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Zinc binding site 6 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:94.9
occ:1.00
 CB I:CYS10 2.2 14.0 1.0
SG I:CYS29 2.3 14.4 1.0
SG I:CYS7 2.3 14.2 1.0
SG I:CYS10 2.3 14.8 1.0
SG I:CYS32 2.3 15.5 1.0
CB I:CYS32 2.3 15.2 1.0
CB I:CYS29 3.0 13.9 1.0
CB I:CYS7 3.2 13.4 1.0
OG1 I:THR31 3.4 14.8 1.0
CA I:CYS10 3.4 14.0 1.0
CA I:CYS32 3.6 15.1 1.0
N I:CYS10 3.6 14.2 1.0
N I:CYS32 3.7 14.9 1.0
CB I:TYR34 4.2 14.1 1.0
C I:CYS32 4.3 15.6 1.0
OH Q:TYR401 4.3 307.1 1.0
C I:THR31 4.4 15.3 1.0
CA I:CYS29 4.4 13.9 1.0
O I:CYS29 4.5 14.8 1.0
C I:CYS10 4.5 14.2 1.0
N I:SER33 4.5 15.1 1.0
N I:TYR34 4.5 14.4 1.0
CA I:CYS7 4.6 13.4 1.0
CB I:THR31 4.7 15.1 1.0
C I:CYS29 4.7 14.6 1.0
CZ Q:TYR401 4.8 307.1 1.0
C I:ASP9 4.8 14.8 1.0
OD1 I:ASN12 4.8 14.9 1.0
N I:ASN11 4.9 13.5 1.0
O I:CYS7 4.9 13.8 1.0
O I:THR31 4.9 15.4 1.0
CA I:THR31 5.0 14.4 1.0

Zinc binding site 7 out of 15 in 7ml4

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Zinc binding site 7 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:67.8
occ:1.00
 CB I:CYS78 1.7 10.9 1.0
SG I:CYS106 2.3 11.4 1.0
SG I:CYS103 2.3 11.4 1.0
SG I:CYS75 2.3 10.2 1.0
SG I:CYS78 2.3 11.2 1.0
CA I:CYS78 2.8 10.9 1.0
CB I:CYS75 2.8 9.6 1.0
CB I:CYS103 3.0 10.7 1.0
N I:CYS78 3.1 10.8 1.0
C I:CYS78 3.4 11.5 1.0
CB I:CYS106 3.6 11.1 1.0
N I:HIS79 3.8 11.2 1.0
N I:CYS106 3.8 11.0 1.0
O I:CYS78 4.1 11.3 1.0
N I:SER80 4.2 10.8 1.0
CA I:CYS106 4.3 11.0 1.0
CA I:CYS75 4.3 9.5 1.0
C I:LYS77 4.4 11.4 1.0
CA I:CYS103 4.5 10.4 1.0
CB I:SER80 4.5 10.9 1.0
CB I:SER105 4.6 11.7 1.0
CA I:HIS79 4.8 11.0 1.0
N I:SER105 4.9 10.9 1.0
C I:SER105 4.9 11.7 1.0
C I:CYS75 4.9 10.3 1.0
C I:CYS106 4.9 11.5 1.0

Zinc binding site 8 out of 15 in 7ml4

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Zinc binding site 8 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:8.4
occ:1.00
 CB J:CYS10 1.7 7.1 1.0
SG J:CYS46 2.1 8.3 1.0
SG J:CYS45 2.3 7.5 1.0
SG J:CYS7 2.3 8.0 1.0
SG J:CYS10 2.5 7.8 1.0
CA J:CYS10 3.1 6.9 1.0
CB J:CYS7 3.2 7.7 1.0
N J:CYS46 3.3 7.5 1.0
CB J:CYS46 3.4 7.8 1.0
C J:CYS45 3.4 7.8 1.0
CB J:CYS45 3.4 6.8 1.0
N J:CYS10 3.5 6.8 1.0
CA J:CYS46 3.6 7.6 1.0
O J:CYS45 3.8 7.7 1.0
NE J:ARG43 3.9 10.3 1.0
C J:CYS10 4.0 7.5 1.0
CA J:CYS45 4.0 7.0 1.0
N J:GLY11 4.2 7.0 1.0
NH2 J:ARG43 4.3 11.3 1.0
CZ J:ARG43 4.4 12.7 1.0
N J:LYS12 4.6 7.9 1.0
CA J:CYS7 4.6 7.5 1.0
CB J:LYS12 4.6 8.6 1.0
CG J:ARG43 4.6 8.7 1.0
CD J:ARG43 4.7 9.3 1.0
O J:CYS7 4.7 7.7 1.0
N J:CYS45 4.8 7.1 1.0
O J:CYS10 4.8 7.5 1.0
C J:CYS7 4.8 7.7 1.0
C J:SER9 4.9 7.3 1.0

Zinc binding site 9 out of 15 in 7ml4

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Zinc binding site 9 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:13.9
occ:1.00
 SG L:CYS48 1.8 15.9 1.0
SG L:CYS31 2.2 15.4 1.0
CB L:CYS48 2.3 15.4 1.0
CB L:CYS31 2.4 14.8 1.0
CB L:CYS34 2.8 16.0 1.0
SG L:CYS34 3.1 16.6 1.0
N L:CYS34 3.3 15.4 1.0
CA L:CYS34 3.7 15.6 1.0
CA L:CYS48 3.7 15.6 1.0
CB L:CYS51 3.8 16.1 1.0
CA L:CYS31 3.8 14.4 1.0
O L:CYS48 4.2 16.8 1.0
N L:CYS51 4.3 16.5 1.0
C L:CYS48 4.3 16.6 1.0
CB L:HIS53 4.4 15.8 1.0
C L:CYS31 4.4 14.8 1.0
C L:GLU33 4.5 15.7 1.0
N L:GLU33 4.6 14.8 1.0
CA L:CYS51 4.6 16.4 1.0
C L:CYS34 4.6 16.0 1.0
N L:CYS48 4.7 15.7 1.0
CB L:GLU33 4.7 15.3 1.0
N L:SER35 4.8 15.1 1.0
N L:ALA32 4.8 14.3 1.0
CA L:GLU33 4.8 14.9 1.0
N L:CYS31 4.9 14.3 1.0
N L:HIS53 4.9 16.1 1.0
O L:CYS31 5.0 14.7 1.0

Zinc binding site 10 out of 15 in 7ml4

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Zinc binding site 10 out of 15 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:0.0
occ:1.00
 SG 4:CYS308 2.3 0.0 1.0
SG 4:CYS289 2.3 0.0 1.0
SG 4:CYS292 2.3 0.0 1.0
SG 4:CYS305 2.3 0.0 1.0
CB 4:CYS292 2.5 0.0 1.0
CB 4:CYS308 3.4 0.0 1.0
CB 4:CYS289 3.6 0.0 1.0
N 4:CYS308 3.8 0.0 1.0
CB 4:CYS305 4.0 0.0 1.0
CA 4:CYS292 4.0 0.0 1.0
CB 4:ALA307 4.1 0.0 1.0
C 4:ALA307 4.1 0.0 1.0
CA 4:CYS308 4.2 0.0 1.0
CZ 4:PHE312 4.4 0.0 1.0
CA 4:ALA307 4.6 0.0 1.0
CB 4:CYS294 4.7 0.0 1.0
C 4:CYS292 4.7 0.0 1.0
O 4:ALA307 4.7 0.0 1.0
N 4:CYS292 4.7 0.0 1.0
N 4:ALA307 4.8 0.0 1.0
O 4:CYS305 4.8 0.0 1.0
CA 4:CYS305 4.9 0.0 1.0
N 4:SER290 4.9 0.0 1.0
N 4:CYS305 4.9 0.0 1.0
C 4:CYS308 4.9 0.0 1.0
O 4:CYS308 4.9 0.0 1.0
CA 4:CYS289 5.0 0.0 1.0

Reference:

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
Page generated: Tue Oct 29 23:32:27 2024

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