Zinc in PDB 6i84: Structure of Transcribing Rna Polymerase II-Nucleosome Complex

Enzymatic activity of Structure of Transcribing Rna Polymerase II-Nucleosome Complex

All present enzymatic activity of Structure of Transcribing Rna Polymerase II-Nucleosome Complex:
2.7.7.6;

Other elements in 6i84:

The structure of Structure of Transcribing Rna Polymerase II-Nucleosome Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex (pdb code 6i84). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex, PDB code: 6i84:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6i84

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Zinc binding site 1 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.7
occ:1.00
 SG A:CYS167 2.5 0.8 1.0
SG A:CYS110 2.5 74.3 1.0
SG A:CYS107 2.5 82.0 1.0
CB A:CYS107 3.0 82.0 1.0
SG A:CYS148 3.5 96.9 1.0
O A:GLY166 3.5 0.5 1.0
O A:CYS167 3.5 0.8 1.0
CB A:CYS110 3.7 74.3 1.0
CB A:CYS167 4.0 0.8 1.0
CB A:LYS112 4.3 80.6 1.0
C A:CYS167 4.3 0.8 1.0
CA A:CYS107 4.4 82.0 1.0
C A:GLY166 4.5 0.5 1.0
CB A:CYS148 4.5 96.9 1.0
O A:CYS107 4.5 82.0 1.0
C A:CYS107 4.6 82.0 1.0
CA A:CYS167 4.6 0.8 1.0
N A:CYS167 5.0 0.8 1.0
CA A:CYS110 5.0 74.3 1.0
N A:LYS112 5.0 80.6 1.0
O A:MET108 5.0 73.8 1.0

Zinc binding site 2 out of 8 in 6i84

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Zinc binding site 2 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:67.0
occ:1.00
 SG A:CYS77 2.5 61.0 1.0
SG A:CYS67 2.5 79.2 1.0
CB A:CYS70 2.5 70.6 1.0
NE2 A:HIS80 2.6 63.3 1.0
SG A:CYS70 3.0 70.6 1.0
O A:CYS67 3.1 79.2 1.0
O A:CYS70 3.2 70.6 1.0
NE2 A:GLN68 3.2 81.0 1.0
CE1 A:HIS80 3.4 63.3 1.0
CB A:CYS67 3.5 79.2 1.0
CA A:CYS70 3.7 70.6 1.0
CD2 A:HIS80 3.7 63.3 1.0
C A:CYS70 3.8 70.6 1.0
O A:PRO78 4.0 56.0 1.0
CB A:CYS77 4.1 61.0 1.0
C A:CYS67 4.1 79.2 1.0
N A:CYS70 4.4 70.6 1.0
CA A:CYS67 4.4 79.2 1.0
CD A:GLN68 4.5 81.0 1.0
ND1 A:HIS80 4.6 63.3 1.0
CG A:HIS80 4.8 63.3 1.0
CA A:CYS77 5.0 61.0 1.0

Zinc binding site 3 out of 8 in 6i84

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Zinc binding site 3 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.8
occ:1.00
 CB B:CYS1166 2.5 62.1 1.0
CB B:CYS1185 2.5 65.2 1.0
SG B:CYS1166 2.6 62.1 1.0
SG B:CYS1185 2.9 65.2 1.0
CA B:CYS1185 3.2 65.2 1.0
N B:CYS1166 3.4 62.1 1.0
CA B:CYS1166 3.5 62.1 1.0
O B:CYS1185 4.0 65.2 1.0
C B:CYS1185 4.1 65.2 1.0
N B:CYS1185 4.3 65.2 1.0
C B:ILE1165 4.5 68.9 1.0
CB B:ILE1165 4.5 68.9 1.0
CG2 B:ILE1165 4.6 68.9 1.0
C B:CYS1166 4.7 62.1 1.0

Zinc binding site 4 out of 8 in 6i84

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Zinc binding site 4 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.6
occ:1.00
 N C:CYS92 2.2 90.0 1.0
SG C:CYS95 2.4 87.0 1.0
SG C:CYS88 2.4 0.6 1.0
CB C:CYS92 2.5 90.0 1.0
SG C:CYS92 2.5 90.0 1.0
C C:HIS91 2.7 0.8 1.0
CA C:CYS92 2.8 90.0 1.0
CA C:HIS91 3.1 0.8 1.0
SG C:CYS86 3.3 0.8 1.0
O C:HIS91 3.5 0.8 1.0
CB C:CYS88 3.6 0.6 1.0
CB C:CYS95 3.7 87.0 1.0
C C:CYS92 3.8 90.0 1.0
N C:HIS91 3.8 0.8 1.0
O C:CYS92 4.2 90.0 1.0
N C:CYS95 4.3 87.0 1.0
CB C:CYS86 4.4 0.8 1.0
CB C:HIS91 4.4 0.8 1.0
CA C:CYS95 4.5 87.0 1.0
N C:ASP93 4.6 80.5 1.0
C C:ASP90 4.7 0.1 1.0
CA C:CYS88 4.9 0.6 1.0
C C:CYS95 4.9 87.0 1.0
OG C:SER96 4.9 86.2 1.0
OG C:SER83 5.0 91.9 1.0
O C:ASP90 5.0 0.1 1.0

Zinc binding site 5 out of 8 in 6i84

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Zinc binding site 5 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1201

b:0.4
occ:1.00
 SG I:CYS6 2.5 0.9 1.0
SG I:CYS31 2.5 0.1 1.0
CB I:CYS28 2.5 0.7 1.0
SG I:CYS28 2.5 0.7 1.0
SG I:CYS9 2.6 0.5 1.0
CB I:CYS6 3.1 0.9 1.0
CB I:CYS31 3.7 0.1 1.0
CA I:CYS28 4.0 0.7 1.0
N I:CYS31 4.0 0.1 1.0
CB I:CYS9 4.2 0.5 1.0
CA I:CYS31 4.3 0.1 1.0
CG I:ARG7 4.3 0.3 1.0
CB I:TYR33 4.3 92.5 1.0
C I:CYS31 4.4 0.1 1.0
N I:ARG7 4.4 0.3 1.0
N I:TYR33 4.5 92.5 1.0
CA I:CYS6 4.5 0.9 1.0
O I:CYS31 4.6 0.1 1.0
O I:ARG7 4.7 0.3 1.0
N I:CYS28 4.7 0.7 1.0
N I:ASN11 4.7 0.8 1.0
N I:ASN10 4.8 0.0 1.0
N I:ARG29 4.8 0.6 1.0
C I:CYS6 4.8 0.9 1.0
N I:SER32 4.8 99.8 1.0
C I:CYS28 4.8 0.7 1.0
NE I:ARG7 4.9 0.3 1.0

Zinc binding site 6 out of 8 in 6i84

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Zinc binding site 6 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1202

b:0.0
occ:1.00
 SG I:CYS74 2.5 0.8 1.0
SG I:CYS77 2.5 0.6 1.0
N I:CYS77 2.5 0.6 1.0
CB I:HIS107 2.6 1.0 1.0
CB I:LYS76 2.7 0.8 1.0
CB I:CYS77 3.1 0.6 1.0
CG I:HIS107 3.3 1.0 1.0
C I:LYS76 3.3 0.8 1.0
CA I:LYS76 3.3 0.8 1.0
CA I:CYS77 3.4 0.6 1.0
N I:LYS76 3.6 0.8 1.0
CA I:HIS107 3.9 1.0 1.0
CG I:LYS76 3.9 0.8 1.0
CD2 I:HIS107 4.0 1.0 1.0
CB I:CYS74 4.0 0.8 1.0
N I:HIS107 4.1 1.0 1.0
CD I:LYS76 4.1 0.8 1.0
ND1 I:HIS107 4.1 1.0 1.0
C I:CYS77 4.3 0.6 1.0
O I:LYS76 4.5 0.8 1.0
N I:HIS78 4.5 0.7 1.0
O I:SER104 4.6 0.9 1.0
SG I:CYS105 4.6 0.5 1.0
CB I:CYS102 4.8 0.2 1.0
SG I:CYS102 4.8 0.2 1.0
C I:PRO75 4.9 0.3 1.0
NE2 I:HIS107 4.9 1.0 1.0
C I:HIS107 5.0 1.0 1.0
CE1 I:HIS107 5.0 1.0 1.0

Zinc binding site 7 out of 8 in 6i84

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Zinc binding site 7 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:42.9
occ:1.00
 O J:CYS7 2.1 45.5 1.0
SG J:CYS10 2.4 42.2 1.0
SG J:CYS7 2.4 45.5 1.0
CB J:CYS7 2.5 45.5 1.0
C J:CYS7 2.6 45.5 1.0
SG J:CYS46 3.0 34.0 1.0
CA J:CYS7 3.1 45.5 1.0
N J:CYS10 3.2 42.2 1.0
CB J:CYS10 3.4 42.2 1.0
N J:PHE8 3.6 42.6 1.0
N J:GLY11 3.6 40.1 1.0
CB J:CYS46 3.6 34.0 1.0
OG J:SER9 3.8 43.7 1.0
CA J:CYS10 3.8 42.2 1.0
N J:SER9 3.8 43.7 1.0
N J:CYS7 3.9 45.5 1.0
C J:CYS10 4.2 42.2 1.0
C J:SER9 4.2 43.7 1.0
CA J:CYS46 4.3 34.0 1.0
CA J:SER9 4.4 43.7 1.0
C J:PHE8 4.4 42.6 1.0
CB J:SER9 4.5 43.7 1.0
CA J:PHE8 4.6 42.6 1.0
O J:LYS12 4.6 38.8 1.0
NH2 J:ARG43 4.6 40.5 1.0
CA J:GLY11 4.6 40.1 1.0
N J:LYS12 4.7 38.8 1.0
C J:ARG6 4.8 39.7 1.0
O J:CYS45 4.8 32.9 1.0

Zinc binding site 8 out of 8 in 6i84

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Zinc binding site 8 out of 8 in the Structure of Transcribing Rna Polymerase II-Nucleosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Transcribing Rna Polymerase II-Nucleosome Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.1
occ:1.00
 OE1 L:GLU33 2.2 1.0 1.0
N L:GLU33 2.2 1.0 1.0
N L:CYS34 2.5 0.7 1.0
SG L:CYS31 2.5 0.8 1.0
CA L:GLU33 2.7 1.0 1.0
CB L:GLU33 2.7 1.0 1.0
C L:GLU33 3.0 1.0 1.0
SG L:CYS51 3.1 89.1 1.0
CD L:GLU33 3.1 1.0 1.0
C L:ALA32 3.2 0.8 1.0
N L:ALA32 3.4 0.8 1.0
CG L:GLU33 3.4 1.0 1.0
CB L:CYS31 3.5 0.8 1.0
CA L:CYS34 3.7 0.7 1.0
CA L:ALA32 3.8 0.8 1.0
C L:CYS31 3.9 0.8 1.0
O L:CYS34 4.0 0.7 1.0
SG L:CYS34 4.1 0.7 1.0
C L:CYS34 4.1 0.7 1.0
CB L:CYS34 4.1 0.7 1.0
O L:ALA32 4.2 0.8 1.0
O L:GLU33 4.2 1.0 1.0
OE2 L:GLU33 4.3 1.0 1.0
CB L:ALA32 4.3 0.8 1.0
CA L:CYS31 4.3 0.8 1.0
O L:CYS31 4.5 0.8 1.0
SG L:CYS48 4.5 95.2 1.0
CB L:CYS51 4.6 89.1 1.0

Reference:

L.Farnung, S.M.Vos, P.Cramer. Structure of Transcribing Rna Polymerase II-Nucleosome Complex. Nat Commun V. 9 5432 2018.
ISSN: ESSN 2041-1723
PubMed: 30575770
DOI: 10.1038/S41467-018-07870-Y
Page generated: Wed Dec 16 11:59:50 2020

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