Zinc in PDB 7nky: Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure

Enzymatic activity of Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure

All present enzymatic activity of Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure:
2.7.7.6;

Other elements in 7nky:

The structure of Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure (pdb code 7nky). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure, PDB code: 7nky:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7nky

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Zinc binding site 1 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:108.6
occ:1.00
 SG A:CYS110 2.4 93.2 1.0
SG A:CYS107 2.4 94.5 1.0
SG A:CYS148 2.5 110.7 1.0
SG A:CYS167 2.6 109.5 1.0
N A:CYS167 3.2 109.5 1.0
O A:CYS167 3.3 109.5 1.0
CB A:CYS148 3.4 110.7 1.0
CB A:CYS107 3.5 94.5 1.0
C A:CYS167 3.8 109.5 1.0
CA A:CYS167 3.8 109.5 1.0
CB A:CYS167 3.8 109.5 1.0
CB A:CYS110 3.9 93.2 1.0
C A:GLY166 4.2 114.9 1.0
CA A:GLY166 4.3 114.9 1.0
NH1 A:ARG164 4.3 118.4 1.0
N A:CYS110 4.5 93.2 1.0
CA A:CYS110 4.8 93.2 1.0
N A:GLY168 4.9 111.3 1.0
CA A:CYS148 4.9 110.7 1.0
CA A:CYS107 4.9 94.5 1.0

Zinc binding site 2 out of 9 in 7nky

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Zinc binding site 2 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:104.2
occ:1.00
 NE2 A:HIS80 2.2 79.8 1.0
SG A:CYS70 2.4 86.4 1.0
SG A:CYS77 2.4 85.3 1.0
SG A:CYS67 2.4 96.2 1.0
CD2 A:HIS80 2.7 79.8 1.0
CE1 A:HIS80 3.3 79.8 1.0
CB A:CYS70 3.5 86.4 1.0
CB A:CYS67 3.6 96.2 1.0
N A:CYS70 3.7 86.4 1.0
CB A:THR69 3.8 86.4 1.0
CG A:HIS80 3.9 79.8 1.0
CB A:CYS77 4.0 85.3 1.0
ND1 A:HIS80 4.2 79.8 1.0
CA A:CYS70 4.2 86.4 1.0
CG2 A:THR69 4.3 86.4 1.0
C A:THR69 4.4 86.4 1.0
CA A:THR69 4.6 86.4 1.0
OG1 A:THR69 4.7 86.4 1.0
CA A:CYS77 4.7 85.3 1.0
CA A:GLY59 4.7 78.4 1.0
N A:THR69 4.9 86.4 1.0

Zinc binding site 3 out of 9 in 7nky

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Zinc binding site 3 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:107.3
occ:1.00
 SG B:CYS1185 2.4 96.8 1.0
SG B:CYS1163 2.4 86.5 1.0
SG B:CYS1182 2.4 89.8 1.0
SG B:CYS1166 2.5 86.1 1.0
CB B:CYS1185 2.9 96.8 1.0
N B:CYS1166 3.6 86.1 1.0
CB B:CYS1166 3.7 86.1 1.0
CB B:CYS1182 3.7 89.8 1.0
CB B:CYS1163 3.9 86.5 1.0
CB B:ILE1165 4.0 92.3 1.0
CA B:CYS1185 4.2 96.8 1.0
CA B:CYS1166 4.3 86.1 1.0
OD1 B:ASN1187 4.3 94.5 1.0
N B:CYS1185 4.4 96.8 1.0
ND2 B:ASN1187 4.4 94.5 1.0
C B:ILE1165 4.6 92.3 1.0
CG2 B:ILE1165 4.6 92.3 1.0
CA B:ILE1165 4.6 92.3 1.0
N B:ILE1165 4.7 92.3 1.0
CG B:ASN1187 4.7 94.5 1.0
CG1 B:ILE1165 4.8 92.3 1.0
N B:GLY1167 4.9 84.2 1.0
O B:CYS1182 4.9 89.8 1.0

Zinc binding site 4 out of 9 in 7nky

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Zinc binding site 4 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:141.1
occ:1.00
 SG C:CYS95 2.4 85.2 1.0
SG C:CYS88 2.4 133.0 1.0
SG C:CYS86 2.4 104.5 1.0
CB C:CYS86 3.2 104.5 1.0
SG C:CYS92 3.3 95.2 1.0
NZ Z:LYS813 3.5 122.8 1.0
CB C:CYS88 3.6 133.0 1.0
CB C:CYS95 3.7 85.2 1.0
NH1 Z:ARG808 3.8 139.2 1.0
C C:CYS86 3.9 104.5 1.0
O C:SER83 4.0 96.6 1.0
N C:PHE87 4.0 122.6 1.0
O C:CYS86 4.1 104.5 1.0
CA C:CYS86 4.1 104.5 1.0
C C:PHE87 4.1 122.6 1.0
N C:CYS88 4.2 133.0 1.0
NH2 Z:ARG808 4.4 139.2 1.0
CA C:PHE87 4.4 122.6 1.0
O C:PHE87 4.5 122.6 1.0
CA C:SER83 4.5 96.6 1.0
CA C:CYS88 4.5 133.0 1.0
CE Z:LYS813 4.5 122.8 1.0
CZ Z:ARG808 4.6 139.2 1.0
C C:SER83 4.7 96.6 1.0
CB C:CYS92 4.9 95.2 1.0
CA C:CYS95 4.9 85.2 1.0
CB C:SER83 5.0 96.6 1.0
N C:CYS86 5.0 104.5 1.0

Zinc binding site 5 out of 9 in 7nky

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Zinc binding site 5 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:195.3
occ:1.00
 SG I:CYS29 2.4 162.7 1.0
SG I:CYS10 2.4 153.0 1.0
SG I:CYS7 2.5 154.9 1.0
SG I:CYS32 2.5 158.3 1.0
OG1 I:THR31 2.5 144.7 1.0
CB I:CYS10 2.6 153.0 1.0
CB I:CYS7 3.4 154.9 1.0
N I:CYS32 3.6 158.3 1.0
CB I:CYS29 3.7 162.7 1.0
CB I:CYS32 3.8 158.3 1.0
CB I:THR31 3.9 144.7 1.0
CA I:CYS10 4.1 153.0 1.0
CA I:CYS32 4.2 158.3 1.0
C I:THR31 4.3 144.7 1.0
CA I:THR31 4.5 144.7 1.0
N I:CYS10 4.5 153.0 1.0
O I:CYS32 4.6 158.3 1.0
O I:ARG8 4.6 147.5 1.0
N I:THR31 4.6 144.7 1.0
C I:CYS10 4.8 153.0 1.0
CA I:CYS7 4.8 154.9 1.0
OD1 I:ASN12 4.9 138.7 1.0
C I:CYS32 4.9 158.3 1.0
CG2 I:THR31 4.9 144.7 1.0

Zinc binding site 6 out of 9 in 7nky

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Zinc binding site 6 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:120.9
occ:1.00
 SG I:CYS103 2.4 104.0 1.0
SG I:CYS75 2.4 108.6 1.0
SG I:CYS106 2.4 114.9 1.0
SG I:CYS78 2.4 106.2 1.0
CB I:CYS103 2.8 104.0 1.0
OG I:SER105 3.3 112.8 1.0
CB I:CYS75 3.5 108.6 1.0
CB I:CYS106 3.8 114.9 1.0
CB I:CYS78 3.9 106.2 1.0
N I:CYS106 4.1 114.9 1.0
N I:CYS78 4.1 106.2 1.0
CA I:CYS103 4.3 104.0 1.0
CB I:SER80 4.5 102.5 1.0
CA I:CYS106 4.6 114.9 1.0
CA I:CYS78 4.6 106.2 1.0
CB I:SER105 4.7 112.8 1.0
CB I:LYS77 4.7 108.0 1.0
CA I:CYS75 4.9 108.6 1.0
C I:CYS103 4.9 104.0 1.0
ND2 I:ASN83 5.0 105.3 1.0

Zinc binding site 7 out of 9 in 7nky

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Zinc binding site 7 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:75.3
occ:1.00
 SG J:CYS10 2.3 63.0 1.0
SG J:CYS45 2.3 59.6 1.0
SG J:CYS7 2.3 61.2 1.0
SG J:CYS46 2.3 58.3 1.0
CB J:CYS7 3.1 61.2 1.0
N J:CYS46 3.5 58.3 1.0
CB J:CYS46 3.6 58.3 1.0
CB J:CYS10 3.8 63.0 1.0
CA J:CYS46 3.8 58.3 1.0
N J:CYS10 3.9 63.0 1.0
CB J:CYS45 3.9 59.6 1.0
C J:CYS45 4.1 59.6 1.0
CB J:SER9 4.3 62.6 1.0
CA J:CYS10 4.4 63.0 1.0
CA J:CYS7 4.6 61.2 1.0
CA J:CYS45 4.6 59.6 1.0
NE J:ARG43 4.6 60.8 1.0
N J:GLY11 4.7 62.2 1.0
O J:CYS45 4.8 59.6 1.0
NH2 J:ARG43 4.8 60.8 1.0
C J:SER9 4.8 62.6 1.0
N J:SER9 4.8 62.6 1.0
N J:LYS12 4.9 60.6 1.0
CB J:LYS12 4.9 60.6 1.0
CA J:SER9 4.9 62.6 1.0
C J:CYS7 5.0 61.2 1.0
C J:CYS10 5.0 63.0 1.0

Zinc binding site 8 out of 9 in 7nky

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Zinc binding site 8 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:104.9
occ:1.00
 SG L:CYS51 2.4 97.8 1.0
SG L:CYS31 2.4 97.8 1.0
SG L:CYS48 2.5 93.0 1.0
CB L:CYS34 3.1 98.4 1.0
CB L:CYS31 3.2 97.8 1.0
CB L:CYS48 3.3 93.0 1.0
OG L:SER36 3.9 93.3 1.0
N L:CYS34 3.9 98.4 1.0
CB L:CYS51 3.9 97.8 1.0
N L:CYS51 3.9 97.8 1.0
CA L:CYS34 4.1 98.4 1.0
O L:HIS53 4.1 90.1 1.0
CB L:ASP50 4.3 100.4 1.0
SG L:CYS34 4.3 98.4 1.0
CA L:CYS51 4.4 97.8 1.0
CA L:CYS31 4.7 97.8 1.0
O L:CYS51 4.7 97.8 1.0
CA L:CYS48 4.7 93.0 1.0
N L:ASP50 4.8 100.4 1.0
C L:ASP50 4.8 100.4 1.0
CA L:ASP50 4.8 100.4 1.0
C L:CYS34 4.9 98.4 1.0
C L:CYS51 4.9 97.8 1.0
N L:SER35 4.9 97.9 1.0
OD1 L:ASP50 5.0 100.4 1.0

Zinc binding site 9 out of 9 in 7nky

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Zinc binding site 9 out of 9 in the Rna Polymerase II-SPT4/5-Nucleosome-Fact Structure


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-SPT4/5-Nucleosome-Fact Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn300

b:291.6
occ:1.00
 SG Y:CYS10 2.4 240.2 1.0
SG Y:CYS24 2.5 244.3 1.0
SG Y:CYS7 2.5 241.4 1.0
SG Y:CYS27 2.5 248.5 1.0
CB Y:CYS27 2.9 248.5 1.0
N Y:CYS10 3.6 240.2 1.0
CB Y:CYS10 3.6 240.2 1.0
CE2 Y:PHE31 3.7 242.5 1.0
CB Y:CYS7 3.8 241.4 1.0
CZ Y:PHE31 3.8 242.5 1.0
CB Y:CYS24 3.9 244.3 1.0
CA Y:CYS27 4.1 248.5 1.0
N Y:CYS27 4.1 248.5 1.0
CA Y:CYS10 4.2 240.2 1.0
CB Y:LEU9 4.3 236.7 1.0
CG2 Y:ILE12 4.4 236.1 1.0
CG Y:LEU9 4.5 236.7 1.0
C Y:LEU9 4.6 236.7 1.0
CD2 Y:LEU9 4.7 236.7 1.0
N Y:LEU9 4.7 236.7 1.0
CA Y:LEU9 4.8 236.7 1.0
CD2 Y:PHE31 4.8 242.5 1.0
CE1 Y:PHE31 4.9 242.5 1.0
N Y:GLY11 5.0 241.0 1.0

Reference:

L.Farnung, M.Ochmann, M.Engeholm, P.Cramer. Structural Basis of Nucleosome Transcription Mediated By CHD1 and Fact. Nat.Struct.Mol.Biol. V. 28 382 2021.
ISSN: ESSN 1545-9985
PubMed: 33846633
DOI: 10.1038/S41594-021-00578-6
Page generated: Wed Oct 30 07:48:59 2024

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