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Zinc in PDB 7nkx: Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure

Enzymatic activity of Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure

All present enzymatic activity of Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure:
2.7.7.6;

Other elements in 7nkx:

The structure of Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Fluorine (F) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure (pdb code 7nkx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure, PDB code: 7nkx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7nkx

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Zinc binding site 1 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure


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-SPT4/5-Nucleosome-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:126.6
occ:1.00
 CB A:CYS148 2.1 105.0 1.0
SG A:CYS167 2.3 101.2 1.0
SG A:CYS148 2.3 105.0 1.0
SG A:CYS107 2.3 99.2 1.0
SG A:CYS110 2.4 97.1 1.0
O A:CYS167 3.0 101.2 1.0
N A:CYS167 3.1 101.2 1.0
CA A:CYS148 3.4 105.0 1.0
C A:CYS167 3.5 101.2 1.0
CB A:CYS167 3.5 101.2 1.0
CA A:CYS167 3.5 101.2 1.0
CB A:CYS107 3.7 99.2 1.0
C A:GLY166 3.9 100.1 1.0
CB A:CYS110 4.0 97.1 1.0
C A:CYS148 4.0 105.0 1.0
O A:CYS148 4.1 105.0 1.0
CA A:GLY166 4.2 100.1 1.0
N A:CYS148 4.5 105.0 1.0
N A:GLY168 4.6 100.5 1.0
OD1 A:ASN169 4.6 99.9 1.0
O A:GLY166 4.7 100.1 1.0
O A:GLU149 5.0 104.7 1.0
N A:GLU149 5.0 104.7 1.0

Zinc binding site 2 out of 8 in 7nkx

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Zinc binding site 2 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure


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-SPT4/5-Nucleosome-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:114.1
occ:1.00
 NE2 A:HIS80 2.0 86.4 1.0
SG A:CYS70 2.1 92.7 1.0
SG A:CYS67 2.2 95.2 1.0
SG A:CYS77 2.4 88.5 1.0
N A:CYS70 2.8 92.7 1.0
CE1 A:HIS80 2.9 86.4 1.0
CB A:CYS70 2.9 92.7 1.0
CD2 A:HIS80 2.9 86.4 1.0
CB A:CYS67 3.3 95.2 1.0
CB A:THR69 3.4 91.2 1.0
CA A:CYS70 3.4 92.7 1.0
C A:THR69 3.6 91.2 1.0
CA A:THR69 3.8 91.2 1.0
CG2 A:THR69 3.8 91.2 1.0
ND1 A:HIS80 3.9 86.4 1.0
CG A:HIS80 4.0 86.4 1.0
N A:THR69 4.0 91.2 1.0
CB A:CYS77 4.1 88.5 1.0
C A:CYS70 4.4 92.7 1.0
N A:GLN71 4.4 95.2 1.0
OG1 A:THR69 4.5 91.2 1.0
O A:THR69 4.6 91.2 1.0
CA A:CYS67 4.7 95.2 1.0
C A:CYS67 4.9 95.2 1.0

Zinc binding site 3 out of 8 in 7nkx

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Zinc binding site 3 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 Structure


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-SPT4/5-Nucleosome-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:116.7
occ:1.00
 SG B:CYS1166 2.2 93.0 1.0
SG B:CYS1182 2.3 96.3 1.0
SG B:CYS1163 2.3 95.1 1.0
SG B:CYS1185 2.3 101.4 1.0
CB B:CYS1185 2.9 101.4 1.0
CB B:CYS1163 3.2 95.1 1.0
CB B:CYS1166 3.3 93.0 1.0
CB B:CYS1182 3.6 96.3 1.0
N B:CYS1166 4.0 93.0 1.0
CA B:CYS1185 4.1 101.4 1.0
N B:CYS1185 4.2 101.4 1.0
O B:CYS1182 4.2 96.3 1.0
CA B:CYS1166 4.2 93.0 1.0
OG1 B:THR1170 4.4 89.3 1.0
CA B:CYS1163 4.6 95.1 1.0
OD1 B:ASN1187 4.6 102.1 1.0
C B:CYS1182 4.8 96.3 1.0
CA B:CYS1182 4.8 96.3 1.0
ND2 B:ASN1187 4.8 102.1 1.0
C B:GLY1184 4.8 95.5 1.0
CB B:ILE1165 4.9 96.7 1.0

Zinc binding site 4 out of 8 in 7nkx

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Zinc binding site 4 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 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-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:108.8
occ:1.00
 SG C:CYS95 2.1 75.7 1.0
SG C:CYS86 2.1 83.9 1.0
SG C:CYS88 2.2 97.7 1.0
SG C:CYS92 2.3 87.3 1.0
CB C:CYS95 2.4 75.7 1.0
CB C:CYS86 3.0 83.9 1.0
N C:CYS92 3.8 87.3 1.0
CA C:CYS95 3.8 75.7 1.0
CB C:CYS92 3.9 87.3 1.0
CB C:CYS88 4.0 97.7 1.0
O C:CYS92 4.1 87.3 1.0
N C:CYS95 4.1 75.7 1.0
CA C:CYS92 4.3 87.3 1.0
CA C:CYS86 4.4 83.9 1.0
N C:CYS88 4.5 97.7 1.0
C C:CYS92 4.6 87.3 1.0
C C:CYS95 4.7 75.7 1.0
C C:CYS86 4.8 83.9 1.0
CA C:CYS88 4.8 97.7 1.0
C C:HIS91 4.8 92.8 1.0
CA C:HIS91 4.8 92.8 1.0
O C:SER83 4.9 77.6 1.0
C C:LYS94 5.0 77.4 1.0

Zinc binding site 5 out of 8 in 7nkx

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Zinc binding site 5 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 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-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:138.0
occ:1.00
 CB I:CYS10 2.0 123.3 1.0
SG I:CYS7 2.3 121.8 1.0
SG I:CYS32 2.3 125.9 1.0
SG I:CYS10 2.4 123.3 1.0
CB I:CYS7 3.0 121.8 1.0
SG I:CYS29 3.0 122.9 1.0
CA I:CYS10 3.5 123.3 1.0
OG1 I:THR31 3.7 119.9 1.0
CB I:CYS29 4.0 122.9 1.0
CB I:CYS32 4.0 125.9 1.0
N I:CYS10 4.1 123.3 1.0
C I:CYS10 4.1 123.3 1.0
O I:ARG8 4.2 124.9 1.0
CA I:CYS7 4.3 121.8 1.0
N I:ASN11 4.4 113.8 1.0
N I:CYS32 4.5 125.9 1.0
C I:CYS7 4.5 121.8 1.0
O I:CYS7 4.5 121.8 1.0
O I:CYS32 4.7 125.9 1.0
CB I:ASN12 4.8 113.4 1.0
CA I:CYS32 4.8 125.9 1.0
O I:CYS10 4.8 123.3 1.0
N I:ASN12 4.8 113.4 1.0
CB I:THR31 5.0 119.9 1.0

Zinc binding site 6 out of 8 in 7nkx

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Zinc binding site 6 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 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-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:114.4
occ:1.00
 SG I:CYS103 2.2 88.7 1.0
SG I:CYS106 2.2 91.7 1.0
SG I:CYS75 2.2 94.1 1.0
SG I:CYS78 2.3 95.8 1.0
CB I:CYS75 2.9 94.1 1.0
CB I:CYS103 3.0 88.7 1.0
OG I:SER105 3.1 90.8 1.0
NZ I:LYS77 3.7 94.6 1.0
CB I:CYS106 3.7 91.7 1.0
CB I:CYS78 4.0 95.8 1.0
N I:CYS106 4.1 91.7 1.0
OG I:SER80 4.2 93.7 1.0
CB I:SER80 4.3 93.7 1.0
CA I:CYS75 4.4 94.1 1.0
CB I:SER105 4.4 90.8 1.0
CA I:CYS103 4.4 88.7 1.0
CE I:LYS77 4.5 94.6 1.0
CA I:CYS106 4.5 91.7 1.0
N I:CYS78 4.5 95.8 1.0
CA I:CYS78 4.8 95.8 1.0
N I:SER80 4.9 93.7 1.0
C I:CYS103 4.9 88.7 1.0
C I:SER105 5.0 90.8 1.0
C I:CYS75 5.0 94.1 1.0

Zinc binding site 7 out of 8 in 7nkx

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Zinc binding site 7 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 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-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:86.1
occ:1.00
 SG J:CYS45 2.1 62.8 1.0
SG J:CYS46 2.1 62.1 1.0
SG J:CYS7 2.1 61.2 1.0
SG J:CYS10 2.2 62.0 1.0
N J:CYS46 2.6 62.1 1.0
CA J:CYS46 3.0 62.1 1.0
CB J:CYS7 3.0 61.2 1.0
CB J:CYS46 3.0 62.1 1.0
C J:CYS45 3.4 62.8 1.0
CB J:CYS45 3.5 62.8 1.0
CB J:CYS10 3.7 62.0 1.0
CA J:CYS45 4.0 62.8 1.0
O J:CYS45 4.1 62.8 1.0
N J:CYS10 4.1 62.0 1.0
CA J:CYS7 4.4 61.2 1.0
C J:CYS46 4.5 62.1 1.0
CA J:CYS10 4.5 62.0 1.0
NE J:ARG43 4.5 62.7 1.0
CB J:LYS12 4.7 60.9 1.0
N J:CYS45 4.7 62.8 1.0
CB J:ARG43 4.8 62.7 1.0
CB J:SER9 4.9 64.2 1.0
O J:ARG43 5.0 62.7 1.0

Zinc binding site 8 out of 8 in 7nkx

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Zinc binding site 8 out of 8 in the Rna Polymerase II-SPT4/5-Nucleosome-CHD1 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-CHD1 Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:110.3
occ:1.00
 CB L:CYS48 2.1 94.1 1.0
SG L:CYS48 2.1 94.1 1.0
SG L:CYS51 2.2 94.2 1.0
SG L:CYS31 2.3 90.5 1.0
SG L:CYS34 2.3 90.2 1.0
CB L:CYS31 3.1 90.5 1.0
CB L:CYS34 3.4 90.2 1.0
CA L:CYS48 3.6 94.1 1.0
O L:HIS53 3.7 89.7 1.0
CB L:CYS51 3.9 94.2 1.0
N L:CYS34 4.1 90.2 1.0
N L:CYS51 4.2 94.2 1.0
O L:CYS51 4.3 94.2 1.0
CB L:HIS53 4.3 89.7 1.0
N L:CYS48 4.4 94.1 1.0
CA L:CYS34 4.4 90.2 1.0
CA L:CYS31 4.4 90.5 1.0
C L:HIS53 4.4 89.7 1.0
CA L:CYS51 4.4 94.2 1.0
C L:CYS48 4.4 94.1 1.0
N L:HIS53 4.5 89.7 1.0
C L:CYS51 4.5 94.2 1.0
CA L:HIS53 4.6 89.7 1.0
N L:ALA32 4.8 86.9 1.0
O L:CYS48 4.9 94.1 1.0
OG L:SER36 5.0 89.3 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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