Atomistry » Zinc » PDB 7n5u-7nsk » 7nkx
Atomistry »
  Zinc »
    PDB 7n5u-7nsk »
      7nkx »

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

Go back to Zinc Binding Sites List in 7nkx
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

Go back to Zinc Binding Sites List in 7nkx
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

Go back to Zinc Binding Sites List in 7nkx
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

Go back to Zinc Binding Sites List in 7nkx
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

Go back to Zinc Binding Sites List in 7nkx
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

Go back to Zinc Binding Sites List in 7nkx
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

Go back to Zinc Binding Sites List in 7nkx
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

Go back to Zinc Binding Sites List in 7nkx
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy