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

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

Go back to Zinc Binding Sites List in 7nky
Zinc binding site 1 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 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

Go back to Zinc Binding Sites List in 7nky
Zinc binding site 2 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 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

Go back to Zinc Binding Sites List in 7nky
Zinc binding site 3 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 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

Go back to Zinc Binding Sites List in 7nky
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

Go back to Zinc Binding Sites List in 7nky
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

Go back to Zinc Binding Sites List in 7nky
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

Go back to Zinc Binding Sites List in 7nky
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

Go back to Zinc Binding Sites List in 7nky
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

Go back to Zinc Binding Sites List in 7nky
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy