Zinc in PDB 8h0v: Rna Polymerase II Transcribing A Chromatosome (Type I)

Enzymatic activity of Rna Polymerase II Transcribing A Chromatosome (Type I)

All present enzymatic activity of Rna Polymerase II Transcribing A Chromatosome (Type I):
2.7.7.6;

Other elements in 8h0v:

The structure of Rna Polymerase II Transcribing A Chromatosome (Type I) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Transcribing A Chromatosome (Type I) (pdb code 8h0v). 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 Transcribing A Chromatosome (Type I), PDB code: 8h0v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 1 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:235.9
occ:1.00
 CE1 A:HIS80 1.6 203.8 1.0
NE2 A:HIS80 2.1 203.8 1.0
SG A:CYS70 2.3 211.3 1.0
SG A:CYS67 2.3 208.8 1.0
SG A:CYS77 2.3 219.7 1.0
ND1 A:HIS80 2.9 203.8 1.0
CB A:CYS67 3.0 208.8 1.0
CB A:CYS70 3.4 211.3 1.0
CD2 A:HIS80 3.4 203.8 1.0
CB A:CYS77 3.5 219.7 1.0
CG A:HIS80 3.8 203.8 1.0
N A:CYS70 3.9 211.3 1.0
CA A:CYS70 4.2 211.3 1.0
CA A:CYS77 4.3 219.7 1.0
CA A:CYS67 4.5 208.8 1.0
CA A:GLY59 4.5 208.4 1.0
CB A:THR69 4.6 207.4 1.0
N A:GLY79 4.7 202.4 1.0
CD A:PRO78 4.8 209.3 1.0
C A:CYS77 4.9 219.7 1.0
C A:THR69 4.9 207.4 1.0
C A:CYS70 4.9 211.3 1.0
N A:PRO78 4.9 209.3 1.0
N A:GLY71 5.0 207.5 1.0

Zinc binding site 2 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 2 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:297.5
occ:1.00
 SG A:CYS107 2.3 253.6 1.0
SG A:CYS148 2.3 281.6 1.0
SG A:CYS168 2.3 280.3 1.0
SG A:CYS110 2.3 254.7 1.0
CB A:CYS148 2.6 281.6 1.0
CB A:CYS107 3.3 253.6 1.0
CB A:CYS168 3.4 280.3 1.0
CB A:CYS110 3.6 254.7 1.0
N A:CYS168 3.7 280.3 1.0
CA A:CYS148 4.1 281.6 1.0
CA A:CYS168 4.2 280.3 1.0
N A:CYS110 4.2 254.7 1.0
O A:CYS148 4.5 281.6 1.0
CA A:CYS110 4.5 254.7 1.0
N A:GLY169 4.6 277.4 1.0
C A:GLY167 4.7 289.0 1.0
CA A:CYS107 4.7 253.6 1.0
C A:CYS148 4.8 281.6 1.0
CA A:GLY167 4.9 289.0 1.0
N A:CYS148 4.9 281.6 1.0
C A:CYS168 4.9 280.3 1.0

Zinc binding site 3 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 3 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:279.6
occ:1.00
 SG B:CYS1163 2.3 240.1 1.0
SG B:CYS1185 2.3 243.9 1.0
SG B:CYS1166 2.3 235.9 1.0
SG B:CYS1182 2.3 231.1 1.0
CB B:CYS1163 2.9 240.1 1.0
CB B:CYS1166 2.9 235.9 1.0
CB B:CYS1185 3.2 243.9 1.0
CB B:CYS1182 3.5 231.1 1.0
N B:CYS1166 3.7 235.9 1.0
CA B:CYS1166 3.9 235.9 1.0
N B:CYS1185 4.2 243.9 1.0
CA B:CYS1185 4.3 243.9 1.0
CA B:CYS1163 4.4 240.1 1.0
OG B:SER1170 4.6 224.8 1.0
C B:CYS1166 4.7 235.9 1.0
C B:ILE1165 4.8 248.4 1.0
CB B:ILE1165 4.8 248.4 1.0
CA B:CYS1182 4.9 231.1 1.0
N B:GLY1167 4.9 227.5 1.0
C B:CYS1163 5.0 240.1 1.0

Zinc binding site 4 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 4 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:310.3
occ:1.00
 SG C:CYS87 2.3 268.4 1.0
SG C:CYS91 2.3 249.7 1.0
SG C:CYS94 2.3 240.0 1.0
SG C:CYS85 2.3 264.4 1.0
CB C:CYS85 3.0 264.4 1.0
CB C:CYS87 3.2 268.4 1.0
CB C:CYS94 3.5 240.0 1.0
CB C:CYS91 3.6 249.7 1.0
CG C:GLU93 4.1 235.5 1.0
N C:CYS94 4.1 240.0 1.0
N C:CYS91 4.2 249.7 1.0
CA C:CYS87 4.3 268.4 1.0
N C:CYS87 4.4 268.4 1.0
CA C:CYS94 4.4 240.0 1.0
OE2 C:GLU93 4.5 235.5 1.0
CA C:CYS85 4.5 264.4 1.0
CA C:CYS91 4.5 249.7 1.0
CD C:GLU93 4.8 235.5 1.0
C C:CYS85 4.8 264.4 1.0
CD C:LYS80 4.9 235.7 1.0

Zinc binding site 5 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 5 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:550.7
occ:1.00
 CB I:CYS106 1.8 508.9 1.0
CB I:CYS78 2.0 540.5 1.0
SG I:CYS103 2.4 484.9 1.0
SG I:CYS75 2.4 521.3 1.0
SG I:CYS78 2.4 540.5 1.0
SG I:CYS106 2.4 508.9 1.0
CA I:CYS106 3.2 508.9 1.0
N I:CYS106 3.4 508.9 1.0
CA I:CYS78 3.4 540.5 1.0
OG I:SER80 3.6 508.4 1.0
N I:CYS78 3.7 540.5 1.0
CB I:CYS103 3.7 484.9 1.0
CB I:CYS75 3.8 521.3 1.0
C I:CYS78 4.2 540.5 1.0
C I:CYS106 4.2 508.9 1.0
O I:CYS78 4.4 540.5 1.0
CB I:SER80 4.5 508.4 1.0
C I:ASN105 4.5 503.9 1.0
CB I:GLU77 4.6 537.7 1.0
CB I:ASN105 4.7 503.9 1.0
C I:GLU77 4.7 537.7 1.0
N I:LYS107 4.8 479.9 1.0
O I:CYS106 4.8 508.9 1.0
OD1 I:ASN105 5.0 503.9 1.0
N I:HIS79 5.0 533.7 1.0

Zinc binding site 6 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 6 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:389.1
occ:1.00
 SG I:CYS29 2.3 333.4 1.0
SG I:CYS32 2.3 355.7 1.0
SG I:CYS7 2.3 361.2 1.0
CB I:CYS29 2.8 333.4 1.0
CB I:CYS7 3.0 361.2 1.0
CB I:CYS10 3.7 367.1 1.0
CB I:CYS32 3.9 355.7 1.0
CD2 I:LEU14 4.0 315.7 1.0
CA I:CYS29 4.2 333.4 1.0
CA I:CYS7 4.3 361.2 1.0
N I:CYS10 4.3 367.1 1.0
N I:CYS32 4.4 355.7 1.0
CA I:CYS10 4.6 367.1 1.0
CA I:CYS32 4.7 355.7 1.0
CB I:TYR34 4.7 355.6 1.0
SG I:CYS10 4.7 367.1 1.0
O I:TYR34 4.9 355.6 1.0

Zinc binding site 7 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 7 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:196.1
occ:1.00
 SG J:CYS10 2.3 186.2 1.0
SG J:CYS45 2.3 192.1 1.0
SG J:CYS7 2.3 185.1 1.0
SG J:CYS44 2.3 186.7 1.0
N J:CYS45 3.1 192.1 1.0
CB J:CYS7 3.3 185.1 1.0
CB J:CYS45 3.5 192.1 1.0
CA J:CYS45 3.5 192.1 1.0
CB J:CYS44 3.5 186.7 1.0
CB J:CYS10 3.6 186.2 1.0
C J:CYS44 3.7 186.7 1.0
N J:CYS10 3.9 186.2 1.0
CA J:CYS44 4.2 186.7 1.0
NE J:ARG42 4.2 175.6 1.0
CA J:CYS10 4.3 186.2 1.0
O J:CYS44 4.5 186.7 1.0
NH2 J:ARG42 4.5 175.6 1.0
N J:GLY11 4.7 191.2 1.0
CB J:SER9 4.7 176.4 1.0
CA J:CYS7 4.7 185.1 1.0
CZ J:ARG42 4.9 175.6 1.0
CB J:ARG42 4.9 175.6 1.0
C J:CYS10 4.9 186.2 1.0
CB J:LYS12 4.9 185.9 1.0
N J:CYS44 4.9 186.7 1.0
C J:SER9 4.9 176.4 1.0
N J:LYS12 5.0 185.9 1.0
C J:CYS45 5.0 192.1 1.0

Zinc binding site 8 out of 8 in 8h0v

Go back to Zinc Binding Sites List in 8h0v
Zinc binding site 8 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type I)


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 Transcribing A Chromatosome (Type I) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:315.7
occ:1.00
 SG L:CYS33 2.3 284.3 1.0
SG L:CYS53 2.3 291.4 1.0
SG L:CYS36 2.3 290.9 1.0
SG L:CYS50 2.4 284.7 1.0
CB L:CYS33 2.6 284.3 1.0
CB L:CYS50 3.0 284.7 1.0
CB L:CYS36 3.5 290.9 1.0
ND1 L:HIS55 3.7 277.3 1.0
CB L:HIS55 3.7 277.3 1.0
N L:CYS36 3.9 290.9 1.0
CG L:HIS55 3.9 277.3 1.0
CA L:CYS33 4.1 284.3 1.0
CB L:CYS53 4.1 291.4 1.0
CA L:CYS36 4.2 290.9 1.0
N L:HIS55 4.3 277.3 1.0
CB L:HIS38 4.5 282.8 1.0
CA L:CYS50 4.5 284.7 1.0
CE1 L:HIS55 4.6 277.3 1.0
C L:CYS36 4.6 290.9 1.0
CA L:HIS55 4.6 277.3 1.0
N L:CYS53 4.7 291.4 1.0
N L:HIS38 4.7 282.8 1.0
N L:ALA37 4.8 288.7 1.0
N L:GLY54 4.9 284.8 1.0
C L:CYS33 4.9 284.3 1.0
CD2 L:HIS55 4.9 277.3 1.0
CA L:CYS53 4.9 291.4 1.0
N L:CYS33 5.0 284.3 1.0

Reference:

R.Hirano, H.Ehara, T.Kujirai, T.Uejima, Y.Takizawa, S.I.Sekine, H.Kurumizaka. Structural Basis of Rna Polymerase II Transcription on the Chromatosome Containing Linker Histone H1. Nat Commun V. 13 7287 2022.
ISSN: ESSN 2041-1723
PubMed: 36435862
DOI: 10.1038/S41467-022-35003-Z
Page generated: Thu Oct 31 06:53:48 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy