Zinc in PDB 8h0w: Rna Polymerase II Transcribing A Chromatosome (Type II)

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

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

Other elements in 8h0w:

The structure of Rna Polymerase II Transcribing A Chromatosome (Type II) 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 II) (pdb code 8h0w). 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 II), PDB code: 8h0w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8h0w

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Zinc binding site 1 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:257.4
occ:1.00
 CE1 A:HIS80 1.6 221.0 1.0
NE2 A:HIS80 2.1 221.0 1.0
SG A:CYS70 2.3 223.4 1.0
SG A:CYS67 2.3 212.1 1.0
SG A:CYS77 2.3 212.1 1.0
ND1 A:HIS80 2.9 221.0 1.0
CB A:CYS67 3.0 212.1 1.0
CB A:CYS70 3.4 223.4 1.0
CD2 A:HIS80 3.4 221.0 1.0
CB A:CYS77 3.5 212.1 1.0
CG A:HIS80 3.8 221.0 1.0
N A:CYS70 3.9 223.4 1.0
CA A:CYS70 4.2 223.4 1.0
CA A:CYS77 4.3 212.1 1.0
CA A:CYS67 4.5 212.1 1.0
CA A:GLY59 4.5 209.2 1.0
CB A:THR69 4.6 211.5 1.0
N A:GLY79 4.7 201.2 1.0
CD A:PRO78 4.8 203.9 1.0
C A:CYS77 4.9 212.1 1.0
C A:THR69 4.9 211.5 1.0
C A:CYS70 4.9 223.4 1.0
N A:PRO78 4.9 203.9 1.0
N A:GLY71 5.0 213.8 1.0

Zinc binding site 2 out of 8 in 8h0w

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Zinc binding site 2 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:202.7
occ:1.00
 SG A:CYS107 2.3 197.6 1.0
SG A:CYS148 2.3 197.3 1.0
SG A:CYS168 2.3 178.8 1.0
SG A:CYS110 2.3 175.3 1.0
CB A:CYS148 2.6 197.3 1.0
CB A:CYS107 3.3 197.6 1.0
CB A:CYS168 3.4 178.8 1.0
CB A:CYS110 3.6 175.3 1.0
N A:CYS168 3.7 178.8 1.0
CA A:CYS148 4.1 197.3 1.0
CA A:CYS168 4.2 178.8 1.0
N A:CYS110 4.2 175.3 1.0
O A:CYS148 4.5 197.3 1.0
CA A:CYS110 4.5 175.3 1.0
N A:GLY169 4.6 183.6 1.0
C A:GLY167 4.7 195.2 1.0
CA A:CYS107 4.8 197.6 1.0
C A:CYS148 4.8 197.3 1.0
CA A:GLY167 4.9 195.2 1.0
N A:CYS148 4.9 197.3 1.0
C A:CYS168 4.9 178.8 1.0

Zinc binding site 3 out of 8 in 8h0w

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Zinc binding site 3 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:312.9
occ:1.00
 SG B:CYS1163 2.3 275.7 1.0
SG B:CYS1185 2.3 247.8 1.0
SG B:CYS1166 2.3 265.9 1.0
SG B:CYS1182 2.3 264.3 1.0
CB B:CYS1163 2.9 275.7 1.0
CB B:CYS1166 2.9 265.9 1.0
CB B:CYS1185 3.2 247.8 1.0
CB B:CYS1182 3.5 264.3 1.0
N B:CYS1166 3.7 265.9 1.0
CA B:CYS1166 3.9 265.9 1.0
N B:CYS1185 4.2 247.8 1.0
CA B:CYS1185 4.3 247.8 1.0
CA B:CYS1163 4.4 275.7 1.0
OG B:SER1170 4.6 249.5 1.0
C B:CYS1166 4.7 265.9 1.0
C B:ILE1165 4.8 291.2 1.0
CB B:ILE1165 4.8 291.2 1.0
CA B:CYS1182 4.9 264.3 1.0
N B:GLY1167 4.9 250.5 1.0
C B:CYS1163 5.0 275.7 1.0

Zinc binding site 4 out of 8 in 8h0w

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Zinc binding site 4 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:260.1
occ:1.00
 SG C:CYS87 2.3 265.7 1.0
SG C:CYS91 2.3 232.3 1.0
SG C:CYS94 2.3 240.4 1.0
SG C:CYS85 2.3 259.2 1.0
CB C:CYS85 3.0 259.2 1.0
CB C:CYS87 3.2 265.7 1.0
CB C:CYS94 3.5 240.4 1.0
CB C:CYS91 3.6 232.3 1.0
CG C:GLU93 4.1 242.7 1.0
N C:CYS94 4.1 240.4 1.0
N C:CYS91 4.2 232.3 1.0
CA C:CYS87 4.3 265.7 1.0
N C:CYS87 4.4 265.7 1.0
CA C:CYS94 4.4 240.4 1.0
OE2 C:GLU93 4.5 242.7 1.0
CA C:CYS85 4.5 259.2 1.0
CA C:CYS91 4.5 232.3 1.0
CD C:GLU93 4.8 242.7 1.0
C C:CYS85 4.8 259.2 1.0
CD C:LYS80 4.9 248.6 1.0

Zinc binding site 5 out of 8 in 8h0w

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Zinc binding site 5 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:877.3
occ:1.00
 CB I:CYS106 1.8 793.9 1.0
CB I:CYS78 2.0 825.3 1.0
SG I:CYS103 2.4 739.6 1.0
SG I:CYS75 2.4 771.3 1.0
SG I:CYS78 2.4 825.3 1.0
SG I:CYS106 2.4 793.9 1.0
CA I:CYS106 3.2 793.9 1.0
N I:CYS106 3.4 793.9 1.0
CA I:CYS78 3.4 825.3 1.0
OG I:SER80 3.6 761.0 1.0
CB I:CYS103 3.7 739.6 1.0
N I:CYS78 3.7 825.3 1.0
CB I:CYS75 3.8 771.3 1.0
C I:CYS78 4.2 825.3 1.0
C I:CYS106 4.2 793.9 1.0
O I:CYS78 4.4 825.3 1.0
CB I:SER80 4.5 761.0 1.0
C I:ASN105 4.5 791.6 1.0
CB I:GLU77 4.6 823.7 1.0
CB I:ASN105 4.7 791.6 1.0
C I:GLU77 4.7 823.7 1.0
N I:LYS107 4.8 749.7 1.0
O I:CYS106 4.8 793.9 1.0
OD1 I:ASN105 5.0 791.6 1.0
N I:HIS79 5.0 794.3 1.0

Zinc binding site 6 out of 8 in 8h0w

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Zinc binding site 6 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:489.0
occ:1.00
 SG I:CYS29 2.3 436.9 1.0
SG I:CYS7 2.3 467.4 1.0
SG I:CYS32 2.3 474.9 1.0
CB I:CYS29 2.8 436.9 1.0
CB I:CYS7 3.0 467.4 1.0
CB I:CYS10 3.7 452.5 1.0
CB I:CYS32 3.9 474.9 1.0
CD2 I:LEU14 4.0 466.9 1.0
CA I:CYS29 4.2 436.9 1.0
CA I:CYS7 4.3 467.4 1.0
N I:CYS10 4.3 452.5 1.0
N I:CYS32 4.4 474.9 1.0
CA I:CYS10 4.6 452.5 1.0
CA I:CYS32 4.7 474.9 1.0
CB I:TYR34 4.7 582.8 1.0
SG I:CYS10 4.7 452.5 1.0
O I:TYR34 4.9 582.8 1.0

Zinc binding site 7 out of 8 in 8h0w

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Zinc binding site 7 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:133.1
occ:1.00
 SG J:CYS10 2.3 156.4 1.0
SG J:CYS45 2.3 146.9 1.0
SG J:CYS7 2.3 163.9 1.0
SG J:CYS44 2.3 141.0 1.0
N J:CYS45 3.1 146.9 1.0
CB J:CYS7 3.3 163.9 1.0
CB J:CYS45 3.5 146.9 1.0
CA J:CYS45 3.5 146.9 1.0
CB J:CYS44 3.5 141.0 1.0
CB J:CYS10 3.6 156.4 1.0
C J:CYS44 3.7 141.0 1.0
N J:CYS10 3.9 156.4 1.0
CA J:CYS44 4.2 141.0 1.0
NE J:ARG42 4.2 137.7 1.0
CA J:CYS10 4.3 156.4 1.0
O J:CYS44 4.5 141.0 1.0
NH2 J:ARG42 4.5 137.7 1.0
N J:GLY11 4.7 153.5 1.0
CB J:SER9 4.7 179.0 1.0
CA J:CYS7 4.7 163.9 1.0
CZ J:ARG42 4.9 137.7 1.0
CB J:ARG42 4.9 137.7 1.0
C J:CYS10 4.9 156.4 1.0
CB J:LYS12 4.9 157.3 1.0
N J:CYS44 4.9 141.0 1.0
C J:SER9 4.9 179.0 1.0
N J:LYS12 5.0 157.3 1.0
C J:CYS45 5.0 146.9 1.0

Zinc binding site 8 out of 8 in 8h0w

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Zinc binding site 8 out of 8 in the Rna Polymerase II Transcribing A Chromatosome (Type II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:257.6
occ:1.00
 SG L:CYS33 2.3 221.5 1.0
SG L:CYS53 2.3 209.3 1.0
SG L:CYS36 2.3 228.8 1.0
SG L:CYS50 2.4 216.7 1.0
CB L:CYS33 2.6 221.5 1.0
CB L:CYS50 3.0 216.7 1.0
CB L:CYS36 3.5 228.8 1.0
ND1 L:HIS55 3.7 213.3 1.0
CB L:HIS55 3.7 213.3 1.0
N L:CYS36 3.9 228.8 1.0
CG L:HIS55 3.9 213.3 1.0
CA L:CYS33 4.1 221.5 1.0
CB L:CYS53 4.1 209.3 1.0
CA L:CYS36 4.2 228.8 1.0
N L:HIS55 4.3 213.3 1.0
CB L:HIS38 4.5 218.1 1.0
CA L:CYS50 4.5 216.7 1.0
CE1 L:HIS55 4.6 213.3 1.0
C L:CYS36 4.6 228.8 1.0
CA L:HIS55 4.6 213.3 1.0
N L:CYS53 4.7 209.3 1.0
N L:HIS38 4.7 218.1 1.0
N L:ALA37 4.8 225.7 1.0
N L:GLY54 4.9 210.4 1.0
C L:CYS33 4.9 221.5 1.0
CD2 L:HIS55 4.9 213.3 1.0
CA L:CYS53 4.9 209.3 1.0
N L:CYS33 5.0 221.5 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: Sat Apr 8 09:10:54 2023

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