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Zinc in PDB 9j0o: Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)

Enzymatic activity of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)

All present enzymatic activity of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc):
2.7.7.6;

Other elements in 9j0o:

The structure of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) (pdb code 9j0o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc), PDB code: 9j0o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9j0o

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Zinc binding site 1 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:65.5
occ:1.00
 NE2 A:HIS84 2.0 45.6 1.0
SG A:CYS71 2.3 60.2 1.0
SG A:CYS81 2.3 49.2 1.0
SG A:CYS74 2.3 58.5 1.0
CD2 A:HIS84 2.7 45.6 1.0
CB A:CYS71 2.9 60.2 1.0
CE1 A:HIS84 3.2 45.6 1.0
CB A:CYS81 3.7 49.2 1.0
O A:CYS74 3.7 58.5 1.0
O A:PRO82 3.8 45.2 1.0
CB A:CYS74 3.9 58.5 1.0
N A:CYS74 3.9 58.5 1.0
CG A:HIS84 3.9 45.6 1.0
ND1 A:HIS84 4.2 45.6 1.0
CA A:CYS74 4.3 58.5 1.0
CA A:CYS71 4.4 60.2 1.0
C A:CYS74 4.5 58.5 1.0
CA A:CYS81 4.5 49.2 1.0
CB A:THR73 4.6 54.5 1.0
CA A:GLY63 4.7 53.3 1.0
O A:GLN62 4.8 49.0 1.0
C A:THR73 4.8 54.5 1.0
C A:CYS81 4.9 49.2 1.0
C A:CYS71 4.9 60.2 1.0
C A:PRO82 5.0 45.2 1.0

Zinc binding site 2 out of 9 in 9j0o

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Zinc binding site 2 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:185.7
occ:1.00
 SG A:CYS114 2.3 130.9 1.0
SG A:CYS111 2.3 127.9 1.0
SG A:CYS184 2.3 173.1 1.0
CB A:CYS114 2.4 130.9 1.0
CD1 A:TYR187 3.3 157.4 1.0
CE1 A:TYR187 3.4 157.4 1.0
CB A:CYS111 3.7 127.9 1.0
CA A:CYS114 4.0 130.9 1.0
CB A:CYS184 4.0 173.1 1.0
O A:PHE112 4.4 122.4 1.0
N A:CYS184 4.5 173.1 1.0
CG A:TYR187 4.5 157.4 1.0
CZ A:TYR187 4.6 157.4 1.0
N A:CYS114 4.7 130.9 1.0
O A:GLY182 4.7 171.7 1.0
CE1 A:PHE113 4.7 129.4 1.0
CB A:LYS116 4.8 134.2 1.0
C A:CYS114 4.8 130.9 1.0
CA A:CYS184 4.8 173.1 1.0
N A:GLY185 4.8 164.2 1.0
C A:GLY182 4.9 171.7 1.0

Zinc binding site 3 out of 9 in 9j0o

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Zinc binding site 3 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:79.5
occ:1.00
 SG B:CYS1122 2.3 61.0 1.0
SG B:CYS1140 2.3 74.8 1.0
SG B:CYS1137 2.3 76.2 1.0
SG B:CYS1119 2.3 56.1 1.0
CB B:CYS1119 2.9 56.1 1.0
CB B:CYS1140 3.2 74.8 1.0
CB B:CYS1137 3.6 76.2 1.0
CB B:CYS1122 3.7 61.0 1.0
N B:CYS1122 3.7 61.0 1.0
O B:CYS1122 4.0 61.0 1.0
CA B:CYS1122 4.2 61.0 1.0
CA B:CYS1140 4.4 74.8 1.0
CA B:CYS1119 4.4 56.1 1.0
CB B:LEU1121 4.4 61.1 1.0
N B:CYS1140 4.5 74.8 1.0
C B:CYS1122 4.5 61.0 1.0
C B:LEU1121 4.8 61.1 1.0
O B:ARG1138 4.9 72.3 1.0
O B:CYS1137 4.9 76.2 1.0
CA B:CYS1137 4.9 76.2 1.0
N B:LEU1121 5.0 61.1 1.0
C B:CYS1119 5.0 56.1 1.0
CA B:LEU1121 5.0 61.1 1.0

Zinc binding site 4 out of 9 in 9j0o

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Zinc binding site 4 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:136.2
occ:1.00
 SG C:CYS94 2.3 49.7 1.0
SG C:CYS90 2.3 73.7 1.0
SG C:CYS88 2.3 64.0 1.0
SG C:CYS97 2.3 44.5 1.0
CB C:CYS88 3.3 64.0 1.0
CB C:CYS97 3.3 44.5 1.0
CB C:CYS90 3.4 73.7 1.0
CB C:CYS94 3.6 49.7 1.0
N C:CYS94 3.7 49.7 1.0
N C:CYS97 4.1 44.5 1.0
CA C:CYS94 4.2 49.7 1.0
CA C:CYS97 4.3 44.5 1.0
O C:CYS94 4.3 49.7 1.0
C C:CYS94 4.6 49.7 1.0
CA C:CYS88 4.6 64.0 1.0
O C:GLU92 4.6 63.4 1.0
CA C:CYS90 4.6 73.7 1.0
C C:GLU96 4.7 45.9 1.0
NZ Z:LYS718 4.7 62.3 1.0
C C:PHE93 4.8 52.2 1.0
N C:CYS90 4.8 73.7 1.0
CA C:PHE93 4.9 52.2 1.0
C C:CYS88 4.9 64.0 1.0
CB C:GLU96 5.0 45.9 1.0

Zinc binding site 5 out of 9 in 9j0o

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Zinc binding site 5 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:232.3
occ:1.00
 SG I:CYS20 2.3 170.1 1.0
SG I:CYS42 2.3 188.2 1.0
SG I:CYS39 2.3 180.8 1.0
SG I:CYS17 2.3 168.9 1.0
CB I:CYS39 3.0 180.8 1.0
CB I:CYS17 3.1 168.9 1.0
OE2 I:GLU19 3.8 173.0 1.0
CB I:CYS20 3.8 170.1 1.0
CB I:CYS42 4.0 188.2 1.0
CD I:GLU19 4.2 173.0 1.0
O I:CYS42 4.2 188.2 1.0
N I:CYS42 4.2 188.2 1.0
CA I:CYS39 4.5 180.8 1.0
CA I:CYS42 4.5 188.2 1.0
N I:CYS20 4.5 170.1 1.0
CB I:ASN22 4.5 164.1 1.0
CA I:CYS17 4.6 168.9 1.0
CG I:GLU19 4.6 173.0 1.0
C I:CYS42 4.7 188.2 1.0
CA I:CYS20 4.7 170.1 1.0
OE1 I:GLU19 4.8 173.0 1.0
CB I:TYR44 4.8 172.9 1.0
ND2 I:ASN22 4.9 164.1 1.0
C I:ASN41 4.9 182.3 1.0
N I:ASN41 5.0 182.3 1.0
CB I:ASN41 5.0 182.3 1.0

Zinc binding site 6 out of 9 in 9j0o

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Zinc binding site 6 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:198.4
occ:1.00
 SG I:CYS89 2.3 158.9 1.0
SG I:CYS119 2.3 157.5 1.0
SG I:CYS114 2.3 144.7 1.0
SG I:CYS86 2.3 158.3 1.0
CB I:CYS86 2.9 158.3 1.0
CB I:CYS114 3.1 144.7 1.0
CB I:CYS89 3.6 158.9 1.0
CB I:CYS119 3.7 157.5 1.0
N I:CYS89 4.4 158.9 1.0
CB I:HIS121 4.4 143.9 1.0
CA I:CYS86 4.4 158.3 1.0
CB I:ALA116 4.4 153.5 1.0
CB I:HIS91 4.5 150.3 1.0
CA I:CYS89 4.5 158.9 1.0
CA I:CYS114 4.6 144.7 1.0
ND1 I:HIS121 4.8 143.9 1.0
N I:HIS91 4.8 150.3 1.0
CG I:LYS88 4.9 162.5 1.0
C I:CYS89 5.0 158.9 1.0
N I:GLY90 5.0 155.6 1.0
NZ I:LYS88 5.0 162.5 1.0

Zinc binding site 7 out of 9 in 9j0o

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Zinc binding site 7 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:43.8
occ:1.00
 SG J:CYS10 2.3 40.2 1.0
SG J:CYS45 2.3 19.5 1.0
SG J:CYS44 2.3 20.8 1.0
SG J:CYS7 2.3 27.5 1.0
CB J:CYS7 3.1 27.5 1.0
N J:CYS45 3.2 19.5 1.0
CB J:CYS45 3.5 19.5 1.0
CA J:CYS45 3.5 19.5 1.0
CB J:CYS10 3.6 40.2 1.0
C J:CYS44 3.6 20.8 1.0
CB J:CYS44 3.6 20.8 1.0
N J:CYS10 3.9 40.2 1.0
O J:CYS44 4.1 20.8 1.0
NH2 J:ARG42 4.1 23.4 1.0
CA J:CYS44 4.2 20.8 1.0
CA J:CYS10 4.3 40.2 1.0
NE J:ARG42 4.5 23.4 1.0
CA J:CYS7 4.6 27.5 1.0
CB J:LYS12 4.7 31.5 1.0
CB J:THR9 4.8 31.6 1.0
N J:GLY11 4.8 64.3 1.0
CZ J:ARG42 4.8 23.4 1.0
N J:LYS12 4.9 31.5 1.0
N J:CYS44 5.0 20.8 1.0
C J:THR9 5.0 31.6 1.0

Zinc binding site 8 out of 9 in 9j0o

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Zinc binding site 8 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:158.5
occ:1.00
 SG L:CYS22 2.3 96.0 1.0
SG L:CYS19 2.3 84.9 1.0
SG L:CYS39 2.3 102.2 1.0
SG L:CYS36 2.3 97.5 1.0
CB L:CYS19 2.9 84.9 1.0
CB L:CYS36 3.1 97.5 1.0
CB L:CYS22 3.2 96.0 1.0
O L:GLU38 3.5 105.6 1.0
N L:CYS22 3.8 96.0 1.0
CA L:CYS22 4.1 96.0 1.0
CB L:CYS39 4.1 102.2 1.0
OG1 L:THR24 4.3 85.8 1.0
C L:GLU38 4.3 105.6 1.0
CB L:TYR41 4.3 83.7 1.0
CA L:CYS19 4.4 84.9 1.0
CG L:GLU38 4.5 105.6 1.0
CA L:CYS36 4.6 97.5 1.0
C L:CYS22 4.7 96.0 1.0
N L:HIS23 4.8 83.0 1.0
CD L:GLU38 4.9 105.6 1.0
N L:TYR41 5.0 83.7 1.0
CA L:CYS39 5.0 102.2 1.0

Zinc binding site 9 out of 9 in 9j0o

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Zinc binding site 9 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC1-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn201

b:297.3
occ:1.00
 SG Y:CYS36 2.3 261.4 1.0
SG Y:CYS33 2.3 260.1 1.0
SG Y:CYS19 2.3 254.6 1.0
SG Y:CYS16 2.3 256.5 1.0
CB Y:CYS19 3.1 254.6 1.0
CB Y:CYS36 3.4 261.4 1.0
CB Y:CYS16 3.5 256.5 1.0
CB Y:CYS33 3.5 260.1 1.0
N Y:CYS36 3.8 261.4 1.0
N Y:CYS19 4.1 254.6 1.0
CA Y:CYS19 4.2 254.6 1.0
CA Y:CYS36 4.2 261.4 1.0
C Y:ASN35 4.5 253.8 1.0
CE Y:MET42 4.7 261.5 1.0
N Y:ASN35 4.7 253.8 1.0
CB Y:ASN35 4.8 253.8 1.0
CA Y:CYS33 4.9 260.1 1.0
CA Y:ASN35 4.9 253.8 1.0
CA Y:CYS16 4.9 256.5 1.0
CB Y:LEU21 5.0 246.5 1.0

Reference:

M.Naganuma, T.Kujirai, H.Ehara, T.Uejima, T.Ito, M.Goto, M.Aoki, M.Henmi, S.Miyamoto-Kohno, M.Shirouzu, H.Kurumizaka, S.Sekine. Structural Insights Into Promoter-Proximal Pausing of Rna Polymerase II at +1 Nucleosome Sci Adv 2025.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADU0577
Page generated: Sun Feb 9 09:13:13 2025

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