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Zinc in PDB 9j0n: Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)

Enzymatic activity of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)

All present enzymatic activity of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc):
2.7.7.6;

Other elements in 9j0n:

The structure of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) (pdb code 9j0n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc), PDB code: 9j0n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9j0n

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Zinc binding site 1 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:91.4
occ:1.00
 NE2 A:HIS84 2.1 66.3 1.0
SG A:CYS74 2.3 93.0 1.0
SG A:CYS81 2.3 74.3 1.0
SG A:CYS71 2.3 86.4 1.0
CB A:CYS71 2.7 86.4 1.0
CB A:CYS81 2.9 74.3 1.0
CD2 A:HIS84 2.9 66.3 1.0
CE1 A:HIS84 3.1 66.3 1.0
O A:PRO82 3.4 62.1 1.0
O A:CYS74 3.6 93.0 1.0
OG1 A:THR73 3.9 83.9 1.0
CB A:CYS74 4.0 93.0 1.0
CA A:GLY63 4.1 78.8 1.0
CG A:HIS84 4.1 66.3 1.0
ND1 A:HIS84 4.2 66.3 1.0
CA A:CYS81 4.2 74.3 1.0
CA A:CYS71 4.2 86.4 1.0
N A:CYS74 4.2 93.0 1.0
C A:CYS81 4.4 74.3 1.0
CA A:CYS74 4.5 93.0 1.0
C A:CYS74 4.5 93.0 1.0
N A:GLY63 4.6 78.8 1.0
C A:PRO82 4.6 62.1 1.0
N A:PRO82 4.7 62.1 1.0
O A:CYS81 4.7 74.3 1.0
N A:VAL64 4.8 79.5 1.0
C A:CYS71 4.8 86.4 1.0
C A:GLY63 4.9 78.8 1.0
N A:CYS71 5.0 86.4 1.0

Zinc binding site 2 out of 9 in 9j0n

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Zinc binding site 2 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:229.8
occ:1.00
 CB A:CYS114 2.2 163.2 1.0
SG A:CYS111 2.3 165.3 1.0
SG A:CYS184 2.3 196.5 1.0
SG A:CYS114 2.3 163.2 1.0
O A:GLY182 3.2 187.8 1.0
CE1 A:TYR187 3.4 195.1 1.0
CB A:CYS184 3.5 196.5 1.0
CD1 A:TYR187 3.5 195.1 1.0
CB A:CYS111 3.6 165.3 1.0
CA A:CYS114 3.7 163.2 1.0
N A:CYS184 3.9 196.5 1.0
C A:GLY182 4.0 187.8 1.0
CA A:CYS184 4.3 196.5 1.0
N A:CYS114 4.4 163.2 1.0
C A:CYS114 4.5 163.2 1.0
CA A:GLY182 4.6 187.8 1.0
CZ A:TYR187 4.7 195.1 1.0
O A:PHE112 4.7 158.2 1.0
CG A:TYR187 4.9 195.1 1.0
O A:CYS114 4.9 163.2 1.0
CB A:LYS116 4.9 159.1 1.0
CA A:CYS111 4.9 165.3 1.0
CG A:LYS116 5.0 159.1 1.0
N A:GLY183 5.0 192.6 1.0

Zinc binding site 3 out of 9 in 9j0n

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Zinc binding site 3 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:111.5
occ:1.00
 SG B:CYS1137 2.3 119.6 1.0
SG B:CYS1122 2.3 88.2 1.0
SG B:CYS1140 2.3 118.2 1.0
SG B:CYS1119 2.3 86.9 1.0
CB B:CYS1119 2.8 86.9 1.0
CB B:CYS1122 3.1 88.2 1.0
CB B:CYS1140 3.1 118.2 1.0
N B:CYS1122 3.4 88.2 1.0
CB B:CYS1137 3.4 119.6 1.0
CE A:MET34 3.6 85.5 1.0
CA B:CYS1122 3.7 88.2 1.0
O B:CYS1122 4.2 88.2 1.0
C B:CYS1122 4.2 88.2 1.0
CA B:CYS1119 4.3 86.9 1.0
CB B:LEU1121 4.4 94.8 1.0
C B:LEU1121 4.5 94.8 1.0
CA B:CYS1140 4.5 118.2 1.0
SD A:MET34 4.6 85.5 1.0
N B:LEU1121 4.7 94.8 1.0
CA B:CYS1137 4.7 119.6 1.0
CA B:LEU1121 4.8 94.8 1.0
C B:CYS1119 4.9 86.9 1.0
N B:CYS1140 4.9 118.2 1.0
O B:CYS1137 5.0 119.6 1.0
CG B:LEU1121 5.0 94.8 1.0

Zinc binding site 4 out of 9 in 9j0n

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Zinc binding site 4 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:156.1
occ:1.00
 SG C:CYS90 2.3 107.8 1.0
SG C:CYS94 2.3 68.6 1.0
SG C:CYS88 2.3 90.4 1.0
SG C:CYS97 2.3 60.2 1.0
CB C:CYS97 3.1 60.2 1.0
CB C:CYS88 3.2 90.4 1.0
CB C:CYS90 3.2 107.8 1.0
CB C:CYS94 3.6 68.6 1.0
N C:CYS97 3.9 60.2 1.0
N C:CYS94 4.0 68.6 1.0
CA C:CYS97 4.1 60.2 1.0
O C:CYS94 4.3 68.6 1.0
CA C:CYS94 4.3 68.6 1.0
CA C:CYS90 4.4 107.8 1.0
N C:CYS90 4.4 107.8 1.0
CA C:CYS88 4.5 90.4 1.0
C C:CYS94 4.6 68.6 1.0
C C:GLU96 4.6 63.7 1.0
NZ Z:LYS718 4.6 101.7 1.0
CB C:GLU96 4.7 63.7 1.0
C C:CYS88 4.9 90.4 1.0
C C:CYS97 5.0 60.2 1.0
C C:PHE93 5.0 80.6 1.0

Zinc binding site 5 out of 9 in 9j0n

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Zinc binding site 5 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:218.1
occ:1.00
 SG I:CYS17 2.3 170.6 1.0
SG I:CYS39 2.3 177.5 1.0
SG I:CYS42 2.3 177.2 1.0
SG I:CYS20 2.3 177.3 1.0
CB I:CYS39 3.2 177.5 1.0
CB I:CYS17 3.4 170.6 1.0
CB I:CYS20 3.8 177.3 1.0
N I:CYS20 4.0 177.3 1.0
CB I:CYS42 4.0 177.2 1.0
N I:CYS42 4.1 177.2 1.0
CA I:CYS20 4.4 177.3 1.0
CB I:ASN22 4.4 164.2 1.0
CB I:ASN41 4.5 177.0 1.0
CB I:GLU19 4.5 176.0 1.0
N I:ASN41 4.5 177.0 1.0
C I:ASN41 4.6 177.0 1.0
CA I:CYS42 4.6 177.2 1.0
CA I:CYS39 4.7 177.5 1.0
ND2 I:ASN22 4.7 164.2 1.0
CA I:ASN41 4.8 177.0 1.0
O I:CYS42 4.8 177.2 1.0
CA I:CYS17 4.8 170.6 1.0
N I:ARG40 4.9 171.2 1.0
C I:CYS20 4.9 177.3 1.0

Zinc binding site 6 out of 9 in 9j0n

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Zinc binding site 6 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:229.2
occ:1.00
 SG I:CYS89 2.3 188.7 1.0
SG I:CYS86 2.3 185.4 1.0
SG I:CYS119 2.3 185.1 1.0
SG I:CYS114 2.3 176.2 1.0
CB I:CYS86 2.9 185.4 1.0
CB I:CYS114 3.1 176.2 1.0
CB I:CYS119 3.7 185.1 1.0
CB I:CYS89 3.8 188.7 1.0
CB I:HIS121 4.1 176.2 1.0
CB I:HIS91 4.2 181.8 1.0
CB I:ALA116 4.3 185.9 1.0
CA I:CYS86 4.4 185.4 1.0
N I:CYS89 4.5 188.7 1.0
ND1 I:HIS121 4.5 176.2 1.0
CA I:CYS114 4.6 176.2 1.0
CA I:CYS89 4.7 188.7 1.0
N I:HIS91 4.7 181.8 1.0
CG I:HIS121 4.8 176.2 1.0

Zinc binding site 7 out of 9 in 9j0n

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Zinc binding site 7 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn201

b:321.6
occ:1.00
 SG Y:CYS33 2.3 294.0 1.0
SG Y:CYS19 2.3 281.4 1.0
SG Y:CYS36 2.3 290.8 1.0
SG Y:CYS16 2.3 285.3 1.0
CB Y:CYS16 3.3 285.3 1.0
CB Y:CYS36 3.6 290.8 1.0
CB Y:CYS19 3.6 281.4 1.0
N Y:CYS19 3.8 281.4 1.0
CB Y:CYS33 3.8 294.0 1.0
CB Y:LEU18 4.2 286.3 1.0
N Y:CYS36 4.3 290.8 1.0
CA Y:CYS19 4.3 281.4 1.0
CB Y:ASN35 4.3 284.7 1.0
C Y:LEU18 4.5 286.3 1.0
C Y:ASN35 4.6 284.7 1.0
CA Y:CYS36 4.6 290.8 1.0
CA Y:CYS16 4.7 285.3 1.0
CA Y:LEU18 4.7 286.3 1.0
CB Y:LEU21 4.8 273.6 1.0
N Y:LEU18 4.8 286.3 1.0
CA Y:ASN35 4.9 284.7 1.0
C Y:CYS19 4.9 281.4 1.0

Zinc binding site 8 out of 9 in 9j0n

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Zinc binding site 8 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:51.4
occ:1.00
 SG J:CYS45 2.3 29.1 1.0
SG J:CYS10 2.3 29.9 1.0
SG J:CYS44 2.3 32.7 1.0
SG J:CYS7 2.3 23.4 1.0
N J:CYS45 3.3 29.1 1.0
CB J:CYS7 3.3 23.4 1.0
CB J:CYS10 3.4 29.9 1.0
CB J:CYS45 3.5 29.1 1.0
CA J:CYS45 3.6 29.1 1.0
C J:CYS44 3.7 32.7 1.0
CB J:CYS44 3.8 32.7 1.0
N J:CYS10 3.8 29.9 1.0
CA J:CYS10 4.2 29.9 1.0
O J:CYS44 4.2 32.7 1.0
CA J:CYS44 4.4 32.7 1.0
NE J:ARG42 4.5 35.3 1.0
NH2 J:ARG42 4.5 35.3 1.0
CB J:LYS12 4.6 29.1 1.0
N J:GLY11 4.6 28.7 1.0
CA J:CYS7 4.7 23.4 1.0
N J:LYS12 4.8 29.1 1.0
CB J:THR9 4.8 29.1 1.0
C J:CYS10 4.9 29.9 1.0
C J:THR9 4.9 29.1 1.0
CZ J:ARG42 5.0 35.3 1.0

Zinc binding site 9 out of 9 in 9j0n

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Zinc binding site 9 out of 9 in the Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Paused Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (PEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:248.4
occ:1.00
 SG L:CYS22 2.3 171.7 1.0
SG L:CYS19 2.3 158.1 1.0
SG L:CYS39 2.3 192.1 1.0
SG L:CYS36 2.3 183.1 1.0
CB L:CYS19 3.0 158.1 1.0
CB L:CYS36 3.1 183.1 1.0
O L:GLU38 3.6 196.0 1.0
CB L:CYS22 3.6 171.7 1.0
CB L:CYS39 4.0 192.1 1.0
OE2 L:GLU21 4.3 169.1 1.0
N L:CYS22 4.3 171.7 1.0
CB L:TYR41 4.3 156.7 1.0
C L:GLU38 4.4 196.0 1.0
CA L:CYS19 4.5 158.1 1.0
CA L:CYS22 4.5 171.7 1.0
OE1 L:GLU38 4.5 196.0 1.0
CG L:GLU38 4.5 196.0 1.0
CD L:GLU38 4.5 196.0 1.0
CA L:CYS36 4.6 183.1 1.0
N L:TYR41 4.8 156.7 1.0
ND2 L:ASN26 4.9 177.6 1.0
N L:HIS23 4.9 157.3 1.0
CG L:GLU21 4.9 169.1 1.0
CA L:CYS39 5.0 192.1 1.0
C L:CYS22 5.0 171.7 1.0
CD L:GLU21 5.0 169.1 1.0
CB L:THR24 5.0 172.2 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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