Zinc in PDB 9j0p: Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-Nuc)

Enzymatic activity of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-Nuc)

All present enzymatic activity of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-Nuc):
2.7.7.6;

Other elements in 9j0p:

The structure of Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) (pdb code 9j0p). 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 (AEC2-Nuc), PDB code: 9j0p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9j0p

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Zinc binding site 1 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:47.3
occ:1.00
 NE2 A:HIS84 2.1 30.4 1.0
SG A:CYS81 2.3 36.7 1.0
SG A:CYS74 2.3 48.5 1.0
SG A:CYS71 2.3 48.0 1.0
CD2 A:HIS84 2.8 30.4 1.0
CB A:CYS71 3.0 48.0 1.0
CE1 A:HIS84 3.2 30.4 1.0
O A:PRO82 3.7 30.4 1.0
CB A:CYS81 3.8 36.7 1.0
O A:CYS74 3.9 48.5 1.0
CB A:CYS74 3.9 48.5 1.0
N A:CYS74 4.0 48.5 1.0
CG A:HIS84 4.0 30.4 1.0
ND1 A:HIS84 4.2 30.4 1.0
CA A:CYS74 4.3 48.5 1.0
CA A:CYS71 4.5 48.0 1.0
CA A:CYS81 4.5 36.7 1.0
C A:CYS74 4.6 48.5 1.0
CA A:GLY63 4.6 44.1 1.0
CB A:THR73 4.7 43.6 1.0
O A:GLN62 4.7 37.2 1.0
C A:CYS81 4.8 36.7 1.0
C A:PRO82 4.9 30.4 1.0
C A:THR73 4.9 43.6 1.0
C A:CYS71 5.0 48.0 1.0

Zinc binding site 2 out of 9 in 9j0p

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Zinc binding site 2 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:204.0
occ:1.00
 SG A:CYS184 2.3 169.7 1.0
SG A:CYS114 2.3 112.3 1.0
SG A:CYS111 2.3 113.2 1.0
CB A:CYS114 3.1 112.3 1.0
CD1 A:TYR187 3.4 146.2 1.0
CB A:CYS111 3.7 113.2 1.0
CE1 A:TYR187 3.9 146.2 1.0
NZ A:LYS116 4.0 114.0 1.0
CB A:CYS184 4.0 169.7 1.0
O A:PHE112 4.3 106.3 1.0
N A:CYS184 4.3 169.7 1.0
CG A:TYR187 4.4 146.2 1.0
N A:GLY185 4.5 162.4 1.0
CA A:TYR187 4.5 146.2 1.0
CA A:CYS114 4.5 112.3 1.0
CA A:CYS184 4.7 169.7 1.0
CB A:TYR187 4.7 146.2 1.0
O A:GLY185 4.7 162.4 1.0
CE A:LYS116 4.7 114.0 1.0
N A:CYS114 4.9 112.3 1.0
O A:GLY182 4.9 156.0 1.0

Zinc binding site 3 out of 9 in 9j0p

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Zinc binding site 3 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:129.9
occ:1.00
 SG B:CYS1122 2.3 51.8 1.0
SG B:CYS1137 2.3 73.9 1.0
SG B:CYS1140 2.3 88.3 1.0
SG B:CYS1119 2.3 54.2 1.0
CB B:CYS1119 2.9 54.2 1.0
CB B:CYS1140 3.2 88.3 1.0
CB B:CYS1137 3.4 73.9 1.0
CB B:CYS1122 3.7 51.8 1.0
N B:CYS1122 3.9 51.8 1.0
O B:CYS1122 4.2 51.8 1.0
CA B:CYS1122 4.3 51.8 1.0
CE A:MET34 4.3 47.9 1.0
CA B:CYS1119 4.4 54.2 1.0
CA B:CYS1140 4.5 88.3 1.0
CB B:LEU1121 4.6 58.5 1.0
N B:CYS1140 4.6 88.3 1.0
C B:CYS1122 4.7 51.8 1.0
CA B:CYS1137 4.8 73.9 1.0
C B:LEU1121 4.9 58.5 1.0
O B:ARG1138 5.0 66.4 1.0

Zinc binding site 4 out of 9 in 9j0p

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Zinc binding site 4 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:115.6
occ:1.00
 SG C:CYS94 2.3 43.4 1.0
SG C:CYS88 2.3 62.0 1.0
SG C:CYS97 2.3 38.0 1.0
SG C:CYS90 2.3 73.0 1.0
CB C:CYS88 3.3 62.0 1.0
CB C:CYS97 3.4 38.0 1.0
CB C:CYS90 3.5 73.0 1.0
CB C:CYS94 3.6 43.4 1.0
N C:CYS94 3.8 43.4 1.0
N C:CYS97 4.1 38.0 1.0
CA C:CYS94 4.2 43.4 1.0
O C:CYS94 4.3 43.4 1.0
CA C:CYS97 4.4 38.0 1.0
C C:CYS94 4.6 43.4 1.0
CA C:CYS88 4.6 62.0 1.0
C C:GLU96 4.7 42.4 1.0
O C:GLU92 4.7 61.2 1.0
CA C:CYS90 4.7 73.0 1.0
C C:CYS88 4.7 62.0 1.0
O C:CYS88 4.8 62.0 1.0
CB C:GLU96 4.8 42.4 1.0
C C:PHE93 4.9 48.9 1.0
N C:CYS90 4.9 73.0 1.0

Zinc binding site 5 out of 9 in 9j0p

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Zinc binding site 5 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:231.9
occ:1.00
 SG I:CYS20 2.3 158.9 1.0
SG I:CYS42 2.3 174.8 1.0
SG I:CYS39 2.3 175.7 1.0
SG I:CYS17 2.3 159.5 1.0
CB I:CYS39 3.1 175.7 1.0
CB I:CYS17 3.3 159.5 1.0
CB I:CYS20 3.8 158.9 1.0
CB I:CYS42 4.0 174.8 1.0
CG I:GLU19 4.1 164.3 1.0
N I:CYS42 4.2 174.8 1.0
N I:CYS20 4.3 158.9 1.0
O I:CYS42 4.5 174.8 1.0
OE2 I:GLU19 4.5 164.3 1.0
CA I:CYS20 4.6 158.9 1.0
CA I:CYS42 4.6 174.8 1.0
CB I:ASN22 4.6 148.7 1.0
CA I:CYS39 4.6 175.7 1.0
CA I:CYS17 4.7 159.5 1.0
ND2 I:ASN22 4.8 148.7 1.0
CD I:GLU19 4.8 164.3 1.0
C I:CYS42 4.9 174.8 1.0
CB I:TYR44 5.0 166.6 1.0
N I:ARG40 5.0 170.5 1.0

Zinc binding site 6 out of 9 in 9j0p

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Zinc binding site 6 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:199.3
occ:1.00
 SG I:CYS89 2.3 148.8 1.0
SG I:CYS114 2.3 127.6 1.0
SG I:CYS86 2.3 145.3 1.0
SG I:CYS119 2.3 143.1 1.0
CB I:CYS86 2.9 145.3 1.0
CB I:CYS114 3.3 127.6 1.0
CB I:CYS89 3.6 148.8 1.0
CB I:CYS119 3.7 143.1 1.0
CB I:HIS121 4.1 135.4 1.0
NZ I:LYS88 4.2 149.0 1.0
N I:CYS89 4.4 148.8 1.0
CA I:CYS86 4.4 145.3 1.0
CB I:ALA116 4.5 137.8 1.0
CA I:CYS89 4.5 148.8 1.0
ND1 I:HIS121 4.6 135.4 1.0
CG I:LYS88 4.7 149.0 1.0
CE I:LYS88 4.7 149.0 1.0
CA I:CYS114 4.8 127.6 1.0
CG I:HIS121 4.8 135.4 1.0
CB I:HIS91 4.9 142.7 1.0
ND1 I:HIS91 5.0 142.7 1.0

Zinc binding site 7 out of 9 in 9j0p

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Zinc binding site 7 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:22.7
occ:1.00
 SG J:CYS10 2.3 15.6 1.0
SG J:CYS45 2.3 14.7 1.0
SG J:CYS44 2.3 14.3 1.0
SG J:CYS7 2.3 13.5 1.0
CB J:CYS7 3.2 13.5 1.0
N J:CYS45 3.2 14.7 1.0
CB J:CYS45 3.5 14.7 1.0
CB J:CYS10 3.6 15.6 1.0
CA J:CYS45 3.6 14.7 1.0
CB J:CYS44 3.7 14.3 1.0
C J:CYS44 3.7 14.3 1.0
N J:CYS10 3.9 15.6 1.0
O J:CYS44 4.2 14.3 1.0
CA J:CYS10 4.3 15.6 1.0
NE J:ARG42 4.3 16.8 1.0
CA J:CYS44 4.3 14.3 1.0
NH2 J:ARG42 4.5 16.8 1.0
CA J:CYS7 4.6 13.5 1.0
N J:GLY11 4.7 14.3 1.0
CB J:THR9 4.7 13.8 1.0
CB J:LYS12 4.8 13.1 1.0
N J:LYS12 4.9 13.1 1.0
CZ J:ARG42 4.9 16.8 1.0
C J:THR9 4.9 13.8 1.0
C J:CYS10 4.9 15.6 1.0
N J:THR9 5.0 13.8 1.0

Zinc binding site 8 out of 9 in 9j0p

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Zinc binding site 8 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:144.1
occ:1.00
 SG L:CYS22 2.3 79.7 1.0
SG L:CYS19 2.3 74.6 1.0
SG L:CYS36 2.3 90.4 1.0
SG L:CYS39 2.3 99.9 1.0
CB L:CYS19 3.0 74.6 1.0
CB L:CYS36 3.2 90.4 1.0
CB L:CYS22 3.3 79.7 1.0
O L:GLU38 3.5 96.7 1.0
N L:CYS22 3.7 79.7 1.0
CA L:CYS22 4.1 79.7 1.0
CB L:CYS39 4.1 99.9 1.0
OG1 L:THR24 4.2 75.4 1.0
C L:GLU38 4.3 96.7 1.0
CB L:TYR41 4.4 72.9 1.0
CG L:GLU38 4.4 96.7 1.0
CA L:CYS19 4.5 74.6 1.0
CA L:CYS36 4.7 90.4 1.0
C L:CYS22 4.7 79.7 1.0
CB L:GLU21 4.8 79.2 1.0
N L:HIS23 4.8 72.4 1.0
C L:GLU21 4.9 79.2 1.0
CD L:GLU38 4.9 96.7 1.0
N L:GLU21 5.0 79.2 1.0
CA L:CYS39 5.0 99.9 1.0

Zinc binding site 9 out of 9 in 9j0p

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Zinc binding site 9 out of 9 in the Arrested Elongation Complex of Mammalian Rna Polymerase II with Nucleosome (AEC2-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 (AEC2-Nuc) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn201

b:256.4
occ:1.00
 SG Y:CYS36 2.3 218.7 1.0
SG Y:CYS19 2.3 224.1 1.0
SG Y:CYS33 2.3 218.0 1.0
SG Y:CYS16 2.3 224.4 1.0
CB Y:CYS19 3.1 224.1 1.0
CB Y:CYS36 3.4 218.7 1.0
CB Y:CYS16 3.7 224.4 1.0
CB Y:CYS33 3.7 218.0 1.0
N Y:CYS19 3.8 224.1 1.0
N Y:CYS36 3.8 218.7 1.0
CA Y:CYS19 4.1 224.1 1.0
CB Y:LEU18 4.2 227.4 1.0
CA Y:CYS36 4.2 218.7 1.0
C Y:LEU18 4.3 227.4 1.0
C Y:ASN35 4.5 214.1 1.0
CB Y:ASN35 4.5 214.1 1.0
CA Y:LEU18 4.7 227.4 1.0
N Y:LEU18 4.8 227.4 1.0
CA Y:ASN35 4.9 214.1 1.0
N Y:ASN35 4.9 214.1 1.0
CG Y:LEU18 5.0 227.4 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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