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Zinc in PDB 8jh3: Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome

Enzymatic activity of Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome

All present enzymatic activity of Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome:
2.7.7.6;

Other elements in 8jh3:

The structure of Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome (pdb code 8jh3). 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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome, PDB code: 8jh3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8jh3

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:103.4
occ:1.00
 NE2 A:HIS80 2.1 34.7 1.0
SG A:CYS70 2.3 49.1 1.0
SG A:CYS67 2.3 56.6 1.0
SG A:CYS77 2.3 40.9 1.0
CD2 A:HIS80 2.8 34.7 1.0
CB A:CYS67 2.9 56.6 1.0
CE1 A:HIS80 3.2 34.7 1.0
CB A:CYS70 3.4 49.1 1.0
CB A:CYS77 3.5 40.9 1.0
N A:CYS70 3.8 49.1 1.0
CG A:HIS80 4.0 34.7 1.0
CA A:CYS70 4.2 49.1 1.0
ND1 A:HIS80 4.2 34.7 1.0
CA A:CYS77 4.2 40.9 1.0
CA A:GLY59 4.4 45.9 1.0
CA A:CYS67 4.4 56.6 1.0
CB A:THR69 4.7 45.5 1.0
N A:GLY79 4.7 38.1 1.0
CD A:PRO78 4.8 36.3 1.0
C A:CYS77 4.8 40.9 1.0
C A:THR69 4.8 45.5 1.0
C A:CYS70 4.9 49.1 1.0
N A:GLY71 4.9 55.3 1.0
N A:PRO78 4.9 36.3 1.0

Zinc binding site 2 out of 8 in 8jh3

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:115.7
occ:1.00
 SG A:CYS148 2.3 102.8 1.0
SG A:CYS107 2.3 95.2 1.0
SG A:CYS110 2.3 92.3 1.0
SG A:CYS168 2.3 90.4 1.0
CB A:CYS148 2.6 102.8 1.0
CB A:CYS107 3.4 95.2 1.0
CB A:CYS168 3.6 90.4 1.0
CB A:CYS110 3.6 92.3 1.0
N A:CYS168 4.0 90.4 1.0
CA A:CYS148 4.1 102.8 1.0
N A:CYS110 4.3 92.3 1.0
CA A:CYS168 4.4 90.4 1.0
O A:CYS148 4.5 102.8 1.0
CA A:CYS110 4.5 92.3 1.0
N A:GLY169 4.6 91.8 1.0
C A:CYS148 4.8 102.8 1.0
CA A:CYS107 4.8 95.2 1.0
N A:CYS148 4.9 102.8 1.0
CB A:LYS112 4.9 83.8 1.0
C A:GLY167 5.0 93.0 1.0

Zinc binding site 3 out of 8 in 8jh3

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:129.1
occ:1.00
 SG B:CYS1182 2.3 71.6 1.0
SG B:CYS1166 2.3 53.4 1.0
SG B:CYS1163 2.3 50.4 1.0
SG B:CYS1185 2.3 76.3 1.0
CB B:CYS1166 2.8 53.4 1.0
CB B:CYS1163 3.0 50.4 1.0
CB B:CYS1185 3.3 76.3 1.0
CB B:CYS1182 3.5 71.6 1.0
N B:CYS1166 3.5 53.4 1.0
CA B:CYS1166 3.7 53.4 1.0
N B:CYS1185 4.1 76.3 1.0
CA B:CYS1185 4.4 76.3 1.0
CA B:CYS1163 4.5 50.4 1.0
C B:CYS1166 4.5 53.4 1.0
C B:ILE1165 4.6 61.8 1.0
N B:GLY1167 4.7 41.3 1.0
CB B:ILE1165 4.7 61.8 1.0
CA B:CYS1182 4.8 71.6 1.0
CG2 B:ILE1165 5.0 61.8 1.0

Zinc binding site 4 out of 8 in 8jh3

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:184.4
occ:1.00
 SG C:CYS87 2.3 103.1 1.0
SG C:CYS94 2.3 63.8 1.0
SG C:CYS85 2.3 93.3 1.0
SG C:CYS91 2.3 86.3 1.0
CB C:CYS85 3.0 93.3 1.0
N C:CYS91 3.2 86.3 1.0
CB C:CYS87 3.3 103.1 1.0
CB C:CYS91 3.4 86.3 1.0
CB C:CYS94 3.5 63.8 1.0
CA C:CYS91 3.8 86.3 1.0
N C:CYS94 4.2 63.8 1.0
C C:TYR90 4.2 90.3 1.0
CA C:TYR90 4.3 90.3 1.0
CA C:CYS94 4.4 63.8 1.0
O C:CYS91 4.4 86.3 1.0
C C:CYS91 4.4 86.3 1.0
N C:CYS87 4.5 103.1 1.0
CA C:CYS85 4.5 93.3 1.0
CA C:CYS87 4.5 103.1 1.0
O C:ASP89 4.5 111.7 1.0
C C:CYS85 4.9 93.3 1.0

Zinc binding site 5 out of 8 in 8jh3

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:167.3
occ:1.00
 SG I:CYS75 2.3 108.8 1.0
SG I:CYS106 2.3 105.8 1.0
SG I:CYS78 2.3 110.0 1.0
SG I:CYS103 2.3 98.4 1.0
CB I:CYS103 3.1 98.4 1.0
CB I:CYS75 3.2 108.8 1.0
N I:CYS106 3.6 105.8 1.0
CB I:CYS106 3.6 105.8 1.0
OG I:SER80 3.8 104.4 1.0
CB I:CYS78 3.9 110.0 1.0
CB I:ASN105 3.9 100.6 1.0
N I:CYS78 4.0 110.0 1.0
CB I:SER80 4.1 104.4 1.0
CA I:CYS106 4.2 105.8 1.0
CB I:GLU77 4.3 107.0 1.0
CA I:CYS78 4.5 110.0 1.0
C I:ASN105 4.6 100.6 1.0
CA I:ASN105 4.6 100.6 1.0
CA I:CYS103 4.6 98.4 1.0
N I:ASN105 4.6 100.6 1.0
CA I:CYS75 4.6 108.8 1.0
N I:SER80 4.8 104.4 1.0
CG I:ASN105 4.9 100.6 1.0
OD1 I:ASN105 4.9 100.6 1.0
C I:CYS78 4.9 110.0 1.0
C I:GLU77 4.9 107.0 1.0
CA I:GLU77 5.0 107.0 1.0

Zinc binding site 6 out of 8 in 8jh3

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:138.1
occ:1.00
 SG I:CYS7 2.3 111.9 1.0
SG I:CYS29 2.3 110.4 1.0
SG I:CYS32 2.3 117.2 1.0
CB I:CYS10 2.5 115.5 1.0
CB I:CYS7 3.1 111.9 1.0
N I:CYS10 3.3 115.5 1.0
CB I:CYS32 3.4 117.2 1.0
CA I:CYS10 3.4 115.5 1.0
CB I:CYS29 3.5 110.4 1.0
SG I:CYS10 3.8 115.5 1.0
N I:CYS32 3.9 117.2 1.0
C I:CYS10 4.2 115.5 1.0
CA I:CYS32 4.2 117.2 1.0
N I:ASN11 4.5 105.1 1.0
CB I:ASN31 4.5 106.9 1.0
C I:GLU9 4.6 112.9 1.0
CA I:CYS7 4.6 111.9 1.0
N I:ASN12 4.7 106.8 1.0
CA I:CYS29 4.8 110.4 1.0
CB I:GLU9 4.8 112.9 1.0
C I:ASN31 4.9 106.9 1.0
CB I:ASN12 5.0 106.8 1.0

Zinc binding site 7 out of 8 in 8jh3

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:34.8
occ:1.00
 SG J:CYS10 2.3 17.5 1.0
SG J:CYS45 2.3 21.1 1.0
SG J:CYS44 2.3 28.2 1.0
SG J:CYS7 2.3 20.3 1.0
N J:CYS45 3.1 21.1 1.0
CB J:CYS7 3.2 20.3 1.0
CB J:CYS45 3.5 21.1 1.0
CB J:CYS44 3.5 28.2 1.0
CA J:CYS45 3.5 21.1 1.0
CB J:CYS10 3.6 17.5 1.0
C J:CYS44 3.8 28.2 1.0
N J:CYS10 4.0 17.5 1.0
NE J:ARG42 4.2 27.7 1.0
CA J:CYS44 4.3 28.2 1.0
CA J:CYS10 4.4 17.5 1.0
NH1 J:ARG42 4.5 27.7 1.0
O J:CYS44 4.5 28.2 1.0
CB J:LYS12 4.7 17.6 1.0
CA J:CYS7 4.7 20.3 1.0
N J:GLY11 4.7 16.7 1.0
CB J:SER9 4.8 19.0 1.0
CB J:ARG42 4.8 27.7 1.0
CZ J:ARG42 4.8 27.7 1.0
N J:LYS12 4.9 17.6 1.0
N J:CYS44 4.9 28.2 1.0
C J:CYS10 5.0 17.5 1.0

Zinc binding site 8 out of 8 in 8jh3

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


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 Elongation Complex Containing 40 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:151.4
occ:1.00
 SG L:CYS53 2.3 90.5 1.0
SG L:CYS36 2.3 85.3 1.0
SG L:CYS33 2.3 71.0 1.0
SG L:CYS50 2.3 79.6 1.0
CB L:CYS33 2.9 71.0 1.0
CB L:CYS50 3.3 79.6 1.0
CB L:CYS36 3.3 85.3 1.0
N L:CYS36 3.6 85.3 1.0
CB L:CYS53 3.8 90.5 1.0
N L:CYS53 3.9 90.5 1.0
CA L:CYS36 3.9 85.3 1.0
CB L:HIS38 4.3 78.0 1.0
CA L:CYS33 4.4 71.0 1.0
C L:CYS36 4.4 85.3 1.0
CA L:CYS53 4.4 90.5 1.0
CB L:GLU52 4.5 96.6 1.0
CB L:HIS55 4.5 69.2 1.0
N L:HIS38 4.6 78.0 1.0
N L:ALA37 4.6 81.3 1.0
C L:ALA35 4.7 75.9 1.0
CA L:CYS50 4.7 79.6 1.0
CB L:ALA35 4.7 75.9 1.0
N L:GLY54 4.8 80.1 1.0
N L:ALA35 4.8 75.9 1.0
N L:GLU52 4.8 96.6 1.0
N L:HIS55 4.8 69.2 1.0
C L:GLU52 4.9 96.6 1.0
CA L:ALA35 5.0 75.9 1.0
CA L:GLU52 5.0 96.6 1.0

Reference:

M.Akatsu, H.Ehara, T.Kujirai, R.Fujita, T.Ito, K.Osumi, M.Ogasawara, Y.Takizawa, S.I.Sekine, H.Kurumizaka. Cryo-Em Structures of Rna Polymerase II-Nucleosome Complexes Rewrapping Transcribed Dna J.Biol.Chem. 05477 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.105477
Page generated: Thu Oct 31 08:16:46 2024

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