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Zinc in PDB 8jh2: Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome

Enzymatic activity of Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome

All present enzymatic activity of Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome:
2.7.7.6;

Other elements in 8jh2:

The structure of Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome (pdb code 8jh2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome, PDB code: 8jh2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8jh2

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Zinc binding site 1 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:96.9
occ:1.00
 NE2 A:HIS80 2.1 61.9 1.0
SG A:CYS77 2.3 74.5 1.0
SG A:CYS67 2.3 103.2 1.0
SG A:CYS70 2.3 94.7 1.0
CE1 A:HIS80 2.8 61.9 1.0
CB A:CYS67 3.0 103.2 1.0
CD2 A:HIS80 3.2 61.9 1.0
CB A:CYS70 3.4 94.7 1.0
CB A:CYS77 3.5 74.5 1.0
N A:CYS70 3.8 94.7 1.0
ND1 A:HIS80 4.0 61.9 1.0
CA A:CYS70 4.2 94.7 1.0
CG A:HIS80 4.2 61.9 1.0
CA A:CYS77 4.4 74.5 1.0
CA A:CYS67 4.5 103.2 1.0
CB A:THR69 4.6 85.3 1.0
C A:THR69 4.8 85.3 1.0
N A:GLY71 4.8 107.2 1.0
C A:CYS70 4.9 94.7 1.0

Zinc binding site 2 out of 10 in 8jh2

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Zinc binding site 2 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:197.5
occ:1.00
 SG A:CYS107 2.3 142.7 1.0
SG A:CYS168 2.3 155.4 1.0
SG A:CYS110 2.3 152.4 1.0
CB A:CYS168 2.7 155.4 1.0
N A:CYS168 3.2 155.4 1.0
CB A:CYS110 3.2 152.4 1.0
N A:CYS110 3.3 152.4 1.0
CB A:CYS107 3.3 142.7 1.0
CA A:CYS168 3.5 155.4 1.0
CA A:CYS110 3.9 152.4 1.0
CB A:ASN109 3.9 151.4 1.0
C A:GLY167 4.0 147.2 1.0
C A:ASN109 4.3 151.4 1.0
SG A:CYS148 4.3 152.7 1.0
N A:ASN109 4.4 151.4 1.0
CA A:GLY167 4.4 147.2 1.0
CA A:ASN109 4.4 151.4 1.0
C A:CYS168 4.6 155.4 1.0
N A:GLY111 4.7 142.2 1.0
CA A:CYS107 4.7 142.7 1.0
C A:CYS110 4.8 152.4 1.0
N A:GLY169 4.9 152.9 1.0
CG A:ASN109 4.9 151.4 1.0
O A:GLY167 4.9 147.2 1.0
CB A:CYS148 5.0 152.7 1.0

Zinc binding site 3 out of 10 in 8jh2

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Zinc binding site 3 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:123.8
occ:1.00
 SG B:CYS1166 2.3 77.9 1.0
SG B:CYS1185 2.3 109.6 1.0
SG B:CYS1163 2.3 76.1 1.0
SG B:CYS1182 2.3 108.4 1.0
CB B:CYS1163 2.8 76.1 1.0
CB B:CYS1166 2.8 77.9 1.0
CB B:CYS1185 3.1 109.6 1.0
N B:CYS1166 3.4 77.9 1.0
CB B:CYS1182 3.6 108.4 1.0
CA B:CYS1166 3.7 77.9 1.0
N B:CYS1185 4.2 109.6 1.0
CA B:CYS1185 4.2 109.6 1.0
CA B:CYS1163 4.3 76.1 1.0
C B:CYS1166 4.6 77.9 1.0
C B:ILE1165 4.6 81.2 1.0
N B:GLY1167 4.7 72.9 1.0
C B:SER1184 4.8 114.3 1.0
CB B:ILE1165 4.8 81.2 1.0
N B:ILE1165 4.8 81.2 1.0
C B:CYS1163 4.8 76.1 1.0
CB B:SER1184 4.9 114.3 1.0
CA B:CYS1182 5.0 108.4 1.0
CA B:ILE1165 5.0 81.2 1.0

Zinc binding site 4 out of 10 in 8jh2

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Zinc binding site 4 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:174.4
occ:1.00
 SG C:CYS94 2.3 108.1 1.0
SG C:CYS85 2.3 126.1 1.0
SG C:CYS91 2.3 108.1 1.0
SG C:CYS87 3.2 137.8 1.0
CB C:CYS94 3.3 108.1 1.0
CB C:CYS85 3.5 126.1 1.0
N C:CYS94 3.7 108.1 1.0
CB C:CYS91 3.7 108.1 1.0
C C:GLU93 4.0 110.7 1.0
CB C:GLU93 4.1 110.7 1.0
CA C:CYS94 4.1 108.1 1.0
N C:GLU93 4.3 110.7 1.0
CA C:GLU93 4.3 110.7 1.0
CB C:CYS87 4.4 137.8 1.0
N C:CYS91 4.4 108.1 1.0
O C:GLU93 4.6 110.7 1.0
CA C:CYS91 4.6 108.1 1.0
NZ W:LYS764 4.8 128.8 1.0
O C:ASP89 4.8 132.0 1.0
CA C:CYS85 4.9 126.1 1.0
C C:CYS91 4.9 108.1 1.0

Zinc binding site 5 out of 10 in 8jh2

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Zinc binding site 5 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:192.9
occ:1.00
 SG I:CYS103 2.3 166.6 1.0
SG I:CYS78 2.3 173.6 1.0
CB I:ASN105 3.0 169.3 1.0
SG I:CYS75 3.1 169.7 1.0
CB I:CYS103 3.3 166.6 1.0
N I:CYS106 3.4 168.9 1.0
SG I:CYS106 3.6 168.9 1.0
CB I:CYS78 3.7 173.6 1.0
CA I:ASN105 3.9 169.3 1.0
CB I:CYS75 3.9 169.7 1.0
N I:ASN105 3.9 169.3 1.0
CB I:CYS106 4.1 168.9 1.0
C I:ASN105 4.1 169.3 1.0
CG I:ASN105 4.2 169.3 1.0
N I:CYS78 4.3 173.6 1.0
CA I:CYS106 4.3 168.9 1.0
OG I:SER80 4.5 168.2 1.0
OD1 I:ASN105 4.5 169.3 1.0
CA I:CYS78 4.6 173.6 1.0
CA I:CYS103 4.7 166.6 1.0
CB I:SER80 4.7 168.2 1.0
N I:LEU104 4.7 162.1 1.0
C I:CYS103 4.8 166.6 1.0
C I:LEU104 4.9 162.1 1.0
N I:LYS107 5.0 157.8 1.0

Zinc binding site 6 out of 10 in 8jh2

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Zinc binding site 6 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:138.8
occ:1.00
 SG I:CYS29 2.3 154.7 1.0
SG I:CYS32 2.3 153.6 1.0
SG I:CYS10 2.3 133.8 1.0
CB I:CYS32 3.2 153.6 1.0
CB I:CYS29 3.2 154.7 1.0
N I:CYS32 3.4 153.6 1.0
CB I:CYS10 3.7 133.8 1.0
CA I:CYS32 3.8 153.6 1.0
C I:ASN31 4.0 147.3 1.0
CB I:ASN31 4.1 147.3 1.0
N I:ASN31 4.2 147.3 1.0
SG I:CYS7 4.3 131.6 1.0
CA I:ASN31 4.3 147.3 1.0
CB I:ASN12 4.5 136.3 1.0
CB I:CYS7 4.6 131.6 1.0
C I:CYS32 4.6 153.6 1.0
CA I:CYS29 4.6 154.7 1.0
OD1 I:ASN12 4.7 136.3 1.0
N I:CYS10 4.7 133.8 1.0
CA I:CYS10 4.8 133.8 1.0
ND2 I:ASN31 4.8 147.3 1.0
O I:ASN31 4.9 147.3 1.0
N I:ARG30 4.9 146.0 1.0

Zinc binding site 7 out of 10 in 8jh2

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Zinc binding site 7 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:68.2
occ:1.00
 SG J:CYS45 2.3 40.5 1.0
SG J:CYS10 2.3 33.6 1.0
SG J:CYS7 2.3 34.6 1.0
SG J:CYS44 2.3 41.0 1.0
CB J:CYS7 3.1 34.6 1.0
N J:CYS45 3.4 40.5 1.0
CB J:CYS44 3.6 41.0 1.0
CB J:CYS45 3.7 40.5 1.0
C J:CYS44 3.7 41.0 1.0
CA J:CYS45 3.8 40.5 1.0
CB J:CYS10 3.8 33.6 1.0
N J:CYS10 4.0 33.6 1.0
O J:CYS44 4.1 41.0 1.0
CA J:CYS44 4.2 41.0 1.0
N J:GLY11 4.4 34.4 1.0
CA J:CYS10 4.4 33.6 1.0
NE J:ARG42 4.5 36.8 1.0
CB J:LYS12 4.5 31.9 1.0
CA J:CYS7 4.6 34.6 1.0
CB J:SER9 4.6 32.7 1.0
N J:LYS12 4.6 31.9 1.0

Zinc binding site 8 out of 10 in 8jh2

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Zinc binding site 8 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:166.6
occ:1.00
 SG L:CYS36 2.3 124.3 1.0
SG L:CYS53 2.3 130.7 1.0
SG L:CYS50 2.3 122.6 1.0
SG L:CYS33 2.3 114.6 1.0
CB L:CYS33 3.3 114.6 1.0
CB L:CYS36 3.4 124.3 1.0
CB L:CYS50 3.5 122.6 1.0
N L:CYS36 3.6 124.3 1.0
CB L:CYS53 3.7 130.7 1.0
N L:CYS53 3.8 130.7 1.0
CA L:CYS36 4.0 124.3 1.0
CA L:CYS53 4.3 130.7 1.0
CB L:HIS55 4.4 105.3 1.0
CB L:GLU52 4.4 131.4 1.0
N L:ALA37 4.5 126.2 1.0
C L:CYS36 4.5 124.3 1.0
N L:HIS55 4.6 105.3 1.0
CB L:ALA35 4.7 116.1 1.0
C L:ALA35 4.7 116.1 1.0
CA L:CYS33 4.7 114.6 1.0
N L:GLY54 4.7 122.2 1.0
CB L:HIS38 4.8 125.1 1.0
N L:ALA35 4.8 116.1 1.0
C L:CYS53 4.8 130.7 1.0
C L:GLU52 4.8 131.4 1.0
CA L:CYS50 4.9 122.6 1.0
N L:GLU52 4.9 131.4 1.0
N L:HIS38 4.9 125.1 1.0
CA L:ALA35 5.0 116.1 1.0
CA L:GLU52 5.0 131.4 1.0

Zinc binding site 9 out of 10 in 8jh2

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Zinc binding site 9 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 9 of Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:325.7
occ:1.00
 SG M:CYS28 2.3 168.8 1.0
SG M:CYS52 2.3 191.4 1.0
SG M:CYS49 2.3 180.6 1.0
SG M:CYS25 2.3 198.3 1.0
CB M:CYS25 3.0 192.5 1.0
CB M:CYS28 3.4 180.0 1.0
CB M:CYS49 3.4 175.7 1.0
CB M:CYS52 3.7 191.1 1.0
N M:CYS28 3.8 182.5 1.0
N M:CYS52 3.9 187.0 1.0
CD2 M:LEU54 4.1 30.0 1.0
CA M:CYS28 4.2 181.3 1.0
CA M:CYS52 4.3 188.6 1.0
CB M:LYS51 4.5 161.4 1.0
CA M:CYS25 4.5 184.7 1.0
CB M:PHE27 4.7 177.7 1.0
CA M:CYS49 4.8 167.4 1.0
CG M:LEU54 4.9 30.0 1.0
C M:CYS28 4.9 177.3 1.0
C M:PHE27 4.9 174.9 1.0
C M:LYS51 4.9 175.2 1.0
N M:ASN29 5.0 178.9 1.0
N M:ASN53 5.0 188.1 1.0

Zinc binding site 10 out of 10 in 8jh2

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Zinc binding site 10 out of 10 in the Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, 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 10 of Rna Polymerase II Elongation Complex Bound with ELF1, SPT4/5 and Foreign Dna, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn300

b:17.1
occ:1.00
 SG V:CYS15 2.3 22.8 1.0
SG V:CYS29 2.3 18.0 1.0
SG V:CYS32 2.3 25.4 1.0
SG V:CYS12 2.3 34.8 1.0
CB V:CYS15 2.9 14.4 1.0
CB V:CYS32 3.1 17.2 1.0
CB V:CYS12 3.2 14.9 1.0
N V:CYS15 3.4 15.3 1.0
CA V:CYS15 3.7 14.2 1.0
CB V:CYS29 3.9 17.4 1.0
N V:CYS32 4.1 16.6 1.0
CA V:CYS32 4.2 17.2 1.0
N V:GLY16 4.2 14.7 1.0
C V:ASN31 4.4 16.7 1.0
C V:CYS15 4.5 17.6 1.0
C V:LEU14 4.6 18.1 1.0
CB V:LEU14 4.6 13.2 1.0
CA V:CYS12 4.7 13.8 1.0
CB V:ASN31 4.7 15.9 1.0
CG2 V:ILE17 4.8 11.7 1.0
N V:ILE17 4.9 13.5 1.0
O V:ASN31 4.9 19.6 1.0
N V:LEU14 4.9 17.1 1.0
CA V:ASN31 5.0 14.6 1.0
N V:ASN31 5.0 16.2 1.0
CA V:LEU14 5.0 17.6 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 08:16:12 2024

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