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Zinc in PDB 8he5: Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome

Enzymatic activity of Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome

All present enzymatic activity of Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome:
2.7.7.6;

Other elements in 8he5:

The structure of Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome (pdb code 8he5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome, PDB code: 8he5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8he5

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Zinc binding site 1 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:554.3
occ:1.00
 NE2 A:HIS80 2.3 558.6 1.0
SG A:CYS70 2.3 543.0 1.0
CD A:PRO78 2.6 519.5 1.0
CD2 A:HIS80 2.8 558.6 1.0
SG A:CYS77 2.9 540.1 1.0
SG A:CYS67 3.1 570.2 1.0
CA A:CYS77 3.2 540.1 1.0
CB A:CYS70 3.2 543.0 1.0
CB A:CYS67 3.2 570.2 1.0
N A:PRO78 3.3 519.5 1.0
CB A:CYS77 3.4 540.1 1.0
CE1 A:HIS80 3.5 558.6 1.0
C A:CYS77 3.6 540.1 1.0
CG A:PRO78 3.7 519.5 1.0
N A:GLY79 3.9 520.8 1.0
CG A:HIS80 4.1 558.6 1.0
N A:CYS70 4.2 543.0 1.0
O A:GLU72 4.3 531.8 1.0
CA A:CYS70 4.3 543.0 1.0
ND1 A:HIS80 4.4 558.6 1.0
CA A:PRO78 4.4 519.5 1.0
N A:CYS77 4.4 540.1 1.0
O A:CYS77 4.6 540.1 1.0
C A:PRO78 4.6 519.5 1.0
CA A:CYS67 4.7 570.2 1.0
CA A:GLY79 4.8 520.8 1.0
CB A:PRO78 4.8 519.5 1.0
O A:GLU76 4.9 546.6 1.0
C A:GLY79 4.9 520.8 1.0

Zinc binding site 2 out of 9 in 8he5

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Zinc binding site 2 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:415.7
occ:1.00
 CB A:CYS168 2.0 364.7 1.0
CB A:CYS110 2.1 342.8 1.0
N A:CYS110 2.2 342.8 1.0
SG A:CYS168 2.3 364.7 1.0
SG A:CYS110 2.3 342.8 1.0
SG A:CYS107 2.3 353.8 1.0
N A:CYS168 2.5 364.7 1.0
CA A:CYS110 2.6 342.8 1.0
CA A:CYS168 2.7 364.7 1.0
CB A:CYS107 3.3 353.8 1.0
C A:ASN109 3.3 362.4 1.0
C A:GLY167 3.6 279.9 1.0
C A:CYS110 3.7 342.8 1.0
CB A:ASN109 3.8 362.4 1.0
CA A:ASN109 3.9 362.4 1.0
C A:CYS168 4.0 364.7 1.0
N A:ASN109 4.0 362.4 1.0
N A:GLY111 4.1 361.3 1.0
CA A:GLY167 4.2 279.9 1.0
CG A:ASN109 4.3 362.4 1.0
O A:ASN109 4.3 362.4 1.0
ND2 A:ASN109 4.4 362.4 1.0
N A:GLY169 4.4 334.5 1.0
O A:GLY167 4.5 279.9 1.0
CA A:CYS107 4.7 353.8 1.0
O A:CYS110 4.7 342.8 1.0
O A:GLY166 4.9 240.9 1.0
O A:CYS168 5.0 364.7 1.0
C A:CYS107 5.0 353.8 1.0

Zinc binding site 3 out of 9 in 8he5

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Zinc binding site 3 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:640.2
occ:1.00
 SG B:CYS1166 2.3 619.1 1.0
SG B:CYS1182 2.3 614.7 1.0
SG B:CYS1163 2.3 650.0 1.0
SG B:CYS1185 2.3 554.4 1.0
CB B:CYS1163 2.8 650.0 1.0
CB B:CYS1166 2.8 619.1 1.0
CB B:CYS1185 2.9 554.4 1.0
N B:CYS1166 3.2 619.1 1.0
CA B:CYS1166 3.6 619.1 1.0
CB B:CYS1182 3.7 614.7 1.0
N B:CYS1185 3.7 554.4 1.0
CA B:CYS1185 3.9 554.4 1.0
OG B:SER1170 4.0 594.4 1.0
CB B:SER1184 4.1 493.5 1.0
CA B:CYS1163 4.3 650.0 1.0
N B:GLY1167 4.4 611.8 1.0
C B:ILE1165 4.4 631.0 1.0
C B:CYS1166 4.4 619.1 1.0
C B:SER1184 4.5 493.5 1.0
CB B:ILE1165 4.5 631.0 1.0
OG B:SER1184 4.5 493.5 1.0
N B:ILE1165 4.6 631.0 1.0
CB B:ASN1187 4.6 674.0 1.0
CA B:ILE1165 4.7 631.0 1.0
CA B:SER1184 4.8 493.5 1.0
C B:CYS1185 4.9 554.4 1.0
C B:CYS1163 4.9 650.0 1.0
CA B:CYS1182 5.0 614.7 1.0

Zinc binding site 4 out of 9 in 8he5

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Zinc binding site 4 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:487.7
occ:1.00
 SG C:CYS87 2.3 423.4 1.0
SG C:CYS91 2.3 392.0 1.0
SG C:CYS85 2.3 481.0 1.0
SG C:CYS94 2.3 410.5 1.0
CB C:CYS85 3.3 481.0 1.0
CB C:CYS94 3.3 410.5 1.0
CB C:CYS91 3.5 392.0 1.0
CB C:CYS87 3.7 423.4 1.0
N C:CYS91 3.7 392.0 1.0
N C:CYS94 4.0 410.5 1.0
CA C:CYS91 4.1 392.0 1.0
CA C:CYS94 4.3 410.5 1.0
O C:CYS91 4.3 392.0 1.0
C C:CYS91 4.4 392.0 1.0
N C:CYS87 4.5 423.4 1.0
CA C:CYS85 4.7 481.0 1.0
CA C:CYS87 4.7 423.4 1.0
C C:TYR90 4.8 358.3 1.0
C C:CYS85 4.9 481.0 1.0
C C:GLU93 5.0 391.5 1.0

Zinc binding site 5 out of 9 in 8he5

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Zinc binding site 5 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:1000.0
occ:1.00
 CB I:CYS75 1.6 1000.0 1.0
SG I:CYS75 2.3 1000.0 1.0
SG I:CYS103 2.3 1000.0 1.0
SG I:CYS78 2.3 1000.0 1.0
CA I:CYS75 2.8 1000.0 1.0
CB I:CYS103 3.1 1000.0 1.0
N I:CYS78 3.1 1000.0 1.0
N I:HIS79 3.2 1000.0 1.0
C I:CYS75 3.3 1000.0 1.0
CB I:CYS78 3.3 1000.0 1.0
CA I:CYS78 3.5 1000.0 1.0
C I:CYS78 3.7 1000.0 1.0
O I:CYS75 3.7 1000.0 1.0
N I:GLU77 3.9 1000.0 1.0
N I:PRO76 4.0 1000.0 1.0
N I:CYS75 4.0 1000.0 1.0
C I:GLU77 4.1 1000.0 1.0
CA I:HIS79 4.2 1000.0 1.0
N I:SER80 4.2 1000.0 1.0
CA I:GLU77 4.5 1000.0 1.0
CB I:CYS106 4.5 1000.0 1.0
CA I:CYS103 4.5 1000.0 1.0
CD I:PRO76 4.6 1000.0 1.0
SG I:CYS106 4.6 1000.0 1.0
C I:HIS79 4.7 1000.0 1.0
C I:PRO76 4.7 1000.0 1.0
CB I:GLU77 4.8 1000.0 1.0
O I:CYS78 4.8 1000.0 1.0
C I:GLU74 4.9 1000.0 1.0
N I:CYS103 4.9 1000.0 1.0
O I:GLU74 4.9 1000.0 1.0
CA I:PRO76 5.0 1000.0 1.0

Zinc binding site 6 out of 9 in 8he5

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Zinc binding site 6 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:888.3
occ:1.00
 CB I:CYS10 1.9 918.7 1.0
SG I:CYS29 2.3 1000.0 1.0
SG I:CYS32 2.3 991.1 1.0
SG I:CYS10 2.3 918.7 1.0
CB I:CYS29 2.6 1000.0 1.0
CA I:CYS10 3.4 918.7 1.0
CB I:CYS7 3.4 945.3 1.0
SG I:CYS7 3.6 945.3 1.0
CB I:CYS32 3.9 991.1 1.0
N I:CYS10 4.0 918.7 1.0
CA I:CYS29 4.0 1000.0 1.0
C I:CYS10 4.1 918.7 1.0
CB I:TYR34 4.1 1000.0 1.0
N I:CYS32 4.1 991.1 1.0
N I:ASN11 4.3 853.5 1.0
C I:CYS29 4.4 1000.0 1.0
CA I:CYS32 4.5 991.1 1.0
O I:CYS29 4.6 1000.0 1.0
N I:ASN12 4.9 881.9 1.0
CG I:TYR34 4.9 1000.0 1.0
O I:CYS10 4.9 918.7 1.0
N I:CYS29 4.9 1000.0 1.0
CB I:ASN31 4.9 909.3 1.0
CA I:CYS7 4.9 945.3 1.0
N I:ASN31 4.9 909.3 1.0
CD2 I:TYR34 4.9 1000.0 1.0
CD2 I:LEU14 5.0 1000.0 1.0
C I:CYS32 5.0 991.1 1.0

Zinc binding site 7 out of 9 in 8he5

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Zinc binding site 7 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:156.7
occ:1.00
 N J:CYS45 2.2 175.4 1.0
SG J:CYS7 2.3 263.6 1.0
SG J:CYS45 2.3 175.4 1.0
SG J:CYS44 2.3 195.9 1.0
SG J:CYS10 2.3 349.9 1.0
CA J:CYS45 2.6 175.4 1.0
C J:CYS44 2.9 195.9 1.0
CB J:CYS45 2.9 175.4 1.0
CB J:CYS44 3.2 195.9 1.0
CB J:CYS10 3.5 349.9 1.0
O J:CYS44 3.6 195.9 1.0
CA J:CYS44 3.6 195.9 1.0
CB J:CYS7 3.8 263.6 1.0
N J:CYS10 4.0 349.9 1.0
C J:CYS45 4.1 175.4 1.0
N J:CYS44 4.3 195.9 1.0
CA J:CYS10 4.4 349.9 1.0
O J:ARG42 4.4 187.0 1.0
NE J:ARG42 4.5 187.0 1.0
CB J:ARG42 4.5 187.0 1.0
CB J:SER9 4.5 446.4 1.0
N J:ARG46 4.8 197.5 1.0
C J:SER9 4.9 446.4 1.0
O J:CYS45 4.9 175.4 1.0
NH2 J:ARG42 4.9 187.0 1.0
CE J:MET48 5.0 191.2 1.0

Zinc binding site 8 out of 9 in 8he5

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Zinc binding site 8 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:215.1
occ:1.00
 CB L:CYS53 2.3 248.2 1.0
SG L:CYS50 2.3 274.0 1.0
SG L:CYS36 2.3 286.3 1.0
SG L:CYS33 2.3 236.4 1.0
CB L:CYS50 3.2 274.0 1.0
N L:CYS53 3.3 248.2 1.0
CB L:CYS33 3.3 236.4 1.0
OE2 L:GLU52 3.3 249.1 1.0
CA L:CYS53 3.3 248.2 1.0
SG L:CYS53 3.5 248.2 1.0
CB L:CYS36 3.7 286.3 1.0
CB L:HIS38 3.8 255.5 1.0
CD L:GLU52 4.0 249.1 1.0
ND1 L:HIS38 4.1 255.5 1.0
CB L:HIS55 4.1 318.0 1.0
C L:CYS53 4.2 248.2 1.0
CG L:GLU52 4.2 249.1 1.0
N L:GLY54 4.4 286.5 1.0
CG L:HIS38 4.4 255.5 1.0
CA L:CYS50 4.5 274.0 1.0
C L:GLU52 4.5 249.1 1.0
C L:CYS50 4.6 274.0 1.0
N L:HIS55 4.6 318.0 1.0
O L:CYS50 4.6 274.0 1.0
CA L:CYS33 4.7 236.4 1.0
N L:GLU52 4.9 249.1 1.0
CA L:CYS36 5.0 286.3 1.0
OE1 L:GLU52 5.0 249.1 1.0

Zinc binding site 9 out of 9 in 8he5

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Zinc binding site 9 out of 9 in the Rna Polymerase II Elongation Complex Bound with RAD26 and ELF1, Stalled at Shl(-3.5) 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 RAD26 and ELF1, Stalled at Shl(-3.5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:581.1
occ:1.00
 SG M:CYS52 2.3 613.6 1.0
SG M:CYS25 2.3 525.1 1.0
SG M:CYS49 2.3 607.0 1.0
SG M:CYS28 2.3 572.6 1.0
CB M:CYS52 3.2 613.6 1.0
N M:CYS52 3.4 613.6 1.0
CB M:CYS49 3.6 607.0 1.0
CB M:CYS28 3.7 572.6 1.0
CA M:CYS52 3.8 613.6 1.0
OG M:SER33 3.9 582.9 1.0
CB M:CYS25 4.0 525.1 1.0
N M:CYS28 4.0 572.6 1.0
CD2 M:LEU54 4.2 578.2 1.0
CB M:SER33 4.3 582.9 1.0
C M:LYS51 4.4 608.8 1.0
CA M:CYS28 4.4 572.6 1.0
C M:CYS52 4.5 613.6 1.0
N M:ASN53 4.5 610.6 1.0
CB M:LYS51 4.5 608.8 1.0
CB M:PHE27 4.6 568.5 1.0
N M:LYS51 4.7 608.8 1.0
CA M:LYS51 4.8 608.8 1.0
CA M:CYS49 4.9 607.0 1.0
CG M:LEU54 5.0 578.2 1.0

Reference:

K.Osumi, T.Kujirai, H.Ehara, M.Ogasawara, C.Kinoshita, M.Saotome, W.Kagawa, S.I.Sekine, Y.Takizawa, H.Kurumizaka. Structural Basis of Damaged Nucleotide Recognition By Transcribing Rna Polymerase II in the Nucleosome. J.Mol.Biol. V. 435 68130 2023.
ISSN: ESSN 1089-8638
PubMed: 37120012
DOI: 10.1016/J.JMB.2023.168130
Page generated: Thu Oct 31 07:11:19 2024

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