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Zinc in PDB 8rap: Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex

Enzymatic activity of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex

All present enzymatic activity of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex:
2.7.7.6;

Other elements in 8rap:

The structure of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Fluorine (F) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex (pdb code 8rap). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex, PDB code: 8rap:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8rap

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Zinc binding site 1 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:196.4
occ:1.00
 SG A:CYS167 2.3 160.8 1.0
SG A:CYS110 2.3 161.5 1.0
SG A:CYS107 2.3 159.9 1.0
CB A:CYS110 2.7 161.5 1.0
N A:CYS110 2.8 161.5 1.0
CA A:CYS110 3.3 161.5 1.0
CB A:CYS107 3.4 159.9 1.0
CB A:CYS167 3.6 160.8 1.0
CB A:HIS109 3.8 167.1 1.0
C A:HIS109 3.8 167.1 1.0
CA A:HIS109 4.2 167.1 1.0
N A:HIS109 4.2 167.1 1.0
N A:CYS167 4.2 160.8 1.0
C A:CYS110 4.4 161.5 1.0
CA A:CYS167 4.6 160.8 1.0
N A:GLY111 4.7 156.4 1.0
CA A:CYS107 4.8 159.9 1.0
CB A:ASN169 4.9 163.5 1.0
O A:HIS109 4.9 167.1 1.0
CG A:HIS109 4.9 167.1 1.0
N A:GLY168 5.0 160.7 1.0

Zinc binding site 2 out of 9 in 8rap

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Zinc binding site 2 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:165.6
occ:1.00
 SG A:CYS67 2.3 166.7 1.0
SG A:CYS77 2.3 156.7 1.0
CB A:CYS67 2.4 166.7 1.0
CA A:GLY59 3.7 148.7 1.0
CB A:CYS77 3.8 156.7 1.0
CE1 A:HIS80 3.8 145.1 1.0
CA A:CYS67 4.0 166.7 1.0
O A:LEU58 4.1 151.4 1.0
ND1 A:HIS80 4.2 145.1 1.0
CB A:CYS70 4.2 167.1 1.0
N A:GLY59 4.3 148.7 1.0
O A:GLU72 4.4 171.6 1.0
C A:GLY59 4.4 148.7 1.0
SG A:CYS70 4.5 167.1 1.0
N A:SER60 4.5 157.4 1.0
C A:LEU58 4.5 151.4 1.0
O A:ARG57 4.5 154.4 1.0
N A:CYS70 4.6 167.1 1.0
C A:CYS67 4.7 166.7 1.0
N A:CYS67 4.7 166.7 1.0
CA A:CYS77 4.7 156.7 1.0
O A:PRO56 4.9 155.1 1.0
CA A:CYS70 5.0 167.1 1.0
O A:CYS67 5.0 166.7 1.0

Zinc binding site 3 out of 9 in 8rap

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Zinc binding site 3 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:212.2
occ:1.00
 SG B:CYS1163 2.3 153.6 1.0
SG B:CYS1185 2.3 161.0 1.0
SG B:CYS1166 2.3 135.2 1.0
SG B:CYS1182 2.3 169.7 1.0
CB B:CYS1182 2.8 169.7 1.0
CB B:CYS1163 3.1 153.6 1.0
CB B:CYS1166 3.6 135.2 1.0
CB B:CYS1185 3.8 161.0 1.0
ND2 B:ASN1187 4.1 167.9 1.0
OD1 B:ASN1187 4.2 167.9 1.0
N B:CYS1185 4.2 161.0 1.0
CA B:CYS1182 4.3 169.7 1.0
CG B:ASN1187 4.5 167.9 1.0
CA B:CYS1163 4.5 153.6 1.0
CA B:CYS1185 4.6 161.0 1.0
CG2 B:VAL1171 4.7 156.9 1.0
CA B:CYS1166 4.7 135.2 1.0
N B:CYS1166 4.7 135.2 1.0
O B:CYS1185 4.7 161.0 1.0
N B:CYS1163 4.8 153.6 1.0
C B:CYS1182 4.8 169.7 1.0
O B:CYS1182 4.9 169.7 1.0

Zinc binding site 4 out of 9 in 8rap

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Zinc binding site 4 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:216.3
occ:1.00
 SG C:CYS88 2.3 156.4 1.0
SG C:CYS95 2.3 146.9 1.0
SG C:CYS92 2.3 143.6 1.0
SG C:CYS86 2.3 158.8 1.0
CB C:CYS88 2.8 156.4 1.0
CB C:CYS95 3.1 146.9 1.0
CB C:CYS92 3.7 143.6 1.0
N C:CYS92 4.0 143.6 1.0
O C:CYS92 4.0 143.6 1.0
CB C:CYS86 4.1 158.8 1.0
N C:CYS95 4.1 146.9 1.0
CA C:CYS88 4.2 156.4 1.0
CA C:CYS95 4.2 146.9 1.0
OG C:SER83 4.3 151.0 1.0
CA C:CYS92 4.3 143.6 1.0
O C:CYS86 4.3 158.8 1.0
CA C:SER83 4.3 151.0 1.0
O C:SER83 4.5 151.0 1.0
C C:CYS92 4.5 143.6 1.0
N C:CYS88 4.5 156.4 1.0
CB C:SER83 4.7 151.0 1.0
C C:CYS86 4.8 158.8 1.0
C C:SER83 4.9 151.0 1.0
C C:LYS94 4.9 137.4 1.0
C C:HIS91 5.0 139.2 1.0

Zinc binding site 5 out of 9 in 8rap

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Zinc binding site 5 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:243.3
occ:1.00
 SG I:CYS7 2.3 224.9 1.0
SG I:CYS32 2.3 222.7 1.0
CB I:CYS7 3.1 224.9 1.0
CB I:CYS29 3.6 225.1 1.0
CB I:CYS32 4.0 222.7 1.0
CB I:TYR34 4.1 210.2 1.0
CD2 I:LEU14 4.2 222.1 1.0
OG1 I:THR31 4.3 227.3 1.0
CB I:CYS10 4.3 229.6 1.0
CA I:CYS7 4.4 224.9 1.0
SG I:CYS29 4.5 225.1 1.0
SG I:CYS10 4.5 229.6 1.0
CD2 I:TYR34 4.6 210.2 1.0
CG I:TYR34 4.7 210.2 1.0
CA I:CYS29 4.7 225.1 1.0
N I:CYS29 4.8 225.1 1.0
CB I:ASN12 4.8 218.0 1.0
N I:CYS32 4.9 222.7 1.0
O I:CYS29 4.9 225.1 1.0
CA I:CYS32 5.0 222.7 1.0

Zinc binding site 6 out of 9 in 8rap

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Zinc binding site 6 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:262.1
occ:1.00
 SG I:CYS78 2.3 237.3 1.0
SG I:CYS75 2.3 225.2 1.0
SG I:CYS103 2.3 226.2 1.0
SG I:CYS106 2.3 229.1 1.0
CB I:CYS103 2.9 226.2 1.0
CB I:CYS75 3.1 225.2 1.0
OG I:SER105 3.1 229.3 1.0
CB I:CYS106 3.8 229.1 1.0
CB I:CYS78 4.0 237.3 1.0
N I:CYS106 4.1 229.1 1.0
CB I:SER80 4.4 230.5 1.0
CA I:CYS103 4.4 226.2 1.0
OG I:SER80 4.4 230.5 1.0
N I:CYS78 4.4 237.3 1.0
CB I:SER105 4.5 229.3 1.0
CA I:CYS106 4.6 229.1 1.0
CA I:CYS75 4.6 225.2 1.0
NZ I:LYS77 4.7 220.8 1.0
CA I:CYS78 4.8 237.3 1.0
C I:CYS103 4.9 226.2 1.0
N I:SER80 5.0 230.5 1.0
C I:SER105 5.0 229.3 1.0

Zinc binding site 7 out of 9 in 8rap

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Zinc binding site 7 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:125.3
occ:1.00
 SG J:CYS45 2.3 112.4 1.0
SG J:CYS10 2.3 121.4 1.0
SG J:CYS7 2.3 113.2 1.0
SG J:CYS46 2.3 118.0 1.0
CB J:CYS7 2.9 113.2 1.0
N J:CYS46 3.3 118.0 1.0
CB J:CYS45 3.4 112.4 1.0
CB J:CYS46 3.7 118.0 1.0
CB J:CYS10 3.7 121.4 1.0
CA J:CYS46 3.8 118.0 1.0
C J:CYS45 3.9 112.4 1.0
N J:CYS10 4.0 121.4 1.0
CA J:CYS45 4.2 112.4 1.0
NE J:ARG43 4.3 124.5 1.0
CA J:CYS7 4.4 113.2 1.0
CA J:CYS10 4.4 121.4 1.0
NH2 J:ARG43 4.5 124.5 1.0
CB J:LYS12 4.5 123.5 1.0
O J:CYS45 4.7 112.4 1.0
N J:LYS12 4.7 123.5 1.0
N J:GLY11 4.7 117.6 1.0
CB J:SER9 4.7 115.1 1.0
CZ J:ARG43 4.9 124.5 1.0
N J:CYS45 4.9 112.4 1.0

Zinc binding site 8 out of 9 in 8rap

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Zinc binding site 8 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:194.2
occ:1.00
 SG L:CYS51 2.3 148.5 1.0
SG L:CYS48 2.3 146.6 1.0
SG L:CYS34 2.3 149.4 1.0
SG L:CYS31 2.3 140.3 1.0
CB L:CYS48 3.2 146.6 1.0
CB L:CYS34 3.2 149.4 1.0
CB L:CYS31 3.4 140.3 1.0
CB L:CYS51 3.4 148.5 1.0
N L:CYS51 3.7 148.5 1.0
N L:CYS34 3.8 149.4 1.0
CA L:CYS51 4.1 148.5 1.0
CA L:CYS34 4.1 149.4 1.0
CB L:ASP50 4.4 151.7 1.0
C L:CYS51 4.6 148.5 1.0
CA L:CYS48 4.6 146.6 1.0
O L:CYS51 4.6 148.5 1.0
C L:ASP50 4.7 151.7 1.0
O L:HIS53 4.7 141.8 1.0
CA L:CYS31 4.8 140.3 1.0
CB L:GLU33 4.9 139.8 1.0
N L:ASP50 4.9 151.7 1.0
CA L:ASP50 4.9 151.7 1.0
C L:GLU33 4.9 139.8 1.0
CB L:HIS53 5.0 141.8 1.0

Zinc binding site 9 out of 9 in 8rap

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Zinc binding site 9 out of 9 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:431.9
occ:1.00
 SG M:CYS49 2.3 374.4 1.0
SG M:CYS52 2.3 383.4 1.0
SG M:CYS28 2.3 392.8 1.0
SG M:CYS25 2.3 387.0 1.0
CB M:CYS25 3.1 387.0 1.0
CB M:CYS49 3.1 374.4 1.0
CB M:CYS52 3.6 383.4 1.0
CB M:CYS28 3.7 392.8 1.0
N M:CYS52 4.0 383.4 1.0
N M:CYS28 4.0 392.8 1.0
CA M:CYS52 4.4 383.4 1.0
CA M:CYS28 4.5 392.8 1.0
OG M:SER33 4.5 380.0 1.0
CA M:CYS25 4.6 387.0 1.0
CA M:CYS49 4.6 374.4 1.0
CB M:PHE27 4.8 372.1 1.0
CB M:SER33 4.9 380.0 1.0
CB M:ILE51 4.9 374.8 1.0

Reference:

S.Rengachari, T.Hainthaler, C.Oberthuer, M.Lidschreiber, P.Cramer. Mechanism of Polyadenylation-Independent Rna Polymerase II Termination. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 39424994
DOI: 10.1038/S41594-024-01409-0
Page generated: Wed Nov 13 13:40:36 2024

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