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Zinc in PDB 8ram: Structure of SEN1 Bound Rna Polymerase II Pre-Termination Complex

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

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

Other elements in 8ram:

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

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of SEN1 Bound Rna Polymerase II Pre-Termination Complex (pdb code 8ram). 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 Bound Rna Polymerase II Pre-Termination Complex, PDB code: 8ram:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8ram

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Zinc binding site 1 out of 9 in the Structure of SEN1 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 1 of Structure of SEN1 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:137.7
occ:1.00
 SG A:CYS167 2.3 113.4 1.0
SG A:CYS107 2.3 100.9 1.0
SG A:CYS110 2.3 104.4 1.0
CB A:CYS110 2.7 104.4 1.0
N A:CYS110 3.0 104.4 1.0
CB A:CYS107 3.3 100.9 1.0
CA A:CYS110 3.4 104.4 1.0
CB A:CYS167 3.7 113.4 1.0
CB A:HIS109 4.0 104.2 1.0
C A:HIS109 4.0 104.2 1.0
N A:CYS167 4.1 113.4 1.0
CA A:HIS109 4.4 104.2 1.0
N A:HIS109 4.4 104.2 1.0
C A:CYS110 4.5 104.4 1.0
CA A:CYS167 4.5 113.4 1.0
CA A:CYS107 4.7 100.9 1.0
N A:GLY111 4.8 97.5 1.0
SG A:CYS148 4.9 108.9 1.0
N A:GLY168 4.9 109.4 1.0

Zinc binding site 2 out of 9 in 8ram

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Zinc binding site 2 out of 9 in the Structure of SEN1 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 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:119.7
occ:1.00
 SG A:CYS67 2.3 95.7 1.0
SG A:CYS77 2.3 84.0 1.0
CB A:CYS67 2.4 95.7 1.0
CA A:GLY59 3.7 86.6 1.0
CB A:CYS77 3.8 84.0 1.0
CA A:CYS67 3.9 95.7 1.0
CE1 A:HIS80 4.0 84.3 1.0
O A:LEU58 4.2 86.4 1.0
N A:SER60 4.3 92.9 1.0
ND1 A:HIS80 4.3 84.3 1.0
C A:GLY59 4.4 86.6 1.0
CB A:CYS70 4.4 95.7 1.0
CA A:CYS77 4.5 84.0 1.0
N A:GLY59 4.5 86.6 1.0
SG A:CYS70 4.6 95.7 1.0
O A:GLU72 4.6 96.7 1.0
N A:CYS67 4.6 95.7 1.0
C A:LEU58 4.7 86.4 1.0
C A:CYS67 4.7 95.7 1.0
N A:CYS70 4.8 95.7 1.0
C A:CYS77 5.0 84.0 1.0

Zinc binding site 3 out of 9 in 8ram

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Zinc binding site 3 out of 9 in the Structure of SEN1 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 3 of Structure of SEN1 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:104.9
occ:1.00
 SG B:CYS1163 2.3 83.6 1.0
SG B:CYS1185 2.3 96.4 1.0
SG B:CYS1166 2.3 79.9 1.0
SG B:CYS1182 2.3 89.4 1.0
CB B:CYS1182 2.8 89.4 1.0
CB B:CYS1163 3.1 83.6 1.0
CB B:CYS1166 3.7 79.9 1.0
CB B:CYS1185 3.8 96.4 1.0
ND2 B:ASN1187 4.1 97.5 1.0
OD1 B:ASN1187 4.2 97.5 1.0
N B:CYS1185 4.2 96.4 1.0
CA B:CYS1182 4.3 89.4 1.0
CG B:ASN1187 4.5 97.5 1.0
CA B:CYS1163 4.5 83.6 1.0
CA B:CYS1185 4.6 96.4 1.0
N B:CYS1166 4.7 79.9 1.0
O B:CYS1185 4.7 96.4 1.0
CA B:CYS1166 4.7 79.9 1.0
C B:CYS1182 4.8 89.4 1.0
N B:CYS1163 4.8 83.6 1.0
CG2 B:VAL1171 4.8 83.9 1.0
O B:CYS1182 4.9 89.4 1.0
O B:THR1170 5.0 80.4 1.0

Zinc binding site 4 out of 9 in 8ram

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Zinc binding site 4 out of 9 in the Structure of SEN1 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 4 of Structure of SEN1 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:92.8
occ:1.00
 SG C:CYS95 2.3 60.6 1.0
SG C:CYS92 2.3 63.0 1.0
SG C:CYS88 2.3 74.0 1.0
SG C:CYS86 2.3 67.9 1.0
CB C:CYS88 2.9 74.0 1.0
CB C:CYS95 3.1 60.6 1.0
CB C:CYS92 3.6 63.0 1.0
N C:CYS92 3.9 63.0 1.0
CB C:CYS86 4.1 67.9 1.0
N C:CYS95 4.2 60.6 1.0
CA C:CYS95 4.2 60.6 1.0
CA C:CYS92 4.3 63.0 1.0
CA C:CYS88 4.3 74.0 1.0
OG C:SER83 4.4 63.5 1.0
O C:CYS92 4.4 63.0 1.0
O C:CYS86 4.4 67.9 1.0
CA C:SER83 4.4 63.5 1.0
O C:SER83 4.5 63.5 1.0
N C:CYS88 4.6 74.0 1.0
C C:CYS92 4.7 63.0 1.0
C C:CYS86 4.8 67.9 1.0
CB C:SER83 4.8 63.5 1.0
NZ Z:LYS813 4.8 69.4 1.0
C C:LYS94 4.9 61.0 1.0
C C:HIS91 5.0 61.8 1.0
C C:CYS95 5.0 60.6 1.0

Zinc binding site 5 out of 9 in 8ram

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Zinc binding site 5 out of 9 in the Structure of SEN1 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 5 of Structure of SEN1 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:145.6
occ:1.00
 SG I:CYS7 2.3 132.4 1.0
SG I:CYS32 2.3 135.6 1.0
CB I:CYS7 3.1 132.4 1.0
CB I:CYS29 3.7 136.1 1.0
CB I:CYS32 4.0 135.6 1.0
CB I:CYS10 4.1 127.4 1.0
CB I:TYR34 4.1 133.2 1.0
OG1 I:THR31 4.2 134.1 1.0
SG I:CYS10 4.2 127.4 1.0
CD2 I:LEU14 4.4 132.9 1.0
SG I:CYS29 4.4 136.1 1.0
CA I:CYS7 4.5 132.4 1.0
CB I:ASN12 4.7 125.6 1.0
CG I:TYR34 4.8 133.2 1.0
N I:CYS32 4.8 135.6 1.0
CA I:CYS29 4.9 136.1 1.0
CD2 I:TYR34 4.9 133.2 1.0
N I:CYS10 4.9 127.4 1.0
CA I:CYS32 4.9 135.6 1.0
OD1 I:ASN12 5.0 125.6 1.0
N I:CYS29 5.0 136.1 1.0

Zinc binding site 6 out of 9 in 8ram

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Zinc binding site 6 out of 9 in the Structure of SEN1 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 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:129.6
occ:1.00
 SG I:CYS78 2.3 111.3 1.0
SG I:CYS75 2.3 108.8 1.0
SG I:CYS103 2.3 101.6 1.0
SG I:CYS106 2.3 103.7 1.0
CB I:CYS103 2.9 101.6 1.0
CB I:CYS75 3.1 108.8 1.0
OG I:SER105 3.2 102.5 1.0
CB I:CYS106 3.8 103.7 1.0
CB I:CYS78 4.0 111.3 1.0
N I:CYS106 4.1 103.7 1.0
CB I:SER80 4.4 108.2 1.0
OG I:SER80 4.4 108.2 1.0
CA I:CYS103 4.4 101.6 1.0
N I:CYS78 4.4 111.3 1.0
CA I:CYS106 4.6 103.7 1.0
CB I:SER105 4.6 102.5 1.0
CA I:CYS75 4.6 108.8 1.0
NZ I:LYS77 4.7 107.3 1.0
CA I:CYS78 4.8 111.3 1.0
C I:CYS103 4.9 101.6 1.0
N I:SER80 4.9 108.2 1.0

Zinc binding site 7 out of 9 in 8ram

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Zinc binding site 7 out of 9 in the Structure of SEN1 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 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:69.6
occ:1.00
 SG J:CYS10 2.3 48.9 1.0
SG J:CYS7 2.3 48.5 1.0
SG J:CYS45 2.3 49.9 1.0
SG J:CYS46 2.3 51.1 1.0
CB J:CYS7 3.0 48.5 1.0
N J:CYS46 3.3 51.1 1.0
CB J:CYS45 3.4 49.9 1.0
CB J:CYS46 3.7 51.1 1.0
CB J:CYS10 3.7 48.9 1.0
CA J:CYS46 3.8 51.1 1.0
C J:CYS45 3.9 49.9 1.0
N J:CYS10 4.0 48.9 1.0
NE J:ARG43 4.2 51.6 1.0
CA J:CYS45 4.2 49.9 1.0
NH2 J:ARG43 4.4 51.6 1.0
CA J:CYS7 4.5 48.5 1.0
CA J:CYS10 4.5 48.9 1.0
CB J:LYS12 4.5 49.8 1.0
O J:CYS45 4.7 49.9 1.0
CB J:SER9 4.7 47.9 1.0
N J:GLY11 4.8 48.7 1.0
N J:LYS12 4.8 49.8 1.0
CZ J:ARG43 4.8 51.6 1.0
N J:CYS45 4.9 49.9 1.0

Zinc binding site 8 out of 9 in 8ram

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Zinc binding site 8 out of 9 in the Structure of SEN1 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 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:98.3
occ:1.00
 SG L:CYS51 2.3 82.0 1.0
SG L:CYS34 2.3 78.6 1.0
SG L:CYS48 2.3 79.9 1.0
SG L:CYS31 2.3 75.6 1.0
CB L:CYS48 3.1 79.9 1.0
CB L:CYS34 3.2 78.6 1.0
CB L:CYS31 3.3 75.6 1.0
CB L:CYS51 3.4 82.0 1.0
N L:CYS51 3.7 82.0 1.0
N L:CYS34 3.8 78.6 1.0
CA L:CYS51 4.1 82.0 1.0
CA L:CYS34 4.1 78.6 1.0
CB L:ASP50 4.4 84.7 1.0
C L:CYS51 4.6 82.0 1.0
CA L:CYS48 4.6 79.9 1.0
O L:CYS51 4.6 82.0 1.0
C L:ASP50 4.7 84.7 1.0
O L:HIS53 4.7 75.2 1.0
CA L:CYS31 4.8 75.6 1.0
CB L:GLU33 4.8 75.9 1.0
CB L:HIS53 4.9 75.2 1.0
N L:ASP50 4.9 84.7 1.0
CA L:ASP50 4.9 84.7 1.0
C L:GLU33 4.9 75.9 1.0

Zinc binding site 9 out of 9 in 8ram

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Zinc binding site 9 out of 9 in the Structure of SEN1 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 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:212.5
occ:1.00
 SG M:CYS49 2.3 191.5 1.0
SG M:CYS52 2.3 196.9 1.0
SG M:CYS25 2.3 194.5 1.0
SG M:CYS28 2.3 198.8 1.0
CB M:CYS25 3.1 194.5 1.0
CB M:CYS49 3.2 191.5 1.0
CB M:CYS52 3.6 196.9 1.0
CB M:CYS28 3.7 198.8 1.0
N M:CYS28 4.0 198.8 1.0
N M:CYS52 4.0 196.9 1.0
CA M:CYS52 4.4 196.9 1.0
CA M:CYS28 4.5 198.8 1.0
CA M:CYS25 4.5 194.5 1.0
CB M:PHE27 4.7 192.4 1.0
CA M:CYS49 4.7 191.5 1.0
OG M:SER33 4.7 192.3 1.0
CB M:ILE51 4.9 194.8 1.0
N M:PHE27 4.9 192.4 1.0
C M:PHE27 5.0 192.4 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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