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Zinc in PDB 8jch: Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)

Enzymatic activity of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)

All present enzymatic activity of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1):
2.7.7.6;

Other elements in 8jch:

The structure of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) (pdb code 8jch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1), PDB code: 8jch:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8jch

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Zinc binding site 1 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:182.7
occ:1.00
 SG A:CYS107 2.3 131.9 1.0
SG A:CYS167 2.3 142.1 1.0
SG A:CYS110 2.3 133.4 1.0
SG A:CYS148 2.3 141.6 1.0
CB A:CYS107 3.1 122.7 1.0
CB A:CYS148 3.5 135.7 1.0
CB A:CYS110 3.6 124.7 1.0
CB A:CYS167 3.7 135.8 1.0
N A:CYS167 3.9 136.9 1.0
N A:CYS110 3.9 125.1 1.0
NE2 A:GLN171 4.2 125.3 1.0
CA A:CYS110 4.3 124.5 1.0
CA A:CYS167 4.3 136.5 1.0
N A:GLY168 4.5 126.7 1.0
CA A:CYS107 4.6 121.5 1.0
O A:CYS110 4.6 123.9 1.0
C A:HIS109 4.8 118.0 1.0
CB A:HIS109 4.8 119.8 1.0
C A:CYS110 4.8 125.7 1.0
CA A:CYS148 4.8 135.3 1.0
O A:ASN169 4.9 127.0 1.0
C A:CYS167 4.9 135.3 1.0
N A:HIS109 4.9 119.1 1.0
N A:ASN169 5.0 125.4 1.0

Zinc binding site 2 out of 8 in 8jch

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Zinc binding site 2 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:147.3
occ:1.00
 NE2 A:HIS80 2.1 92.2 1.0
SG A:CYS70 2.3 115.0 1.0
SG A:CYS77 2.3 110.1 1.0
SG A:CYS67 2.3 133.4 1.0
CE1 A:HIS80 3.0 84.9 1.0
CD2 A:HIS80 3.0 89.8 1.0
CB A:CYS67 3.1 125.9 1.0
CB A:CYS77 3.7 103.3 1.0
CB A:CYS70 3.9 116.3 1.0
ND1 A:HIS80 4.0 80.9 1.0
CG A:HIS80 4.0 80.9 1.0
N A:CYS70 4.1 114.3 1.0
CB A:THR69 4.5 108.2 1.0
CA A:CYS67 4.5 125.3 1.0
CA A:CYS77 4.5 99.8 1.0
CA A:CYS70 4.6 115.7 1.0
CA A:GLY59 4.6 104.5 1.0
N A:GLY79 4.8 90.5 1.0
C A:CYS67 4.9 124.5 1.0
O A:CYS67 4.9 121.7 1.0
N A:THR69 5.0 109.0 1.0
C A:THR69 5.0 108.0 1.0

Zinc binding site 3 out of 8 in 8jch

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Zinc binding site 3 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:164.2
occ:1.00
 SG B:CYS1166 2.3 103.8 1.0
SG B:CYS1185 2.3 129.8 1.0
SG B:CYS1182 2.3 114.0 1.0
SG B:CYS1163 2.3 105.4 1.0
CB B:CYS1166 3.3 87.7 1.0
CB B:CYS1163 3.4 90.0 1.0
N B:CYS1166 3.5 89.9 1.0
CB B:CYS1182 3.6 106.1 1.0
CB B:CYS1185 3.6 117.5 1.0
N B:CYS1185 3.9 113.3 1.0
CA B:CYS1166 4.0 87.3 1.0
CB B:ILE1165 4.2 84.4 1.0
CA B:CYS1185 4.3 115.2 1.0
CB B:ASN1187 4.5 107.7 1.0
C B:ILE1165 4.6 84.2 1.0
CG1 B:ILE1165 4.7 85.3 1.0
C B:GLY1184 4.7 109.1 1.0
N B:ILE1165 4.8 88.7 1.0
CA B:ILE1165 4.8 81.8 1.0
CA B:CYS1163 4.8 85.5 1.0
O B:CYS1182 4.8 109.3 1.0
CA B:GLY1184 4.9 108.6 1.0
CA B:CYS1182 4.9 105.3 1.0
ND2 B:ASN1187 5.0 110.8 1.0
C B:CYS1185 5.0 118.1 1.0

Zinc binding site 4 out of 8 in 8jch

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Zinc binding site 4 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:162.8
occ:1.00
 SG C:CYS92 2.3 92.5 1.0
SG C:CYS88 2.3 127.1 1.0
SG C:CYS86 2.3 107.6 1.0
SG C:CYS95 2.3 95.1 1.0
CB C:CYS95 3.0 78.0 1.0
CB C:CYS86 3.1 96.4 1.0
CB C:CYS88 3.4 118.9 1.0
N C:CYS92 3.7 78.4 1.0
CB C:CYS92 3.8 84.9 1.0
CA C:CYS95 4.2 73.1 1.0
N C:CYS95 4.2 77.9 1.0
CA C:CYS92 4.3 77.5 1.0
CA C:CYS86 4.4 94.7 1.0
CG C:LYS94 4.4 76.7 1.0
C C:HIS91 4.5 87.5 1.0
CA C:HIS91 4.6 89.9 1.0
C C:CYS86 4.6 99.6 1.0
CA C:CYS88 4.7 114.8 1.0
N C:CYS88 4.7 117.3 1.0
NZ W:LYS813 4.8 132.6 1.0
C C:CYS92 4.9 80.2 1.0
N C:PHE87 4.9 110.6 1.0
C C:LYS94 4.9 75.0 1.0
O C:CYS92 5.0 88.6 1.0
C C:CYS95 5.0 73.9 1.0

Zinc binding site 5 out of 8 in 8jch

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Zinc binding site 5 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:211.6
occ:1.00
 SG I:CYS32 2.3 163.5 1.0
SG I:CYS29 2.3 160.5 1.0
SG I:CYS7 2.3 150.8 1.0
SG I:CYS10 2.3 163.6 1.0
OG1 I:THR31 2.9 157.4 1.0
CB I:CYS7 3.2 145.4 1.0
CB I:CYS29 3.2 158.3 1.0
O I:ASP9 3.4 155.2 1.0
N I:CYS32 3.8 158.7 1.0
CB I:CYS10 3.8 156.0 1.0
CB I:CYS32 3.9 158.8 1.0
C I:ASP9 3.9 154.3 1.0
O I:CYS32 4.1 158.8 1.0
CA I:CYS32 4.3 158.3 1.0
CB I:THR31 4.3 157.5 1.0
CB I:ASP9 4.4 154.4 1.0
N I:CYS10 4.5 156.0 1.0
C I:CYS32 4.5 157.2 1.0
C I:THR31 4.6 157.4 1.0
CA I:CYS7 4.6 146.5 1.0
CA I:CYS10 4.7 156.7 1.0
CA I:CYS29 4.7 157.2 1.0
CA I:ASP9 4.7 153.7 1.0
N I:THR31 4.7 157.7 1.0
CA I:THR31 4.8 158.7 1.0

Zinc binding site 6 out of 8 in 8jch

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Zinc binding site 6 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:197.8
occ:1.00
 SG I:CYS78 2.3 142.2 1.0
SG I:CYS75 2.3 135.1 1.0
SG I:CYS106 2.3 128.1 1.0
SG I:CYS103 2.3 126.4 1.0
CB I:CYS103 3.0 114.0 1.0
OG I:SER105 3.3 123.8 1.0
CB I:CYS75 3.3 128.2 1.0
CB I:CYS78 3.5 133.2 1.0
CB I:CYS106 3.7 123.6 1.0
N I:CYS106 4.0 123.3 1.0
OG I:SER80 4.1 127.5 1.0
N I:CYS78 4.4 133.6 1.0
CB I:SER80 4.4 125.8 1.0
CA I:CYS106 4.4 123.8 1.0
CA I:CYS78 4.4 134.1 1.0
CA I:CYS103 4.5 111.7 1.0
CB I:SER105 4.6 122.3 1.0
CA I:CYS75 4.8 127.0 1.0
CB I:HIS108 4.9 106.2 1.0
C I:CYS78 4.9 135.0 1.0
N I:SER80 4.9 128.9 1.0
C I:SER105 4.9 124.8 1.0

Zinc binding site 7 out of 8 in 8jch

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Zinc binding site 7 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:123.3
occ:1.00
 SG J:CYS10 2.3 68.2 1.0
SG J:CYS46 2.3 86.6 1.0
SG J:CYS45 2.3 81.3 1.0
SG J:CYS7 2.3 70.1 1.0
CB J:CYS7 3.2 51.8 1.0
N J:CYS46 3.3 54.9 1.0
CB J:CYS46 3.6 60.4 1.0
CB J:CYS10 3.6 65.6 1.0
CA J:CYS46 3.6 59.1 1.0
CB J:CYS45 3.7 67.0 1.0
C J:CYS45 3.8 65.0 1.0
N J:CYS10 3.9 58.7 1.0
O J:CYS45 4.3 77.2 1.0
CA J:CYS10 4.3 58.9 1.0
NE J:ARG43 4.3 67.8 1.0
CA J:CYS45 4.3 63.3 1.0
NH2 J:ARG43 4.5 73.7 1.0
N J:GLY11 4.5 41.4 1.0
CB J:LYS12 4.5 45.6 1.0
CA J:CYS7 4.6 41.2 1.0
N J:LYS12 4.7 53.1 1.0
CB J:SER9 4.8 63.9 1.0
CZ J:ARG43 4.9 68.2 1.0
C J:CYS10 5.0 59.6 1.0

Zinc binding site 8 out of 8 in 8jch

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Zinc binding site 8 out of 8 in the Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 1 (Pol II RAT1-PTTC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:166.0
occ:1.00
 SG L:CYS51 2.3 133.3 1.0
SG L:CYS34 2.3 109.5 1.0
SG L:CYS31 2.3 117.0 1.0
SG L:CYS48 2.3 126.9 1.0
CB L:CYS48 3.0 113.2 1.0
CB L:CYS34 3.1 109.7 1.0
CB L:CYS51 3.3 120.6 1.0
CB L:CYS31 3.6 103.8 1.0
N L:CYS51 3.6 119.3 1.0
CA L:CYS51 4.0 119.3 1.0
O L:ALA32 4.1 102.8 1.0
N L:GLY52 4.4 102.8 1.0
CB L:HIS53 4.4 90.2 1.0
N L:HIS53 4.5 89.5 1.0
CA L:CYS48 4.5 111.4 1.0
C L:CYS51 4.5 118.0 1.0
CA L:CYS34 4.5 107.6 1.0
CB L:ASP50 4.7 119.4 1.0
C L:ASP50 4.7 117.6 1.0
N L:CYS34 4.9 109.0 1.0
N L:ASP50 4.9 115.8 1.0
CA L:CYS31 4.9 96.7 1.0
CA L:ASP50 5.0 116.8 1.0
C L:CYS48 5.0 115.8 1.0

Reference:

Y.Zeng, H.Zhang, X.Wu, Y.Zhang. Structural Basis of Exoribonuclease-Mediated Mrna Transcription Termination To Be Published.
Page generated: Thu Oct 31 08:15:36 2024

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