Zinc in PDB 8k5p: Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2)

Enzymatic activity of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2)

All present enzymatic activity of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2):
2.7.7.6;

Other elements in 8k5p:

The structure of Cryo-Em Structure of Yeast RAT1-Bound Pol II Pre-Termination Transcription Complex 2 (Pol II RAT1-PTTC2) 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 2 (Pol II RAT1-PTTC2) (pdb code 8k5p). 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 2 (Pol II RAT1-PTTC2), PDB code: 8k5p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:188.5
occ:1.00
 SG A:CYS107 2.3 141.2 1.0
SG A:CYS167 2.3 145.8 1.0
SG A:CYS110 2.3 130.5 1.0
SG A:CYS148 2.3 142.5 1.0
CB A:CYS148 3.1 140.9 1.0
CB A:CYS107 3.2 127.6 1.0
CB A:CYS167 3.5 139.8 1.0
CB A:CYS110 3.7 124.5 1.0
N A:CYS167 3.8 140.6 1.0
N A:CYS110 4.0 129.2 1.0
CA A:CYS167 4.2 138.2 1.0
NE2 A:GLN171 4.3 129.9 1.0
N A:GLY168 4.3 128.1 1.0
CA A:CYS110 4.4 126.8 1.0
CA A:CYS148 4.5 138.1 1.0
CB A:HIS109 4.6 129.9 1.0
CA A:CYS107 4.7 126.0 1.0
C A:CYS167 4.7 138.4 1.0
O A:CYS110 4.7 126.9 1.0
C A:HIS109 4.8 128.2 1.0
O A:ASN169 4.9 132.6 1.0
C A:GLY166 4.9 138.1 1.0
N A:ASN169 4.9 129.7 1.0
N A:HIS109 5.0 127.8 1.0
C A:CYS110 5.0 128.9 1.0

Zinc binding site 2 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:154.8
occ:1.00
 NE2 A:HIS80 2.1 93.2 1.0
SG A:CYS70 2.3 125.6 1.0
SG A:CYS67 2.3 131.2 1.0
SG A:CYS77 2.3 110.9 1.0
CE1 A:HIS80 2.8 87.0 1.0
CB A:CYS70 3.2 119.0 1.0
CD2 A:HIS80 3.2 87.6 1.0
CB A:CYS67 3.4 124.0 1.0
N A:CYS70 3.7 117.5 1.0
CB A:CYS77 3.7 97.9 1.0
ND1 A:HIS80 4.0 78.0 1.0
CA A:CYS70 4.0 119.0 1.0
CG A:HIS80 4.2 80.2 1.0
CB A:THR69 4.5 105.8 1.0
O A:CYS67 4.5 125.8 1.0
CA A:CYS77 4.5 97.4 1.0
CA A:CYS67 4.6 125.1 1.0
C A:THR69 4.7 107.9 1.0
C A:CYS70 4.8 122.0 1.0
C A:CYS67 4.8 125.9 1.0
O A:GLU72 4.9 137.9 1.0
OE1 A:GLU72 4.9 138.2 1.0
CA A:THR69 5.0 104.9 1.0

Zinc binding site 3 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:153.4
occ:1.00
 SG B:CYS1166 2.3 120.6 1.0
SG B:CYS1185 2.3 114.0 1.0
SG B:CYS1182 2.3 118.0 1.0
SG B:CYS1163 2.3 91.6 1.0
CB B:CYS1166 2.9 103.5 1.0
CB B:CYS1163 3.2 88.6 1.0
N B:CYS1166 3.3 97.0 1.0
CA B:CYS1166 3.6 96.9 1.0
CB B:CYS1182 3.6 110.2 1.0
CB B:CYS1185 3.7 109.5 1.0
N B:CYS1185 4.1 108.2 1.0
C B:ILE1165 4.4 86.0 1.0
CA B:CYS1185 4.5 107.7 1.0
CB B:ILE1165 4.5 88.8 1.0
CA B:CYS1163 4.7 82.3 1.0
C B:GLY1184 4.8 109.3 1.0
CA B:ILE1165 4.9 84.8 1.0
N B:ILE1165 4.9 88.7 1.0
CA B:GLY1184 4.9 107.2 1.0
CA B:CYS1182 5.0 109.0 1.0

Zinc binding site 4 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:179.0
occ:1.00
 SG C:CYS92 2.3 105.3 1.0
SG C:CYS88 2.3 129.4 1.0
SG C:CYS86 2.3 120.4 1.0
SG C:CYS95 2.3 110.4 1.0
CB C:CYS95 3.1 97.0 1.0
CB C:CYS86 3.1 110.8 1.0
CB C:CYS88 3.3 122.0 1.0
N C:CYS92 3.7 96.8 1.0
CB C:CYS92 3.7 97.7 1.0
C C:HIS91 4.2 106.0 1.0
CA C:CYS92 4.2 94.4 1.0
N C:CYS95 4.2 92.2 1.0
CA C:CYS95 4.2 88.5 1.0
N C:CYS88 4.3 118.0 1.0
CA C:HIS91 4.4 107.7 1.0
CG C:LYS94 4.4 95.2 1.0
CA C:CYS88 4.4 117.6 1.0
CA C:CYS86 4.6 107.2 1.0
O C:CYS92 4.7 110.8 1.0
C C:CYS92 4.7 97.8 1.0
NZ W:LYS813 4.9 145.4 1.0
O C:HIS91 4.9 107.4 1.0
C C:CYS95 5.0 89.2 1.0
C C:CYS86 5.0 114.0 1.0
C C:LYS94 5.0 91.1 1.0

Zinc binding site 5 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:219.4
occ:1.00
 SG I:CYS32 2.3 171.4 1.0
SG I:CYS29 2.3 177.5 1.0
SG I:CYS7 2.3 160.4 1.0
SG I:CYS10 2.3 164.8 1.0
CB I:CYS7 2.9 157.2 1.0
CB I:CYS29 3.1 169.5 1.0
O I:ASP9 3.4 161.9 1.0
CB I:CYS10 3.8 159.2 1.0
OG1 I:THR31 3.8 161.6 1.0
CB I:CYS32 4.0 167.9 1.0
C I:ASP9 4.1 161.1 1.0
CA I:CYS7 4.4 158.2 1.0
N I:CYS32 4.5 167.2 1.0
OD2 I:ASP9 4.6 161.4 1.0
CB I:ASN12 4.6 147.4 1.0
CA I:CYS29 4.6 167.9 1.0
N I:CYS10 4.7 159.3 1.0
CA I:CYS10 4.7 159.5 1.0
N I:ASN12 4.7 145.1 1.0
CB I:TYR34 4.7 159.4 1.0
CG I:ASP9 4.8 162.4 1.0
CA I:CYS32 4.9 168.7 1.0
CB I:ASP9 4.9 160.9 1.0
O I:ASN12 4.9 147.8 1.0
CD2 I:LEU14 5.0 157.7 1.0

Zinc binding site 6 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:200.8
occ:1.00
 SG I:CYS78 2.3 145.9 1.0
SG I:CYS75 2.3 133.8 1.0
SG I:CYS103 2.3 138.9 1.0
SG I:CYS106 2.3 144.3 1.0
CB I:CYS75 3.1 129.2 1.0
CB I:CYS103 3.3 126.9 1.0
O I:SER105 3.4 137.6 1.0
CB I:CYS78 3.5 137.4 1.0
CB I:CYS106 3.6 141.8 1.0
N I:CYS78 3.8 135.9 1.0
OG I:SER105 4.2 132.2 1.0
CA I:CYS78 4.2 136.8 1.0
C I:SER105 4.2 134.7 1.0
OG I:SER80 4.3 131.9 1.0
CB I:HIS108 4.4 118.7 1.0
CA I:CYS75 4.6 127.3 1.0
CB I:SER80 4.6 130.5 1.0
CB I:LYS77 4.6 131.7 1.0
CA I:CYS106 4.7 141.8 1.0
C I:CYS78 4.7 136.6 1.0
CA I:CYS103 4.8 121.7 1.0
N I:CYS106 4.8 138.8 1.0
N I:HIS79 4.8 132.7 1.0
C I:LYS77 4.9 130.0 1.0
N I:SER80 5.0 133.6 1.0

Zinc binding site 7 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:118.8
occ:1.00
 SG J:CYS10 2.3 87.3 1.0
SG J:CYS46 2.3 99.2 1.0
SG J:CYS45 2.3 92.6 1.0
SG J:CYS7 2.3 83.1 1.0
CB J:CYS7 3.2 67.4 1.0
N J:CYS46 3.3 70.5 1.0
CB J:CYS46 3.5 78.1 1.0
CA J:CYS46 3.6 70.5 1.0
CB J:CYS10 3.7 78.8 1.0
CB J:CYS45 3.7 75.2 1.0
C J:CYS45 3.7 72.7 1.0
N J:CYS10 3.9 67.2 1.0
O J:CYS45 4.2 83.0 1.0
CA J:CYS45 4.4 71.6 1.0
CA J:CYS10 4.4 73.5 1.0
NE J:ARG43 4.4 75.2 1.0
N J:GLY11 4.5 59.3 1.0
NH2 J:ARG43 4.5 77.7 1.0
CB J:LYS12 4.6 62.1 1.0
CA J:CYS7 4.6 58.7 1.0
N J:LYS12 4.7 69.0 1.0
CB J:SER9 4.8 79.7 1.0
CZ J:ARG43 5.0 77.1 1.0

Zinc binding site 8 out of 8 in 8k5p

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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 2 (Pol II RAT1-PTTC2)


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 2 (Pol II RAT1-PTTC2) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:168.2
occ:1.00
 SG L:CYS48 2.3 121.1 1.0
SG L:CYS34 2.3 112.4 1.0
SG L:CYS31 2.3 128.8 1.0
SG L:CYS51 2.3 132.4 1.0
CB L:CYS48 3.1 119.5 1.0
CB L:CYS31 3.1 109.8 1.0
CB L:CYS51 3.7 123.5 1.0
CB L:CYS34 3.7 111.8 1.0
N L:CYS34 3.9 107.7 1.0
N L:CYS51 3.9 125.8 1.0
CA L:CYS51 4.3 122.7 1.0
CA L:CYS34 4.4 110.7 1.0
CB L:HIS53 4.4 101.4 1.0
CA L:CYS48 4.6 116.8 1.0
O L:CYS51 4.6 122.8 1.0
C L:CYS51 4.6 121.8 1.0
CA L:CYS31 4.6 105.0 1.0
C L:ASP50 4.6 130.7 1.0
OG L:SER36 4.7 115.8 1.0
CB L:GLU33 4.7 113.1 1.0
CB L:SER36 4.8 108.5 1.0
CB L:ASP50 4.8 130.6 1.0
N L:ASP50 4.9 126.1 1.0
C L:GLU33 5.0 112.0 1.0
C L:CYS34 5.0 106.1 1.0
N L:HIS53 5.0 107.8 1.0
N L:GLU33 5.0 113.9 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 08:34:11 2024

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