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

Go back to Zinc Binding Sites List in 8jch
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

Go back to Zinc Binding Sites List in 8jch
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

Go back to Zinc Binding Sites List in 8jch
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

Go back to Zinc Binding Sites List in 8jch
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

Go back to Zinc Binding Sites List in 8jch
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

Go back to Zinc Binding Sites List in 8jch
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

Go back to Zinc Binding Sites List in 8jch
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

Go back to Zinc Binding Sites List in 8jch
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy