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:
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 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
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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
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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
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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
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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
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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
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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
|