Zinc in PDB 9bvt: Rna Pol II - High Mn(+2) Concentration
Enzymatic activity of Rna Pol II - High Mn(+2) Concentration
All present enzymatic activity of Rna Pol II - High Mn(+2) Concentration:
2.7.7.6;
Protein crystallography data
The structure of Rna Pol II - High Mn(+2) Concentration, PDB code: 9bvt
was solved by
G.Calero,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.25 /
3.40
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
221.19,
393.97,
283.28,
90,
90,
90
|
R / Rfree (%)
|
22 /
24.9
|
Other elements in 9bvt:
The structure of Rna Pol II - High Mn(+2) Concentration also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Rna Pol II - High Mn(+2) Concentration
(pdb code 9bvt). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Rna Pol II - High Mn(+2) Concentration, PDB code: 9bvt:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 1 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1801
b:159.6
occ:1.00
|
SG
|
A:CYS110
|
2.3
|
207.4
|
1.0
|
SG
|
A:CYS167
|
2.3
|
225.8
|
1.0
|
SG
|
A:CYS107
|
2.3
|
217.2
|
1.0
|
CB
|
A:CYS167
|
2.9
|
198.8
|
1.0
|
CB
|
A:CYS107
|
3.0
|
198.3
|
1.0
|
SG
|
A:CYS148
|
3.4
|
212.3
|
1.0
|
CB
|
A:CYS110
|
3.5
|
209.1
|
1.0
|
CB
|
A:CYS148
|
3.7
|
187.0
|
1.0
|
N
|
A:CYS110
|
3.8
|
208.2
|
1.0
|
CA
|
A:CYS110
|
4.2
|
209.9
|
1.0
|
CA
|
A:CYS167
|
4.2
|
207.1
|
1.0
|
C
|
A:CYS167
|
4.3
|
211.5
|
1.0
|
CA
|
A:CYS107
|
4.5
|
195.1
|
1.0
|
ND1
|
A:HIS109
|
4.5
|
218.1
|
1.0
|
N
|
A:GLY168
|
4.5
|
193.8
|
1.0
|
CB
|
A:HIS109
|
4.6
|
192.4
|
1.0
|
N
|
A:GLY111
|
4.7
|
182.9
|
1.0
|
O
|
A:CYS167
|
4.8
|
215.4
|
1.0
|
C
|
A:HIS109
|
4.8
|
184.0
|
1.0
|
C
|
A:CYS110
|
4.9
|
190.6
|
1.0
|
C
|
A:CYS107
|
4.9
|
183.2
|
1.0
|
N
|
A:ASN169
|
4.9
|
173.8
|
1.0
|
CG
|
A:HIS109
|
5.0
|
211.1
|
1.0
|
O
|
A:CYS107
|
5.0
|
178.2
|
1.0
|
CA
|
A:CYS148
|
5.0
|
203.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 2 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1802
b:116.0
occ:1.00
|
SG
|
A:CYS70
|
2.3
|
115.3
|
1.0
|
NE2
|
A:HIS80
|
2.3
|
144.7
|
1.0
|
SG
|
A:CYS77
|
2.3
|
118.8
|
1.0
|
SG
|
A:CYS67
|
2.3
|
120.9
|
1.0
|
CD2
|
A:HIS80
|
2.5
|
103.3
|
1.0
|
CB
|
A:CYS67
|
3.2
|
153.2
|
1.0
|
OG1
|
A:THR69
|
3.2
|
141.8
|
1.0
|
CE1
|
A:HIS80
|
3.6
|
174.6
|
1.0
|
CB
|
A:CYS77
|
3.6
|
112.7
|
1.0
|
O
|
A:CYS70
|
3.8
|
153.0
|
1.0
|
CB
|
A:CYS70
|
3.8
|
162.4
|
1.0
|
N
|
A:CYS70
|
3.8
|
112.0
|
1.0
|
CG
|
A:HIS80
|
3.9
|
119.3
|
1.0
|
CA
|
A:CYS70
|
4.2
|
127.4
|
1.0
|
ND1
|
A:HIS80
|
4.3
|
177.0
|
1.0
|
CA
|
A:CYS77
|
4.4
|
116.0
|
1.0
|
C
|
A:CYS70
|
4.5
|
134.1
|
1.0
|
CB
|
A:THR69
|
4.6
|
122.8
|
1.0
|
CA
|
A:CYS67
|
4.7
|
147.8
|
1.0
|
C
|
A:THR69
|
4.8
|
127.2
|
1.0
|
C
|
A:CYS77
|
4.9
|
112.8
|
1.0
|
N
|
A:THR69
|
5.0
|
126.6
|
1.0
|
N
|
A:GLY79
|
5.0
|
99.8
|
1.0
|
|
Zinc binding site 3 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 3 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1301
b:135.3
occ:1.00
|
SG
|
B:CYS1185
|
2.3
|
84.8
|
1.0
|
SG
|
B:CYS1166
|
2.3
|
126.7
|
1.0
|
SG
|
B:CYS1163
|
2.3
|
137.3
|
1.0
|
CB
|
B:CYS1163
|
2.9
|
124.2
|
1.0
|
N
|
B:CYS1166
|
2.9
|
106.6
|
1.0
|
CB
|
B:CYS1166
|
3.4
|
138.6
|
1.0
|
CB
|
B:CYS1185
|
3.5
|
131.2
|
1.0
|
CB
|
B:ILE1165
|
3.6
|
126.0
|
1.0
|
CA
|
B:CYS1166
|
3.6
|
124.3
|
1.0
|
SG
|
B:CYS1182
|
3.7
|
143.3
|
1.0
|
O
|
B:CYS1166
|
3.9
|
105.7
|
1.0
|
C
|
B:ILE1165
|
3.9
|
119.6
|
1.0
|
N
|
B:ILE1165
|
3.9
|
111.6
|
1.0
|
CA
|
B:ILE1165
|
4.0
|
121.0
|
1.0
|
C
|
B:CYS1166
|
4.1
|
123.1
|
1.0
|
CD1
|
B:ILE1165
|
4.2
|
84.7
|
1.0
|
CA
|
B:CYS1163
|
4.3
|
95.3
|
1.0
|
CG2
|
B:ILE1165
|
4.4
|
163.3
|
1.0
|
CG1
|
B:ILE1165
|
4.4
|
85.0
|
1.0
|
ND2
|
B:ASN1187
|
4.5
|
185.8
|
1.0
|
CB
|
B:CYS1182
|
4.6
|
158.8
|
1.0
|
O
|
B:CYS1185
|
4.7
|
157.2
|
1.0
|
C
|
B:CYS1163
|
4.7
|
110.2
|
1.0
|
N
|
B:GLY1164
|
4.8
|
113.6
|
1.0
|
CA
|
B:CYS1185
|
4.9
|
148.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 4 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:114.0
occ:1.00
|
SG
|
C:CYS88
|
2.3
|
102.3
|
1.0
|
SG
|
C:CYS92
|
2.3
|
136.9
|
1.0
|
SG
|
C:CYS95
|
2.3
|
119.0
|
1.0
|
SG
|
C:CYS86
|
2.3
|
118.4
|
1.0
|
CB
|
C:CYS95
|
3.4
|
128.6
|
1.0
|
CB
|
C:CYS86
|
3.4
|
132.0
|
1.0
|
CB
|
C:CYS88
|
3.5
|
135.6
|
1.0
|
CB
|
C:CYS92
|
3.5
|
133.0
|
1.0
|
N
|
C:CYS92
|
3.6
|
120.1
|
1.0
|
N
|
C:CYS95
|
4.0
|
142.0
|
1.0
|
C
|
C:HIS91
|
4.1
|
137.2
|
1.0
|
CA
|
C:CYS92
|
4.1
|
103.3
|
1.0
|
N
|
C:CYS88
|
4.2
|
87.2
|
1.0
|
CA
|
C:HIS91
|
4.2
|
123.0
|
1.0
|
CA
|
C:CYS95
|
4.3
|
139.8
|
1.0
|
CB
|
C:LYS94
|
4.4
|
142.4
|
1.0
|
CA
|
C:CYS88
|
4.5
|
112.8
|
1.0
|
C
|
C:LYS94
|
4.6
|
137.4
|
1.0
|
O
|
C:ASP90
|
4.6
|
153.6
|
1.0
|
N
|
C:LYS94
|
4.7
|
113.5
|
1.0
|
C
|
C:CYS92
|
4.7
|
121.5
|
1.0
|
CD
|
C:LYS94
|
4.8
|
156.4
|
1.0
|
CA
|
C:CYS86
|
4.8
|
112.4
|
1.0
|
CA
|
C:LYS94
|
4.8
|
120.4
|
1.0
|
CG
|
C:LYS94
|
4.9
|
148.0
|
1.0
|
N
|
C:PHE87
|
4.9
|
118.8
|
1.0
|
O
|
C:HIS91
|
4.9
|
133.4
|
1.0
|
|
Zinc binding site 5 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 5 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:150.9
occ:1.00
|
SG
|
I:CYS32
|
2.3
|
140.9
|
1.0
|
SG
|
I:CYS29
|
2.3
|
175.9
|
1.0
|
SG
|
I:CYS7
|
2.3
|
155.0
|
1.0
|
CB
|
I:CYS7
|
2.8
|
157.0
|
1.0
|
CB
|
I:CYS10
|
3.0
|
162.6
|
1.0
|
SG
|
I:CYS10
|
3.2
|
158.6
|
1.0
|
CB
|
I:CYS29
|
3.5
|
189.5
|
1.0
|
N
|
I:CYS10
|
3.7
|
147.0
|
1.0
|
CB
|
I:CYS32
|
3.8
|
157.3
|
1.0
|
CA
|
I:CYS10
|
4.0
|
174.1
|
1.0
|
N
|
I:CYS32
|
4.0
|
143.1
|
1.0
|
CB
|
I:TYR34
|
4.1
|
143.1
|
1.0
|
CA
|
I:CYS7
|
4.3
|
147.6
|
1.0
|
CA
|
I:CYS32
|
4.4
|
165.1
|
1.0
|
CB
|
I:THR31
|
4.7
|
187.6
|
1.0
|
C
|
I:ASP9
|
4.7
|
166.5
|
1.0
|
C
|
I:CYS10
|
4.8
|
156.7
|
1.0
|
C
|
I:CYS32
|
4.8
|
194.1
|
1.0
|
CG
|
I:TYR34
|
4.9
|
143.6
|
1.0
|
CA
|
I:CYS29
|
4.9
|
157.6
|
1.0
|
O
|
I:ASN12
|
4.9
|
176.8
|
1.0
|
CB
|
I:ASP9
|
4.9
|
185.6
|
1.0
|
N
|
I:TYR34
|
4.9
|
156.4
|
1.0
|
CB
|
I:ASN12
|
4.9
|
177.9
|
1.0
|
N
|
I:ASP9
|
5.0
|
172.8
|
1.0
|
N
|
I:ASN11
|
5.0
|
148.1
|
1.0
|
C
|
I:CYS7
|
5.0
|
143.0
|
1.0
|
|
Zinc binding site 6 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 6 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn202
b:216.0
occ:1.00
|
SG
|
I:CYS106
|
2.3
|
207.4
|
1.0
|
SG
|
I:CYS78
|
2.3
|
236.1
|
1.0
|
SG
|
I:CYS75
|
2.3
|
246.3
|
1.0
|
CB
|
I:CYS78
|
3.2
|
227.4
|
1.0
|
CB
|
I:CYS106
|
3.3
|
186.4
|
1.0
|
CB
|
I:CYS75
|
3.4
|
205.3
|
1.0
|
N
|
I:CYS78
|
3.5
|
255.1
|
1.0
|
OG
|
I:SER105
|
3.6
|
235.9
|
1.0
|
CA
|
I:CYS78
|
3.8
|
250.8
|
1.0
|
CB
|
I:CYS103
|
3.9
|
225.1
|
1.0
|
SG
|
I:CYS103
|
4.0
|
252.1
|
1.0
|
N
|
I:CYS106
|
4.1
|
241.4
|
1.0
|
N
|
I:HIS79
|
4.2
|
298.1
|
1.0
|
CA
|
I:CYS106
|
4.3
|
200.2
|
1.0
|
C
|
I:CYS78
|
4.3
|
260.6
|
1.0
|
OG
|
I:SER80
|
4.7
|
238.9
|
1.0
|
C
|
I:LYS77
|
4.7
|
249.0
|
1.0
|
CA
|
I:CYS75
|
4.8
|
212.6
|
1.0
|
CB
|
I:SER105
|
4.8
|
239.5
|
1.0
|
N
|
I:SER80
|
4.8
|
253.8
|
1.0
|
CB
|
I:LYS77
|
4.8
|
216.9
|
1.0
|
N
|
I:LYS77
|
4.9
|
246.2
|
1.0
|
C
|
I:SER105
|
4.9
|
242.4
|
1.0
|
C
|
I:CYS106
|
4.9
|
216.1
|
1.0
|
CB
|
I:SER80
|
5.0
|
238.2
|
1.0
|
|
Zinc binding site 7 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 7 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:133.5
occ:1.00
|
SG
|
J:CYS46
|
2.3
|
125.7
|
1.0
|
SG
|
J:CYS10
|
2.3
|
131.9
|
1.0
|
SG
|
J:CYS45
|
2.3
|
134.2
|
1.0
|
SG
|
J:CYS7
|
2.3
|
126.8
|
1.0
|
OG
|
J:SER9
|
2.8
|
148.3
|
1.0
|
N
|
J:CYS46
|
3.3
|
155.2
|
1.0
|
CB
|
J:CYS7
|
3.3
|
108.4
|
1.0
|
CB
|
J:CYS46
|
3.5
|
123.8
|
1.0
|
CA
|
J:CYS46
|
3.6
|
132.1
|
1.0
|
C
|
J:CYS45
|
3.7
|
141.2
|
1.0
|
CB
|
J:CYS45
|
3.7
|
155.2
|
1.0
|
CB
|
J:CYS10
|
3.8
|
127.4
|
1.0
|
NH2
|
J:ARG43
|
3.9
|
145.6
|
1.0
|
N
|
J:CYS10
|
3.9
|
137.7
|
1.0
|
NE
|
J:ARG43
|
3.9
|
144.0
|
1.0
|
O
|
J:CYS45
|
4.2
|
125.7
|
1.0
|
CB
|
J:SER9
|
4.2
|
138.8
|
1.0
|
CA
|
J:CYS45
|
4.3
|
130.9
|
1.0
|
CZ
|
J:ARG43
|
4.4
|
150.4
|
1.0
|
CA
|
J:CYS10
|
4.4
|
138.5
|
1.0
|
CA
|
J:CYS7
|
4.7
|
123.8
|
1.0
|
N
|
J:SER9
|
4.9
|
116.3
|
1.0
|
C
|
J:SER9
|
4.9
|
139.3
|
1.0
|
CA
|
J:SER9
|
4.9
|
132.2
|
1.0
|
CB
|
J:ARG43
|
4.9
|
156.8
|
1.0
|
N
|
J:CYS45
|
5.0
|
123.5
|
1.0
|
|
Zinc binding site 8 out
of 8 in 9bvt
Go back to
Zinc Binding Sites List in 9bvt
Zinc binding site 8 out
of 8 in the Rna Pol II - High Mn(+2) Concentration
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Rna Pol II - High Mn(+2) Concentration within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:166.7
occ:1.00
|
SG
|
L:CYS34
|
2.3
|
168.1
|
1.0
|
SG
|
L:CYS51
|
2.3
|
229.4
|
1.0
|
SG
|
L:CYS31
|
2.3
|
229.8
|
1.0
|
SG
|
L:CYS48
|
2.3
|
147.5
|
1.0
|
CB
|
L:CYS51
|
2.5
|
216.1
|
1.0
|
CB
|
L:CYS31
|
3.2
|
188.1
|
1.0
|
CB
|
L:CYS34
|
3.4
|
167.0
|
1.0
|
CB
|
L:CYS48
|
3.4
|
155.3
|
1.0
|
OG
|
L:SER36
|
3.7
|
166.3
|
1.0
|
CA
|
L:CYS51
|
3.8
|
243.8
|
1.0
|
N
|
L:CYS51
|
3.9
|
257.0
|
1.0
|
CB
|
L:SER36
|
4.2
|
181.8
|
1.0
|
N
|
L:CYS34
|
4.3
|
211.8
|
1.0
|
CA
|
L:CYS34
|
4.4
|
192.6
|
1.0
|
OE1
|
L:GLU33
|
4.4
|
218.4
|
1.0
|
N
|
L:SER36
|
4.4
|
190.4
|
1.0
|
C
|
L:ASP50
|
4.5
|
242.5
|
1.0
|
N
|
L:SER35
|
4.6
|
233.4
|
1.0
|
O
|
L:CYS48
|
4.6
|
206.5
|
1.0
|
CA
|
L:CYS31
|
4.7
|
181.2
|
1.0
|
N
|
L:GLY52
|
4.7
|
188.8
|
1.0
|
CA
|
L:CYS48
|
4.8
|
146.4
|
1.0
|
C
|
L:CYS34
|
4.8
|
208.7
|
1.0
|
C
|
L:CYS51
|
4.8
|
225.7
|
1.0
|
O
|
L:ASP50
|
4.9
|
235.8
|
1.0
|
CA
|
L:SER36
|
5.0
|
173.8
|
1.0
|
N
|
L:ALA32
|
5.0
|
176.8
|
1.0
|
|
Reference:
G.Lin,
C.O.Barnes,
S.Weiss,
B.Dutagaci,
C.Qiu,
M.Feig,
J.Song,
A.Lyubimov,
A.E.Cohen,
C.D.Kaplan,
G.Calero.
Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser. Proc.Natl.Acad.Sci.Usa V. 121 27121 2024.
ISSN: ESSN 1091-6490
PubMed: 39190355
DOI: 10.1073/PNAS.2318527121
Page generated: Thu Oct 31 14:42:26 2024
|