Zinc in PDB 4y7n: The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Enzymatic activity of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
All present enzymatic activity of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.:
2.7.7.6;
Protein crystallography data
The structure of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y7n
was solved by
L.Wang,
J.Chong,
D.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.88 /
3.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
168.181,
222.614,
192.829,
90.00,
101.59,
90.00
|
R / Rfree (%)
|
20.7 /
25
|
Other elements in 4y7n:
The structure of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
(pdb code 4y7n). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation., PDB code: 4y7n:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 1 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1801
b:0.1
occ:0.96
|
SG
|
A:CYS110
|
2.3
|
0.7
|
1.0
|
SG
|
A:CYS167
|
2.3
|
0.5
|
1.0
|
SG
|
A:CYS148
|
2.4
|
0.2
|
1.0
|
SG
|
A:CYS107
|
2.4
|
0.6
|
1.0
|
N
|
A:CYS110
|
2.8
|
0.1
|
1.0
|
CB
|
A:CYS110
|
3.0
|
0.9
|
1.0
|
CB
|
A:CYS167
|
3.4
|
0.0
|
1.0
|
CA
|
A:CYS110
|
3.4
|
0.2
|
1.0
|
CB
|
A:HIS109
|
3.5
|
0.3
|
1.0
|
CB
|
A:CYS148
|
3.7
|
0.8
|
1.0
|
CB
|
A:CYS107
|
3.8
|
0.0
|
1.0
|
N
|
A:GLY111
|
3.8
|
0.7
|
1.0
|
C
|
A:HIS109
|
3.9
|
0.8
|
1.0
|
C
|
A:CYS110
|
4.0
|
1.0
|
1.0
|
CA
|
A:HIS109
|
4.1
|
0.3
|
1.0
|
N
|
A:CYS167
|
4.2
|
0.1
|
1.0
|
OD1
|
A:ASN169
|
4.2
|
0.2
|
1.0
|
N
|
A:HIS109
|
4.3
|
0.0
|
1.0
|
CA
|
A:CYS167
|
4.3
|
0.3
|
1.0
|
CG
|
A:HIS109
|
4.6
|
0.7
|
1.0
|
O
|
A:CYS167
|
4.7
|
1.0
|
1.0
|
C
|
A:CYS167
|
4.9
|
1.0
|
1.0
|
CA
|
A:GLY111
|
4.9
|
0.7
|
1.0
|
O
|
A:HIS109
|
5.0
|
0.7
|
1.0
|
CA
|
A:CYS148
|
5.0
|
0.4
|
1.0
|
|
Zinc binding site 2 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 2 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1802
b:0.7
occ:1.00
|
SG
|
A:CYS67
|
2.3
|
0.8
|
1.0
|
NE2
|
A:HIS80
|
2.3
|
0.4
|
1.0
|
SG
|
A:CYS70
|
2.4
|
0.2
|
1.0
|
SG
|
A:CYS77
|
2.4
|
0.6
|
1.0
|
OE1
|
A:GLN68
|
2.7
|
0.8
|
1.0
|
CE1
|
A:HIS80
|
3.1
|
0.6
|
1.0
|
CD2
|
A:HIS80
|
3.4
|
0.4
|
1.0
|
CB
|
A:CYS67
|
3.5
|
0.8
|
1.0
|
CB
|
A:CYS77
|
3.5
|
0.5
|
1.0
|
CD
|
A:GLN68
|
3.5
|
0.7
|
1.0
|
NE2
|
A:GLN68
|
3.6
|
0.5
|
1.0
|
CB
|
A:CYS70
|
3.7
|
0.8
|
1.0
|
O
|
A:CYS67
|
3.9
|
0.1
|
1.0
|
ND1
|
A:HIS80
|
4.2
|
0.4
|
1.0
|
CA
|
A:CYS77
|
4.4
|
0.5
|
1.0
|
CG
|
A:HIS80
|
4.4
|
0.3
|
1.0
|
CD
|
A:PRO78
|
4.4
|
0.5
|
1.0
|
C
|
A:CYS67
|
4.5
|
0.5
|
1.0
|
O
|
A:GLN71
|
4.6
|
0.9
|
1.0
|
CA
|
A:CYS67
|
4.6
|
0.9
|
1.0
|
CG
|
A:GLN68
|
4.9
|
0.8
|
1.0
|
N
|
A:PRO78
|
5.0
|
0.9
|
1.0
|
C
|
A:CYS77
|
5.0
|
0.4
|
1.0
|
|
Zinc binding site 3 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 3 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1301
b:0.1
occ:1.00
|
SG
|
B:CYS1182
|
2.3
|
0.2
|
1.0
|
SG
|
B:CYS1163
|
2.3
|
0.4
|
1.0
|
SG
|
B:CYS1166
|
2.4
|
0.8
|
1.0
|
SG
|
B:CYS1185
|
2.4
|
0.1
|
1.0
|
CB
|
B:CYS1166
|
2.8
|
0.4
|
1.0
|
CB
|
B:CYS1163
|
3.0
|
0.8
|
1.0
|
N
|
B:CYS1166
|
3.2
|
0.4
|
1.0
|
CA
|
B:CYS1166
|
3.6
|
0.1
|
1.0
|
CB
|
B:CYS1182
|
3.9
|
0.1
|
1.0
|
CB
|
B:ILE1165
|
4.2
|
0.9
|
1.0
|
CB
|
B:CYS1185
|
4.2
|
0.6
|
1.0
|
N
|
B:CYS1185
|
4.2
|
0.5
|
1.0
|
C
|
B:ILE1165
|
4.3
|
0.6
|
1.0
|
CA
|
B:GLY1184
|
4.3
|
0.8
|
1.0
|
C
|
B:GLY1184
|
4.4
|
0.1
|
1.0
|
N
|
B:GLY1167
|
4.5
|
0.5
|
1.0
|
CA
|
B:CYS1163
|
4.5
|
0.4
|
1.0
|
C
|
B:CYS1166
|
4.6
|
0.4
|
1.0
|
CA
|
B:ILE1165
|
4.6
|
0.7
|
1.0
|
O
|
B:CYS1182
|
4.6
|
0.9
|
1.0
|
N
|
B:ILE1165
|
4.7
|
0.3
|
1.0
|
CG1
|
B:ILE1165
|
4.8
|
0.3
|
1.0
|
N
|
B:GLY1184
|
4.8
|
0.5
|
1.0
|
C
|
B:CYS1163
|
4.9
|
0.6
|
1.0
|
CA
|
B:CYS1185
|
5.0
|
0.8
|
1.0
|
|
Zinc binding site 4 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 4 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:0.4
occ:1.00
|
SG
|
C:CYS92
|
2.2
|
76.6
|
1.0
|
SG
|
C:CYS86
|
2.4
|
91.5
|
1.0
|
SG
|
C:CYS88
|
2.4
|
79.6
|
1.0
|
SG
|
C:CYS95
|
2.4
|
90.7
|
1.0
|
CB
|
C:CYS92
|
2.9
|
83.2
|
1.0
|
N
|
C:CYS92
|
3.3
|
90.1
|
1.0
|
CB
|
C:CYS95
|
3.4
|
81.0
|
1.0
|
CB
|
C:CYS86
|
3.5
|
83.3
|
1.0
|
CB
|
C:CYS88
|
3.6
|
86.7
|
1.0
|
CA
|
C:CYS92
|
3.7
|
84.7
|
1.0
|
C
|
C:HIS91
|
3.7
|
94.0
|
1.0
|
CA
|
C:HIS91
|
4.1
|
89.7
|
1.0
|
O
|
C:ASP90
|
4.3
|
85.1
|
1.0
|
O
|
C:HIS91
|
4.4
|
89.9
|
1.0
|
N
|
C:CYS95
|
4.4
|
92.5
|
1.0
|
C
|
C:CYS92
|
4.4
|
85.0
|
1.0
|
CA
|
C:CYS95
|
4.5
|
86.1
|
1.0
|
N
|
C:CYS88
|
4.6
|
84.7
|
1.0
|
CA
|
C:CYS88
|
4.7
|
87.0
|
1.0
|
CA
|
C:CYS86
|
4.8
|
86.1
|
1.0
|
C
|
C:CYS86
|
4.9
|
86.8
|
1.0
|
N
|
C:ASP93
|
5.0
|
80.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 5 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn201
b:0.1
occ:1.00
|
SG
|
I:CYS29
|
2.2
|
97.2
|
1.0
|
SG
|
I:CYS32
|
2.2
|
0.4
|
1.0
|
SG
|
I:CYS10
|
2.3
|
98.7
|
1.0
|
SG
|
I:CYS7
|
2.4
|
89.5
|
1.0
|
CB
|
I:CYS10
|
2.8
|
88.6
|
1.0
|
CB
|
I:CYS7
|
3.0
|
90.3
|
1.0
|
CB
|
I:CYS29
|
3.3
|
93.7
|
1.0
|
CB
|
I:CYS32
|
3.5
|
0.5
|
1.0
|
N
|
I:CYS32
|
3.8
|
0.6
|
1.0
|
N
|
I:CYS10
|
4.0
|
98.5
|
1.0
|
CA
|
I:CYS10
|
4.0
|
93.7
|
1.0
|
CA
|
I:CYS32
|
4.2
|
0.9
|
1.0
|
CB
|
I:THR31
|
4.3
|
0.3
|
1.0
|
CB
|
I:TYR34
|
4.5
|
80.6
|
1.0
|
CA
|
I:CYS7
|
4.5
|
96.4
|
1.0
|
C
|
I:THR31
|
4.6
|
0.7
|
1.0
|
N
|
I:SER33
|
4.7
|
0.4
|
1.0
|
CA
|
I:CYS29
|
4.7
|
93.0
|
1.0
|
OG1
|
I:THR31
|
4.7
|
0.9
|
1.0
|
N
|
I:THR31
|
4.7
|
0.6
|
1.0
|
N
|
I:TYR34
|
4.8
|
84.3
|
1.0
|
CB
|
I:ASP9
|
4.8
|
0.5
|
1.0
|
CA
|
I:THR31
|
4.8
|
0.3
|
1.0
|
C
|
I:CYS29
|
4.9
|
99.1
|
1.0
|
C
|
I:ASP9
|
4.9
|
0.2
|
1.0
|
O
|
I:CYS29
|
4.9
|
0.1
|
1.0
|
C
|
I:CYS10
|
5.0
|
94.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 6 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn202
b:93.9
occ:1.00
|
SG
|
I:CYS78
|
2.2
|
0.5
|
1.0
|
SG
|
I:CYS106
|
2.2
|
0.3
|
1.0
|
SG
|
I:CYS103
|
2.4
|
91.0
|
1.0
|
SG
|
I:CYS75
|
2.4
|
0.4
|
1.0
|
CB
|
I:CYS78
|
2.7
|
0.7
|
1.0
|
CB
|
I:CYS75
|
2.8
|
95.3
|
1.0
|
N
|
I:CYS78
|
3.4
|
0.2
|
1.0
|
CA
|
I:CYS78
|
3.6
|
0.7
|
1.0
|
CB
|
I:CYS106
|
3.6
|
0.3
|
1.0
|
CB
|
I:CYS103
|
3.7
|
92.2
|
1.0
|
N
|
I:CYS106
|
3.7
|
0.2
|
1.0
|
CB
|
I:SER105
|
4.1
|
0.0
|
1.0
|
CA
|
I:CYS106
|
4.3
|
99.8
|
1.0
|
CA
|
I:CYS75
|
4.3
|
95.3
|
1.0
|
C
|
I:LYS77
|
4.3
|
83.3
|
1.0
|
C
|
I:CYS78
|
4.4
|
0.7
|
1.0
|
N
|
I:HIS79
|
4.4
|
0.9
|
1.0
|
N
|
I:LYS77
|
4.6
|
88.1
|
1.0
|
CB
|
I:LYS77
|
4.6
|
90.4
|
1.0
|
N
|
I:SER80
|
4.7
|
77.4
|
1.0
|
CA
|
I:LYS77
|
4.8
|
87.4
|
1.0
|
CB
|
I:SER80
|
4.8
|
71.0
|
1.0
|
C
|
I:SER105
|
4.8
|
0.3
|
1.0
|
C
|
I:CYS75
|
4.8
|
99.0
|
1.0
|
CA
|
I:SER105
|
4.9
|
0.9
|
1.0
|
CB
|
I:HIS108
|
4.9
|
91.7
|
1.0
|
C
|
I:CYS106
|
4.9
|
0.1
|
1.0
|
N
|
I:SER105
|
4.9
|
0.6
|
1.0
|
|
Zinc binding site 7 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 7 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn101
b:92.2
occ:1.00
|
SG
|
J:CYS10
|
2.2
|
83.2
|
1.0
|
SG
|
J:CYS7
|
2.2
|
76.5
|
1.0
|
SG
|
J:CYS45
|
2.2
|
93.4
|
1.0
|
SG
|
J:CYS46
|
2.2
|
67.4
|
1.0
|
CB
|
J:CYS46
|
2.5
|
77.4
|
1.0
|
N
|
J:CYS46
|
2.8
|
91.5
|
1.0
|
CA
|
J:CYS46
|
2.9
|
88.0
|
1.0
|
CB
|
J:CYS7
|
3.1
|
77.5
|
1.0
|
C
|
J:CYS45
|
3.2
|
88.2
|
1.0
|
CB
|
J:CYS10
|
3.4
|
68.3
|
1.0
|
O
|
J:CYS45
|
3.6
|
83.7
|
1.0
|
CB
|
J:CYS45
|
3.6
|
86.1
|
1.0
|
N
|
J:CYS10
|
3.7
|
69.3
|
1.0
|
CA
|
J:CYS45
|
4.1
|
80.5
|
1.0
|
CA
|
J:CYS10
|
4.1
|
72.5
|
1.0
|
NH2
|
J:ARG43
|
4.3
|
92.7
|
1.0
|
C
|
J:CYS46
|
4.4
|
84.5
|
1.0
|
CB
|
J:SER9
|
4.4
|
70.8
|
1.0
|
CA
|
J:CYS7
|
4.5
|
75.6
|
1.0
|
OG
|
J:SER9
|
4.6
|
67.4
|
1.0
|
N
|
J:GLY11
|
4.7
|
60.7
|
1.0
|
N
|
J:CYS45
|
4.7
|
77.9
|
1.0
|
C
|
J:SER9
|
4.8
|
60.3
|
1.0
|
CB
|
J:LYS12
|
4.8
|
52.2
|
1.0
|
N
|
J:SER9
|
4.8
|
61.1
|
1.0
|
CA
|
J:SER9
|
4.9
|
60.1
|
1.0
|
C
|
J:CYS7
|
5.0
|
77.6
|
1.0
|
C
|
J:CYS10
|
5.0
|
69.6
|
1.0
|
|
Zinc binding site 8 out
of 8 in 4y7n
Go back to
Zinc Binding Sites List in 4y7n
Zinc binding site 8 out
of 8 in the The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation.
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of The Structure Insight Into 5-Carboxycytosine Recognition By Rna Polymerase II During Transcription Elongation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Zn101
b:0.5
occ:1.00
|
SG
|
L:CYS48
|
2.3
|
0.8
|
1.0
|
SG
|
L:CYS51
|
2.4
|
0.4
|
1.0
|
SG
|
L:CYS31
|
2.4
|
0.1
|
1.0
|
SG
|
L:CYS34
|
2.4
|
0.9
|
1.0
|
CB
|
L:CYS51
|
2.5
|
0.4
|
1.0
|
CB
|
L:CYS34
|
2.7
|
0.1
|
1.0
|
CB
|
L:CYS31
|
3.4
|
0.5
|
1.0
|
CB
|
L:CYS48
|
3.8
|
0.9
|
1.0
|
O
|
L:LYS49
|
3.9
|
0.7
|
1.0
|
CA
|
L:CYS51
|
3.9
|
0.1
|
1.0
|
CA
|
L:CYS34
|
4.0
|
0.8
|
1.0
|
N
|
L:CYS51
|
4.2
|
0.7
|
1.0
|
N
|
L:CYS34
|
4.3
|
0.2
|
1.0
|
O
|
L:ASP50
|
4.4
|
0.3
|
1.0
|
C
|
L:ASP50
|
4.5
|
0.2
|
1.0
|
O
|
L:CYS34
|
4.6
|
0.4
|
1.0
|
C
|
L:CYS34
|
4.6
|
0.9
|
1.0
|
C
|
L:LYS49
|
4.7
|
0.8
|
1.0
|
N
|
L:LYS49
|
4.7
|
0.9
|
1.0
|
CA
|
L:CYS31
|
4.8
|
0.0
|
1.0
|
C
|
L:CYS51
|
5.0
|
0.7
|
1.0
|
O
|
L:HIS53
|
5.0
|
0.9
|
1.0
|
|
Reference:
L.Wang,
Y.Zhou,
L.Xu,
R.Xiao,
X.Lu,
L.Chen,
J.Chong,
H.Li,
C.He,
X.D.Fu,
D.Wang.
Molecular Basis For 5-Carboxycytosine Recognition By Rna Polymerase II Elongation Complex. Nature V. 523 621 2015.
ISSN: ESSN 1476-4687
PubMed: 26123024
DOI: 10.1038/NATURE14482
Page generated: Sun Oct 27 10:58:16 2024
|