Magnesium in PDB 1tfy: How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template
Enzymatic activity of How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template
All present enzymatic activity of How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template:
2.7.7.25;
Protein crystallography data
The structure of How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template, PDB code: 1tfy
was solved by
Y.Xiong,
T.A.Steitz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.28 /
3.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
114.092,
84.023,
134.561,
90.00,
102.38,
90.00
|
R / Rfree (%)
|
23.5 /
29
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template
(pdb code 1tfy). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template, PDB code: 1tfy:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1tfy
Go back to
Magnesium Binding Sites List in 1tfy
Magnesium binding site 1 out
of 4 in the How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:0.1
occ:1.00
|
O2B
|
A:CTP501
|
2.6
|
0.5
|
1.0
|
O3G
|
A:CTP501
|
3.0
|
0.1
|
1.0
|
O1A
|
A:CTP501
|
3.0
|
0.5
|
1.0
|
OD2
|
A:ASP61
|
3.1
|
0.3
|
1.0
|
O3B
|
A:CTP501
|
3.4
|
0.7
|
1.0
|
PB
|
A:CTP501
|
3.5
|
0.3
|
1.0
|
CB
|
A:SER47
|
3.5
|
0.0
|
1.0
|
PG
|
A:CTP501
|
3.7
|
0.1
|
1.0
|
O
|
A:GLU59
|
3.8
|
0.2
|
1.0
|
O3A
|
A:CTP501
|
3.9
|
0.1
|
1.0
|
CB
|
A:GLU59
|
4.0
|
0.2
|
1.0
|
OG
|
A:SER47
|
4.0
|
0.1
|
1.0
|
PA
|
A:CTP501
|
4.1
|
0.2
|
1.0
|
OE1
|
A:GLU59
|
4.1
|
0.1
|
1.0
|
N
|
A:SER47
|
4.2
|
0.0
|
1.0
|
CG
|
A:ASP61
|
4.2
|
0.9
|
1.0
|
O1G
|
A:CTP501
|
4.3
|
0.6
|
1.0
|
CG
|
A:GLU59
|
4.4
|
0.8
|
1.0
|
CA
|
A:SER47
|
4.5
|
0.0
|
1.0
|
C
|
A:GLU59
|
4.5
|
0.1
|
1.0
|
OD1
|
A:ASP61
|
4.6
|
0.1
|
1.0
|
CD
|
A:GLU59
|
4.7
|
0.7
|
1.0
|
CA
|
A:GLU59
|
4.8
|
0.2
|
1.0
|
O1B
|
A:CTP501
|
4.9
|
0.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1tfy
Go back to
Magnesium Binding Sites List in 1tfy
Magnesium binding site 2 out
of 4 in the How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:95.4
occ:1.00
|
O3G
|
B:CTP502
|
2.0
|
0.8
|
1.0
|
O2B
|
B:CTP502
|
2.1
|
0.5
|
1.0
|
OD2
|
B:ASP61
|
2.1
|
0.9
|
1.0
|
O1A
|
B:CTP502
|
2.6
|
0.8
|
1.0
|
OE2
|
B:GLU59
|
2.6
|
0.3
|
1.0
|
OG
|
B:SER47
|
3.1
|
0.2
|
1.0
|
CG
|
B:ASP61
|
3.2
|
0.1
|
1.0
|
PB
|
B:CTP502
|
3.3
|
0.6
|
1.0
|
PG
|
B:CTP502
|
3.4
|
0.8
|
1.0
|
CD
|
B:GLU59
|
3.4
|
0.0
|
1.0
|
CG
|
B:GLU59
|
3.5
|
0.7
|
1.0
|
O3B
|
B:CTP502
|
3.7
|
0.7
|
1.0
|
PA
|
B:CTP502
|
3.7
|
1.0
|
1.0
|
OD1
|
B:ASP61
|
3.7
|
0.1
|
1.0
|
O3A
|
B:CTP502
|
3.8
|
0.8
|
1.0
|
N
|
B:SER47
|
3.9
|
0.0
|
1.0
|
CB
|
B:SER47
|
4.0
|
0.1
|
1.0
|
O2G
|
B:CTP502
|
4.2
|
0.3
|
1.0
|
O
|
B:GLU59
|
4.2
|
0.2
|
1.0
|
CB
|
B:ASP61
|
4.4
|
0.1
|
1.0
|
O1G
|
B:CTP502
|
4.4
|
0.6
|
1.0
|
OE1
|
B:GLU59
|
4.5
|
0.1
|
1.0
|
O1B
|
B:CTP502
|
4.5
|
0.0
|
1.0
|
C5'
|
B:CTP502
|
4.5
|
0.2
|
1.0
|
O5'
|
B:CTP502
|
4.6
|
0.7
|
1.0
|
CA
|
B:SER47
|
4.6
|
0.0
|
1.0
|
CB
|
B:GLU59
|
4.8
|
0.4
|
1.0
|
C
|
B:GLU59
|
4.8
|
0.2
|
1.0
|
CA
|
B:GLY46
|
4.8
|
0.0
|
1.0
|
C
|
B:GLY46
|
4.8
|
1.0
|
1.0
|
O2A
|
B:CTP502
|
4.9
|
0.7
|
1.0
|
N
|
B:ASP61
|
4.9
|
0.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1tfy
Go back to
Magnesium Binding Sites List in 1tfy
Magnesium binding site 3 out
of 4 in the How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg603
b:0.9
occ:1.00
|
O3G
|
C:CTP503
|
2.2
|
0.3
|
1.0
|
O2B
|
C:CTP503
|
2.3
|
0.6
|
1.0
|
OD2
|
C:ASP61
|
2.3
|
0.5
|
1.0
|
O1A
|
C:CTP503
|
2.8
|
1.0
|
1.0
|
CG
|
C:ASP61
|
3.3
|
0.5
|
1.0
|
O
|
C:GLU59
|
3.3
|
0.3
|
1.0
|
OE1
|
C:GLU59
|
3.5
|
0.2
|
1.0
|
PB
|
C:CTP503
|
3.5
|
0.1
|
1.0
|
OG
|
C:SER47
|
3.5
|
0.2
|
1.0
|
PG
|
C:CTP503
|
3.5
|
0.3
|
1.0
|
OD1
|
C:ASP61
|
3.6
|
0.7
|
1.0
|
CB
|
C:GLU59
|
3.8
|
0.4
|
1.0
|
CG
|
C:GLU59
|
3.9
|
0.7
|
1.0
|
O3B
|
C:CTP503
|
3.9
|
0.6
|
1.0
|
CD
|
C:GLU59
|
4.0
|
0.1
|
1.0
|
PA
|
C:CTP503
|
4.0
|
0.1
|
1.0
|
O3A
|
C:CTP503
|
4.1
|
1.0
|
1.0
|
C
|
C:GLU59
|
4.2
|
0.3
|
1.0
|
O1G
|
C:CTP503
|
4.2
|
0.0
|
1.0
|
N
|
C:SER47
|
4.3
|
0.0
|
1.0
|
CA
|
C:GLU59
|
4.6
|
0.3
|
1.0
|
CB
|
C:SER47
|
4.6
|
0.0
|
1.0
|
O2G
|
C:CTP503
|
4.7
|
0.9
|
1.0
|
CB
|
C:ASP61
|
4.7
|
0.3
|
1.0
|
O1B
|
C:CTP503
|
4.8
|
0.7
|
1.0
|
CA
|
C:GLY46
|
4.9
|
0.1
|
1.0
|
CA
|
C:SER47
|
5.0
|
0.0
|
1.0
|
OE2
|
C:GLU59
|
5.0
|
0.3
|
1.0
|
N
|
C:TYR48
|
5.0
|
0.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1tfy
Go back to
Magnesium Binding Sites List in 1tfy
Magnesium binding site 4 out
of 4 in the How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of How Cca Is Added to the 3' End of Immature Trna Without the Use of An Oligonucleotide Template within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg604
b:0.5
occ:1.00
|
O2B
|
D:CTP504
|
2.0
|
0.4
|
1.0
|
OD2
|
D:ASP61
|
2.3
|
0.7
|
1.0
|
O1A
|
D:CTP504
|
2.4
|
1.0
|
1.0
|
O3G
|
D:CTP504
|
2.4
|
0.6
|
1.0
|
OE2
|
D:GLU59
|
2.4
|
0.7
|
1.0
|
PB
|
D:CTP504
|
3.1
|
0.6
|
1.0
|
CD
|
D:GLU59
|
3.3
|
0.5
|
1.0
|
CG
|
D:ASP61
|
3.3
|
0.0
|
1.0
|
O3A
|
D:CTP504
|
3.4
|
0.0
|
1.0
|
PA
|
D:CTP504
|
3.4
|
0.2
|
1.0
|
PG
|
D:CTP504
|
3.5
|
0.6
|
1.0
|
O3B
|
D:CTP504
|
3.5
|
0.6
|
1.0
|
OG
|
D:SER47
|
3.6
|
0.3
|
1.0
|
OD1
|
D:ASP61
|
3.7
|
0.1
|
1.0
|
CG
|
D:GLU59
|
4.0
|
0.9
|
1.0
|
O
|
D:GLU59
|
4.0
|
0.2
|
1.0
|
OE1
|
D:GLU59
|
4.1
|
0.8
|
1.0
|
N
|
D:SER47
|
4.4
|
0.1
|
1.0
|
O1B
|
D:CTP504
|
4.4
|
0.3
|
1.0
|
O2A
|
D:CTP504
|
4.4
|
0.2
|
1.0
|
O2G
|
D:CTP504
|
4.4
|
0.7
|
1.0
|
CB
|
D:SER47
|
4.6
|
0.1
|
1.0
|
O5'
|
D:CTP504
|
4.6
|
1.0
|
1.0
|
O1G
|
D:CTP504
|
4.6
|
0.4
|
1.0
|
CB
|
D:ASP61
|
4.7
|
0.1
|
1.0
|
C5'
|
D:CTP504
|
4.8
|
1.0
|
1.0
|
C
|
D:GLU59
|
4.9
|
0.2
|
1.0
|
CB
|
D:GLU59
|
4.9
|
0.4
|
1.0
|
|
Reference:
Y.Xiong,
T.A.Steitz.
Mechanism of Transfer Rna Maturation By Cca-Adding Enzyme Without Using An Oligonucleotide Template. Nature V. 430 640 2004.
ISSN: ISSN 0028-0836
PubMed: 15295590
DOI: 10.1038/NATURE02711
Page generated: Tue Aug 13 14:32:37 2024
|