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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

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