Phosphorus in PDB 1ajl: Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron

Phosphorus Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Phosphorus atom in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron (pdb code 1ajl). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 17 binding sites of Phosphorus where determined in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, PDB code: 1ajl:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 17 in 1ajl

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Phosphorus binding site 1 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:G3 0.0 0.0 1.0
OP2 A:G3 1.5 0.0 1.0
OP1 A:G3 1.5 0.0 1.0
O3' A:G2 1.6 0.0 1.0
O5' A:G3 1.6 0.0 1.0
H8 A:G3 2.6 0.0 1.0
C3' A:G2 2.7 0.0 1.0
C5' A:G3 2.7 0.0 1.0
HO2' A:G2 2.7 0.0 1.0
H5'' A:G3 2.8 0.0 1.0
H3' A:G2 2.9 0.0 1.0
H3' A:G3 3.2 0.0 1.0
H5' A:G3 3.2 0.0 1.0
C2' A:G2 3.2 0.0 1.0
O2' A:G2 3.3 0.0 1.0
H2' A:G2 3.3 0.0 1.0
H5 A:U4 3.6 0.0 1.0
C8 A:G3 3.7 0.0 1.0
C4' A:G3 3.9 0.0 1.0
C4' A:G2 3.9 0.0 1.0
C3' A:G3 4.0 0.0 1.0
H4' A:G2 4.1 0.0 1.0
C5 A:U4 4.1 0.0 1.0
H5'' A:G2 4.3 0.0 1.0
N7 A:G3 4.4 0.0 1.0
OP2 A:U4 4.4 0.0 1.0
O4' A:G3 4.5 0.0 1.0
O4 A:U4 4.5 0.0 1.0
C4 A:U4 4.6 0.0 1.0
C1' A:G2 4.7 0.0 1.0
C5' A:G2 4.7 0.0 1.0
N9 A:G3 4.7 0.0 1.0
H4' A:G3 4.8 0.0 1.0
O3' A:G3 4.9 0.0 1.0
C6 A:U4 4.9 0.0 1.0
O4' A:G2 4.9 0.0 1.0

Phosphorus binding site 2 out of 17 in 1ajl

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Phosphorus binding site 2 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:U4 0.0 0.0 1.0
OP2 A:U4 1.5 0.0 1.0
OP1 A:U4 1.5 0.0 1.0
O3' A:G3 1.6 0.0 1.0
O5' A:U4 1.6 0.0 1.0
C3' A:G3 2.7 0.0 1.0
C5' A:U4 2.7 0.0 1.0
H3' A:G3 2.7 0.0 1.0
H5' A:U4 2.8 0.0 1.0
HO2' A:G3 2.9 0.0 1.0
H5'' A:U4 3.1 0.0 1.0
H6 A:U4 3.1 0.0 1.0
C2' A:G3 3.4 0.0 1.0
H2' A:G3 3.4 0.0 1.0
O2' A:G3 3.6 0.0 1.0
C4' A:G3 3.9 0.0 1.0
C4' A:U4 4.0 0.0 1.0
C6 A:U4 4.1 0.0 1.0
H4' A:G3 4.1 0.0 1.0
O4' A:U4 4.2 0.0 1.0
H5 A:U4 4.2 0.0 1.0
H5'' A:G3 4.2 0.0 1.0
H3' A:U4 4.2 0.0 1.0
C5' A:G3 4.5 0.0 1.0
C5 A:U4 4.6 0.0 1.0
C3' A:U4 4.7 0.0 1.0
O5' A:G3 4.7 0.0 1.0
H4' A:U4 4.7 0.0 1.0
C1' A:G3 4.8 0.0 1.0
H8 A:G3 4.9 0.0 1.0
O4' A:G3 5.0 0.0 1.0

Phosphorus binding site 3 out of 17 in 1ajl

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Phosphorus binding site 3 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:A5 0.0 0.0 1.0
OP1 A:A5 1.5 0.0 1.0
OP2 A:A5 1.5 0.0 1.0
O5' A:A5 1.6 0.0 1.0
O3' A:U4 1.6 0.0 1.0
C5' A:A5 2.7 0.0 1.0
C3' A:U4 2.7 0.0 1.0
H5'' A:A5 2.9 0.0 1.0
H3' A:U4 2.9 0.0 1.0
H5' A:A5 2.9 0.0 1.0
H2' A:U4 3.2 0.0 1.0
C2' A:U4 3.2 0.0 1.0
O2' A:U4 3.3 0.0 1.0
HO2' A:U4 3.6 0.0 1.0
C4' A:U4 3.9 0.0 1.0
C4' A:A5 4.0 0.0 1.0
H4' A:U4 4.1 0.0 1.0
H4' A:A5 4.2 0.0 1.0
H5'' A:U4 4.4 0.0 1.0
O4' A:A5 4.4 0.0 1.0
C1' A:U4 4.6 0.0 1.0
C5' A:U4 4.7 0.0 1.0
O4' A:U4 4.9 0.0 1.0

Phosphorus binding site 4 out of 17 in 1ajl

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Phosphorus binding site 4 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:A6 0.0 0.0 1.0
OP1 A:A6 1.5 0.0 1.0
OP2 A:A6 1.5 0.0 1.0
O5' A:A6 1.6 0.0 1.0
O3' A:A5 1.6 0.0 1.0
C3' A:A5 2.7 0.0 1.0
C5' A:A6 2.7 0.0 1.0
H3' A:A5 2.7 0.0 1.0
H5' A:A6 2.8 0.0 1.0
H5'' A:A6 3.0 0.0 1.0
H5 A:U7 3.0 0.0 1.0
HO2' A:A5 3.1 0.0 1.0
C2' A:A5 3.6 0.0 1.0
H5' A:A5 3.7 0.0 1.0
C4' A:A5 3.8 0.0 1.0
H2' A:A5 3.8 0.0 1.0
O2' A:A5 3.9 0.0 1.0
C4' A:A6 4.0 0.0 1.0
H4' A:A5 4.0 0.0 1.0
C5 A:U7 4.0 0.0 1.0
H3' A:A6 4.0 0.0 1.0
C5' A:A5 4.2 0.0 1.0
O4' A:A6 4.3 0.0 1.0
H8 A:A6 4.3 0.0 1.0
O4 A:U7 4.4 0.0 1.0
H5'' A:A5 4.5 0.0 1.0
C3' A:A6 4.6 0.0 1.0
C4 A:U7 4.6 0.0 1.0
H4' A:A6 4.8 0.0 1.0
O4' A:A5 4.9 0.0 1.0
C1' A:A5 4.9 0.0 1.0
H6 A:U7 5.0 0.0 1.0
C6 A:U7 5.0 0.0 1.0

Phosphorus binding site 5 out of 17 in 1ajl

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Phosphorus binding site 5 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:U7 0.0 0.0 1.0
OP1 A:U7 1.5 0.0 1.0
OP2 A:U7 1.5 0.0 1.0
O5' A:U7 1.6 0.0 1.0
O3' A:A6 1.6 0.0 1.0
C5' A:U7 2.7 0.0 1.0
C3' A:A6 2.7 0.0 1.0
HO2' A:A6 2.7 0.0 1.0
H5'' A:U7 2.8 0.0 1.0
H3' A:A6 2.8 0.0 1.0
H62 A:A8 2.9 0.0 1.0
H5' A:U7 3.1 0.0 1.0
O2' A:A6 3.1 0.0 1.0
C2' A:A6 3.4 0.0 1.0
H62 A:A9 3.4 0.0 1.0
H61 A:A9 3.7 0.0 1.0
N6 A:A9 3.7 0.0 1.0
N7 A:A8 3.7 0.0 1.0
C4' A:A6 3.9 0.0 1.0
H2' A:A6 3.9 0.0 1.0
N6 A:A8 3.9 0.0 1.0
C4' A:U7 3.9 0.0 1.0
H4' A:A6 3.9 0.0 1.0
H6 A:U7 4.0 0.0 1.0
O4' A:U7 4.2 0.0 1.0
H4' A:U7 4.2 0.0 1.0
H5'' A:A6 4.3 0.0 1.0
C6 A:A9 4.5 0.0 1.0
C5 A:A8 4.5 0.0 1.0
H61 A:A8 4.5 0.0 1.0
C1' A:A6 4.7 0.0 1.0
C5' A:A6 4.7 0.0 1.0
C6 A:A8 4.7 0.0 1.0
C8 A:A8 4.7 0.0 1.0
H1' A:A6 4.8 0.0 1.0
O4' A:A6 4.9 0.0 1.0
H8 A:A8 4.9 0.0 1.0
C6 A:U7 5.0 0.0 1.0

Phosphorus binding site 6 out of 17 in 1ajl

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Phosphorus binding site 6 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:A8 0.0 0.0 1.0
OP1 A:A8 1.5 0.0 1.0
OP2 A:A8 1.5 0.0 1.0
O5' A:A8 1.6 0.0 1.0
O3' A:U7 1.6 0.0 1.0
C3' A:U7 2.7 0.0 1.0
C5' A:A8 2.7 0.0 1.0
H5'' A:A8 2.7 0.0 1.0
H3' A:U7 2.7 0.0 1.0
HO2' A:U7 3.0 0.0 1.0
H5' A:A8 3.2 0.0 1.0
H2' A:A8 3.3 0.0 1.0
O2' A:U7 3.4 0.0 1.0
C2' A:U7 3.6 0.0 1.0
H8 A:A8 3.7 0.0 1.0
H4' A:U7 3.7 0.0 1.0
C4' A:U7 3.8 0.0 1.0
H3' A:A8 3.8 0.0 1.0
C4' A:A8 3.9 0.0 1.0
H1' A:U7 4.1 0.0 1.0
C3' A:A8 4.1 0.0 1.0
C2' A:A8 4.1 0.0 1.0
C1' A:U7 4.3 0.0 1.0
H2' A:U7 4.4 0.0 1.0
O4' A:A8 4.5 0.0 1.0
O4' A:U7 4.6 0.0 1.0
C8 A:A8 4.6 0.0 1.0
H4' A:A8 4.7 0.0 1.0
H5' A:U7 4.8 0.0 1.0
C1' A:A8 4.9 0.0 1.0
C5' A:U7 4.9 0.0 1.0

Phosphorus binding site 7 out of 17 in 1ajl

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Phosphorus binding site 7 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:A9 0.0 0.0 1.0
OP1 A:A9 1.5 0.0 1.0
OP2 A:A9 1.5 0.0 1.0
O5' A:A9 1.6 0.0 1.0
O3' A:A8 1.6 0.0 1.0
C5' A:A9 2.7 0.0 1.0
C3' A:A8 2.7 0.0 1.0
H5'' A:A9 2.7 0.0 1.0
HO2' A:A8 2.8 0.0 1.0
H3' A:A8 2.9 0.0 1.0
O2' A:A8 2.9 0.0 1.0
H5' A:A9 3.1 0.0 1.0
C2' A:A8 3.3 0.0 1.0
H1' A:A8 3.6 0.0 1.0
C4' A:A8 3.9 0.0 1.0
C4' A:A9 3.9 0.0 1.0
C1' A:A8 4.0 0.0 1.0
H4' A:A8 4.0 0.0 1.0
O4' A:A9 4.2 0.0 1.0
H2' A:A8 4.2 0.0 1.0
H4' A:A9 4.3 0.0 1.0
O4' A:A8 4.5 0.0 1.0

Phosphorus binding site 8 out of 17 in 1ajl

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Phosphorus binding site 8 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:G10 0.0 0.0 1.0
OP1 A:G10 1.5 0.0 1.0
OP2 A:G10 1.5 0.0 1.0
O3' A:A9 1.6 0.0 1.0
O5' A:G10 1.6 0.0 1.0
HO2' A:A9 2.3 0.0 1.0
H3' A:G10 2.5 0.0 1.0
C3' A:A9 2.7 0.0 1.0
C5' A:G10 2.7 0.0 1.0
O2' A:A9 2.7 0.0 1.0
H5' A:G10 2.8 0.0 1.0
H3' A:A9 3.0 0.0 1.0
C2' A:A9 3.2 0.0 1.0
C3' A:G10 3.3 0.0 1.0
OP2 A:C11 3.4 0.0 1.0
H5'' A:G10 3.5 0.0 1.0
C4' A:G10 3.6 0.0 1.0
H2' A:A9 3.7 0.0 1.0
O3' A:G10 3.8 0.0 1.0
C4' A:A9 3.9 0.0 1.0
H4' A:A9 4.0 0.0 1.0
P A:C11 4.2 0.0 1.0
H8 A:G10 4.3 0.0 1.0
O4' A:G10 4.3 0.0 1.0
H5 A:C11 4.4 0.0 1.0
H4' A:G10 4.4 0.0 1.0
C1' A:A9 4.4 0.0 1.0
H1' A:A9 4.6 0.0 1.0
C2' A:G10 4.6 0.0 1.0
H5' A:A9 4.6 0.0 1.0
C8 A:G10 4.7 0.0 1.0
O4' A:A9 4.8 0.0 1.0
H2' A:G10 4.9 0.0 1.0
C5' A:A9 4.9 0.0 1.0
C1' A:G10 4.9 0.0 1.0

Phosphorus binding site 9 out of 17 in 1ajl

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Phosphorus binding site 9 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:0.0
occ:1.00
P A:C11 0.0 0.0 1.0
OP1 A:C11 1.5 0.0 1.0
OP2 A:C11 1.5 0.0 1.0
O5' A:C11 1.6 0.0 1.0
O3' A:G10 1.6 0.0 1.0
C3' A:G10 2.6 0.0 1.0
C5' A:C11 2.7 0.0 1.0
H6 A:C11 2.7 0.0 1.0
H3' A:G10 2.8 0.0 1.0
H5'' A:C11 2.8 0.0 1.0
HO2' A:G10 3.1 0.0 1.0
H5' A:C11 3.1 0.0 1.0
H2' A:G10 3.2 0.0 1.0
H3' A:C11 3.2 0.0 1.0
C2' A:G10 3.3 0.0 1.0
O2' A:G10 3.5 0.0 1.0
H5 A:C11 3.6 0.0 1.0
C6 A:C11 3.7 0.0 1.0
OP2 A:G10 3.9 0.0 1.0
C4' A:G10 3.9 0.0 1.0
C4' A:C11 3.9 0.0 1.0
O5' A:G10 3.9 0.0 1.0
C3' A:C11 4.0 0.0 1.0
C5 A:C11 4.1 0.0 1.0
H4' A:G10 4.1 0.0 1.0
P A:G10 4.2 0.0 1.0
OP1 A:G10 4.3 0.0 1.0
O4' A:C11 4.5 0.0 1.0
C5' A:G10 4.6 0.0 1.0
C1' A:G10 4.7 0.0 1.0
HO2' A:A9 4.7 0.0 1.0
H4' A:C11 4.8 0.0 1.0
OP2 A:U12 4.8 0.0 1.0
N1 A:C11 4.8 0.0 1.0
O3' A:C11 4.9 0.0 1.0
O4' A:G10 4.9 0.0 1.0

Phosphorus binding site 10 out of 17 in 1ajl

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Phosphorus binding site 10 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P12

b:0.0
occ:1.00
P A:U12 0.0 0.0 1.0
OP1 A:U12 1.5 0.0 1.0
OP2 A:U12 1.5 0.0 1.0
O3' A:C11 1.6 0.0 1.0
O5' A:U12 1.6 0.0 1.0
HO2' A:C11 2.6 0.0 1.0
C3' A:C11 2.7 0.0 1.0
C5' A:U12 2.7 0.0 1.0
H3' A:C11 2.8 0.0 1.0
H5'' A:U12 2.8 0.0 1.0
H6 A:U12 2.9 0.0 1.0
H3' A:U12 3.2 0.0 1.0
H5' A:U12 3.2 0.0 1.0
C2' A:C11 3.2 0.0 1.0
H2' A:C11 3.2 0.0 1.0
O2' A:C11 3.3 0.0 1.0
C4' A:U12 3.9 0.0 1.0
C4' A:C11 4.0 0.0 1.0
C6 A:U12 4.0 0.0 1.0
C3' A:U12 4.0 0.0 1.0
H5 A:U12 4.1 0.0 1.0
H4' A:C11 4.1 0.0 1.0
O4' A:U12 4.5 0.0 1.0
C5 A:U12 4.5 0.0 1.0
H5'' A:C11 4.5 0.0 1.0
C5' A:C11 4.7 0.0 1.0
C1' A:C11 4.7 0.0 1.0
O5' A:C11 4.8 0.0 1.0
H4' A:U12 4.8 0.0 1.0
OP2 A:C13 4.8 0.0 1.0
O3' A:U12 4.9 0.0 1.0
O4' A:C11 4.9 0.0 1.0

Reference:

K.J.Luebke, S.M.Landry, I.Tinoco. Solution Conformation of A Five-Nucleotide Rna Bulge Loop From A Group I Intron. Biochemistry V. 36 10246 1997.
ISSN: ISSN 0006-2960
PubMed: 9254623
DOI: 10.1021/BI9701540
Page generated: Fri Sep 25 13:01:54 2020

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