Phosphorus in PDB 1ajt: Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure

Phosphorus Binding Sites:

Pages:

>>> 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, uc(Nmr), 1 Structure (pdb code 1ajt). 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, uc(Nmr), 1 Structure, PDB code: 1ajt:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 1 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


Mono view


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, uc(Nmr), 1 Structure 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
OP1 A:G3 1.5 0.0 1.0
OP2 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
C3' A:G2 2.7 0.0 1.0
H8 A:G3 2.7 0.0 1.0
C5' A:G3 2.7 0.0 1.0
H5'' A:G3 2.8 0.0 1.0
HO2' A:G2 2.9 0.0 1.0
H3' A:G2 2.9 0.0 1.0
H3' A:G3 3.2 0.0 1.0
C2' A:G2 3.2 0.0 1.0
H5' A:G3 3.2 0.0 1.0
H2' A:G2 3.2 0.0 1.0
O2' A:G2 3.3 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
H5 A:U4 4.1 0.0 1.0
H5'' A:G2 4.4 0.0 1.0
N7 A:G3 4.4 0.0 1.0
O4' A:G3 4.5 0.0 1.0
OP2 A:U4 4.6 0.0 1.0
C5 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 4.8 0.0 1.0
H4' A:G3 4.8 0.0 1.0
O3' A:G3 4.9 0.0 1.0
O4' A:G2 4.9 0.0 1.0
O4 A:U4 4.9 0.0 1.0

Phosphorus binding site 2 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 2 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


Mono view


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, uc(Nmr), 1 Structure 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
OP1 A:U4 1.5 0.0 1.0
OP2 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 2.8 0.0 1.0
H5' A:U4 2.8 0.0 1.0
H5'' A:U4 3.0 0.0 1.0
H6 A:U4 3.1 0.0 1.0
C2' A:G3 3.3 0.0 1.0
H2' A:G3 3.3 0.0 1.0
O2' A:G3 3.5 0.0 1.0
C4' A:G3 3.9 0.0 1.0
C4' A:U4 4.0 0.0 1.0
HO2' A:G3 4.1 0.0 1.0
C6 A:U4 4.1 0.0 1.0
H4' A:G3 4.1 0.0 1.0
H3' A:U4 4.2 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 4.3 0.0 1.0
C5' A:G3 4.6 0.0 1.0
C5 A:U4 4.6 0.0 1.0
C3' A:U4 4.6 0.0 1.0
C1' A:G3 4.7 0.0 1.0
H4' A:U4 4.8 0.0 1.0
O5' A:G3 4.8 0.0 1.0
O4' A:G3 5.0 0.0 1.0
H8 A:G3 5.0 0.0 1.0

Phosphorus binding site 3 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 3 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


Mono view


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, uc(Nmr), 1 Structure 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
O3' A:U4 1.6 0.0 1.0
O5' A:A5 1.6 0.0 1.0
C5' A:A5 2.6 0.0 1.0
C3' A:U4 2.7 0.0 1.0
H5'' A:A5 2.8 0.0 1.0
HO2' A:U4 2.8 0.0 1.0
H3' A:U4 2.9 0.0 1.0
H5' A:A5 3.0 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 3.4 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 4.0 0.0 1.0
H4' A:A5 4.3 0.0 1.0
O4' A:A5 4.3 0.0 1.0
H5'' A:U4 4.3 0.0 1.0
C1' A:U4 4.7 0.0 1.0
C5' A:U4 4.7 0.0 1.0
H8 A:A5 4.9 0.0 1.0
O4' A:U4 4.9 0.0 1.0

Phosphorus binding site 4 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 4 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


Mono view


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, uc(Nmr), 1 Structure 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
OP2 A:A6 1.5 0.0 1.0
OP1 A:A6 1.5 0.0 1.0
O3' A:A5 1.6 0.0 1.0
O5' A:A6 1.6 0.0 1.0
C3' A:A5 2.7 0.0 1.0
C5' A:A6 2.7 0.0 1.0
H8 A:A6 2.7 0.0 1.0
H5'' A:A6 2.8 0.0 1.0
H3' A:A5 2.8 0.0 1.0
H5' A:A6 3.0 0.0 1.0
C2' A:A5 3.4 0.0 1.0
H2' A:A5 3.4 0.0 1.0
O2' A:A5 3.6 0.0 1.0
H2' A:A6 3.6 0.0 1.0
C8 A:A6 3.8 0.0 1.0
C4' A:A5 3.9 0.0 1.0
H5 A:U7 3.9 0.0 1.0
C4' A:A6 4.0 0.0 1.0
H4' A:A5 4.1 0.0 1.0
H5' A:A5 4.1 0.0 1.0
H3' A:A6 4.2 0.0 1.0
HO2' A:A5 4.3 0.0 1.0
C3' A:A6 4.4 0.0 1.0
C2' A:A6 4.4 0.0 1.0
O4' A:A6 4.5 0.0 1.0
C5' A:A5 4.5 0.0 1.0
N7 A:A6 4.6 0.0 1.0
N9 A:A6 4.7 0.0 1.0
H5'' A:A5 4.8 0.0 1.0
H4' A:A6 4.8 0.0 1.0
C1' A:A5 4.8 0.0 1.0
C1' A:A6 4.8 0.0 1.0
O4' A:A5 4.9 0.0 1.0
C5 A:U7 5.0 0.0 1.0

Phosphorus binding site 5 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 5 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


Mono view


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, uc(Nmr), 1 Structure 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
O3' A:A6 1.6 0.0 1.0
O5' A:U7 1.6 0.0 1.0
C5' A:U7 2.7 0.0 1.0
C3' A:A6 2.7 0.0 1.0
H3' A:A6 2.7 0.0 1.0
H5'' A:U7 2.9 0.0 1.0
HO2' A:A6 2.9 0.0 1.0
H5' A:U7 2.9 0.0 1.0
H4' A:A6 3.5 0.0 1.0
N7 A:A8 3.5 0.0 1.0
H62 A:A8 3.6 0.0 1.0
O2' A:A6 3.6 0.0 1.0
C4' A:A6 3.7 0.0 1.0
C2' A:A6 3.7 0.0 1.0
C4' A:U7 4.0 0.0 1.0
H4' A:U7 4.2 0.0 1.0
C8 A:A8 4.2 0.0 1.0
C5 A:A8 4.2 0.0 1.0
N6 A:A8 4.3 0.0 1.0
H8 A:A8 4.4 0.0 1.0
O4' A:U7 4.4 0.0 1.0
H1' A:A6 4.4 0.0 1.0
O4' A:A6 4.5 0.0 1.0
C1' A:A6 4.5 0.0 1.0
H2' A:A6 4.5 0.0 1.0
H6 A:U7 4.6 0.0 1.0
C6 A:A8 4.6 0.0 1.0
H5'' A:A6 4.7 0.0 1.0
C5' A:A6 4.8 0.0 1.0

Phosphorus binding site 6 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 6 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


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, uc(Nmr), 1 Structure 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
C5' A:A8 2.6 0.0 1.0
C3' A:U7 2.7 0.0 1.0
H5' A:A8 2.7 0.0 1.0
H3' A:U7 2.8 0.0 1.0
H5'' A:A8 3.1 0.0 1.0
H4' A:U7 3.1 0.0 1.0
HO2' A:U7 3.4 0.0 1.0
C4' A:U7 3.5 0.0 1.0
C2' A:U7 3.9 0.0 1.0
C4' A:A8 3.9 0.0 1.0
O2' A:U7 4.0 0.0 1.0
H4' A:A8 4.0 0.0 1.0
H1' A:U7 4.2 0.0 1.0
O4' A:U7 4.4 0.0 1.0
H5' A:U7 4.4 0.0 1.0
C1' A:U7 4.4 0.0 1.0
O4' A:A8 4.5 0.0 1.0
C5' A:U7 4.6 0.0 1.0
H2' A:U7 4.7 0.0 1.0

Phosphorus binding site 7 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 7 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


Mono view


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, uc(Nmr), 1 Structure 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
O3' A:A8 1.6 0.0 1.0
O5' A:A9 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
H3' A:A8 2.7 0.0 1.0
HO2' A:A8 2.9 0.0 1.0
H5' A:A9 3.3 0.0 1.0
O2' A:A8 3.3 0.0 1.0
C2' A:A8 3.5 0.0 1.0
H4' A:A8 3.8 0.0 1.0
C4' A:A9 3.8 0.0 1.0
C4' A:A8 3.8 0.0 1.0
O4' A:A9 3.9 0.0 1.0
H1' A:A8 3.9 0.0 1.0
H4' A:A9 4.2 0.0 1.0
C1' A:A8 4.2 0.0 1.0
H2' A:A8 4.4 0.0 1.0
O4' A:A8 4.5 0.0 1.0
H5' A:A8 4.9 0.0 1.0

Phosphorus binding site 8 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 8 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


Mono view


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, uc(Nmr), 1 Structure 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 2.2 0.0 1.0
H3' A:G10 2.4 0.0 1.0
C3' A:A9 2.7 0.0 1.0
C5' A:G10 2.7 0.0 1.0
H5' A:G10 2.8 0.0 1.0
O2' A:A9 2.8 0.0 1.0
H3' A:A9 2.9 0.0 1.0
C2' A:A9 3.2 0.0 1.0
C3' A:G10 3.3 0.0 1.0
H8 A:G10 3.4 0.0 1.0
C4' A:G10 3.5 0.0 1.0
H5'' A:G10 3.6 0.0 1.0
H2' A:A9 3.6 0.0 1.0
O3' A:G10 3.9 0.0 1.0
C4' A:A9 3.9 0.0 1.0
H4' A:A9 4.0 0.0 1.0
O4' A:G10 4.2 0.0 1.0
OP2 A:C11 4.2 0.0 1.0
C8 A:G10 4.4 0.0 1.0
H4' A:G10 4.4 0.0 1.0
H5' A:A9 4.5 0.0 1.0
C1' A:A9 4.5 0.0 1.0
C2' A:G10 4.6 0.0 1.0
P A:C11 4.7 0.0 1.0
H1' A:A9 4.7 0.0 1.0
H2' A:G10 4.8 0.0 1.0
C5' A:A9 4.8 0.0 1.0
O4' 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 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 9 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


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, uc(Nmr), 1 Structure 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 2.7 0.0 1.0
C5' A:C11 2.7 0.0 1.0
H6 A:C11 2.8 0.0 1.0
H3' A:G10 2.9 0.0 1.0
H5'' A:C11 2.9 0.0 1.0
H5' A:C11 3.0 0.0 1.0
H2' A:G10 3.1 0.0 1.0
C2' A:G10 3.1 0.0 1.0
O2' A:G10 3.2 0.0 1.0
H3' A:C11 3.4 0.0 1.0
H5 A:C11 3.5 0.0 1.0
HO2' A:G10 3.6 0.0 1.0
C6 A:C11 3.6 0.0 1.0
C5 A:C11 3.9 0.0 1.0
C4' A:G10 4.0 0.0 1.0
C4' A:C11 4.0 0.0 1.0
H4' A:G10 4.1 0.0 1.0
OP2 A:G10 4.1 0.0 1.0
C3' A:C11 4.2 0.0 1.0
O5' A:G10 4.3 0.0 1.0
O4' A:C11 4.5 0.0 1.0
C1' A:G10 4.6 0.0 1.0
P A:G10 4.7 0.0 1.0
N1 A:C11 4.7 0.0 1.0
C5' A:G10 4.8 0.0 1.0
H4' A:C11 4.8 0.0 1.0
HO2' A:A9 4.9 0.0 1.0
O4' A:G10 4.9 0.0 1.0
OP1 A:G10 5.0 0.0 1.0
H5 A:U12 5.0 0.0 1.0

Phosphorus binding site 10 out of 17 in 1ajt

Go back to Phosphorus Binding Sites List in 1ajt
Phosphorus binding site 10 out of 17 in the Five-Nucleotide Bulge Loop From Tetrahymena Thermophila Group I Intron, uc(Nmr), 1 Structure


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, uc(Nmr), 1 Structure 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
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
HO2' A:C11 2.8 0.0 1.0
H6 A:U12 3.1 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
H3' A:U12 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
C3' A:U12 4.0 0.0 1.0
H4' A:C11 4.1 0.0 1.0
C6 A:U12 4.2 0.0 1.0
H5 A:U12 4.3 0.0 1.0
O4' A:U12 4.5 0.0 1.0
H5'' A:C11 4.6 0.0 1.0
OP2 A:C13 4.6 0.0 1.0
C1' A:C11 4.7 0.0 1.0
H6 A:C11 4.7 0.0 1.0
C5' A:C11 4.7 0.0 1.0
C5 A:U12 4.7 0.0 1.0
H4' A:U12 4.8 0.0 1.0
O5' A:C11 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 13:03:39 2020

Last articles

Na in 5U4H
Na in 5U2T
Na in 5U4U
Na in 5U2S
Na in 5U63
Na in 5U35
Na in 5U2R
Na in 5U24
Na in 5U23
Na in 5U21
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy