Phosphorus in PDB 1ajf: Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure

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 Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure (pdb code 1ajf). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 17 binding sites of Phosphorus where determined in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure, PDB code: 1ajf:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 17 in 1ajf

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Phosphorus binding site 1 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:A2 0.0 0.0 1.0
OP1 A:A2 1.5 0.0 1.0
OP2 A:A2 1.5 0.0 1.0
O3' A:G1 1.6 0.0 1.0
O5' A:A2 1.6 0.0 1.0
C3' A:G1 2.6 0.0 1.0
C5' A:A2 2.7 0.0 1.0
H3' A:G1 2.8 0.0 1.0
H5' A:A2 2.8 0.0 1.0
H5'' A:A2 3.0 0.0 1.0
H8 A:A2 3.2 0.0 1.0
HO2' A:G1 3.3 0.0 1.0
H2' A:G1 3.4 0.0 1.0
C2' A:G1 3.4 0.0 1.0
O2' A:G1 3.8 0.0 1.0
C4' A:G1 3.9 0.0 1.0
C4' A:A2 4.0 0.0 1.0
H5'' A:G1 4.0 0.0 1.0
H4' A:G1 4.1 0.0 1.0
H3' A:A2 4.1 0.0 1.0
O4' A:A2 4.3 0.0 1.0
C8 A:A2 4.3 0.0 1.0
C5' A:G1 4.5 0.0 1.0
C3' A:A2 4.6 0.0 1.0
H4' A:A2 4.8 0.0 1.0
C1' A:G1 4.8 0.0 1.0
O5' A:G1 4.9 0.0 1.0
O4' A:G1 4.9 0.0 1.0

Phosphorus binding site 2 out of 17 in 1ajf

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Phosphorus binding site 2 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:C3 0.0 0.0 1.0
OP2 A:C3 1.5 0.0 1.0
OP1 A:C3 1.5 0.0 1.0
O3' A:A2 1.6 0.0 1.0
O5' A:C3 1.6 0.0 1.0
C3' A:A2 2.6 0.0 1.0
C5' A:C3 2.6 0.0 1.0
H3' A:A2 2.8 0.0 1.0
H5' A:C3 2.8 0.0 1.0
H5'' A:C3 3.0 0.0 1.0
HO2' A:A2 3.1 0.0 1.0
H6 A:C3 3.4 0.0 1.0
C2' A:A2 3.4 0.0 1.0
H2' A:A2 3.4 0.0 1.0
O2' A:A2 3.8 0.0 1.0
C4' A:A2 3.9 0.0 1.0
C4' A:C3 4.0 0.0 1.0
H5'' A:A2 4.0 0.0 1.0
H4' A:A2 4.1 0.0 1.0
H3' A:C3 4.2 0.0 1.0
O4' A:C3 4.3 0.0 1.0
C6 A:C3 4.4 0.0 1.0
C5' A:A2 4.5 0.0 1.0
C3' A:C3 4.6 0.0 1.0
H5 A:C3 4.7 0.0 1.0
H4' A:C3 4.8 0.0 1.0
C1' A:A2 4.8 0.0 1.0
O5' A:A2 4.9 0.0 1.0
O4' A:A2 4.9 0.0 1.0

Phosphorus binding site 3 out of 17 in 1ajf

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Phosphorus binding site 3 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:A4 0.0 0.0 1.0
OP1 A:A4 1.5 0.0 1.0
OP2 A:A4 1.5 0.0 1.0
O5' A:A4 1.6 0.0 1.0
O3' A:C3 1.6 0.0 1.0
C3' A:C3 2.6 0.0 1.0
C5' A:A4 2.6 0.0 1.0
H3' A:C3 2.8 0.0 1.0
H5' A:A4 2.8 0.0 1.0
H5'' A:A4 3.0 0.0 1.0
HO2' A:C3 3.2 0.0 1.0
C2' A:C3 3.5 0.0 1.0
H8 A:A4 3.5 0.0 1.0
H2' A:C3 3.5 0.0 1.0
O2' A:C3 3.8 0.0 1.0
C4' A:C3 3.9 0.0 1.0
C4' A:A4 4.0 0.0 1.0
H5'' A:C3 4.0 0.0 1.0
H4' A:C3 4.1 0.0 1.0
H3' A:A4 4.1 0.0 1.0
O4' A:A4 4.3 0.0 1.0
C5' A:C3 4.4 0.0 1.0
C8 A:A4 4.5 0.0 1.0
C3' A:A4 4.6 0.0 1.0
H4' A:A4 4.8 0.0 1.0
C1' A:C3 4.8 0.0 1.0
O5' A:C3 4.9 0.0 1.0
O4' A:C3 4.9 0.0 1.0

Phosphorus binding site 4 out of 17 in 1ajf

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Phosphorus binding site 4 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:G5 0.0 0.0 1.0
OP2 A:G5 1.5 0.0 1.0
OP1 A:G5 1.5 0.0 1.0
O5' A:G5 1.6 0.0 1.0
O3' A:A4 1.6 0.0 1.0
C3' A:A4 2.6 0.0 1.0
C5' A:G5 2.7 0.0 1.0
H5'' A:G5 2.8 0.0 1.0
H3' A:A4 2.8 0.0 1.0
HO2' A:A4 3.0 0.0 1.0
H5' A:G5 3.0 0.0 1.0
H2' A:A4 3.4 0.0 1.0
C2' A:A4 3.4 0.0 1.0
O2' A:A4 3.7 0.0 1.0
H8 A:G5 3.8 0.0 1.0
H3' A:G5 3.8 0.0 1.0
C4' A:A4 3.9 0.0 1.0
C4' A:G5 4.0 0.0 1.0
H4' A:A4 4.1 0.0 1.0
H5'' A:A4 4.1 0.0 1.0
C3' A:G5 4.4 0.0 1.0
O4' A:G5 4.5 0.0 1.0
C5' A:A4 4.5 0.0 1.0
C1' A:A4 4.8 0.0 1.0
H4' A:G5 4.8 0.0 1.0
C8 A:G5 4.8 0.0 1.0
HN63 A:NCO19 4.9 0.0 1.0
O4' A:A4 4.9 0.0 1.0
O5' A:A4 5.0 0.0 1.0
O3' A:G5 5.0 0.0 1.0

Phosphorus binding site 5 out of 17 in 1ajf

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Phosphorus binding site 5 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:G6 0.0 0.0 1.0
OP2 A:G6 1.5 0.0 1.0
OP1 A:G6 1.5 0.0 1.0
O3' A:G5 1.6 0.0 1.0
O5' A:G6 1.6 0.0 1.0
C5' A:G6 2.6 0.0 1.0
C3' A:G5 2.6 0.0 1.0
H3' A:G5 2.8 0.0 1.0
H5' A:G6 2.8 0.0 1.0
H5'' A:G6 3.0 0.0 1.0
H2' A:G5 3.3 0.0 1.0
C2' A:G5 3.3 0.0 1.0
O2' A:G5 3.6 0.0 1.0
H8 A:G6 3.7 0.0 1.0
C4' A:G5 3.9 0.0 1.0
HO2' A:G5 4.0 0.0 1.0
C4' A:G6 4.0 0.0 1.0
H4' A:G5 4.1 0.0 1.0
H3' A:G6 4.2 0.0 1.0
H5'' A:G5 4.3 0.0 1.0
O4' A:G6 4.3 0.0 1.0
HN62 A:NCO19 4.5 0.0 1.0
C5' A:G5 4.6 0.0 1.0
C3' A:G6 4.6 0.0 1.0
C8 A:G6 4.7 0.0 1.0
C1' A:G5 4.7 0.0 1.0
H4' A:G6 4.8 0.0 1.0
O5' A:G5 4.9 0.0 1.0
O4' A:G5 4.9 0.0 1.0

Phosphorus binding site 6 out of 17 in 1ajf

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Phosphorus binding site 6 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:G7 0.0 0.0 1.0
OP2 A:G7 1.5 0.0 1.0
OP1 A:G7 1.5 0.0 1.0
O3' A:G6 1.6 0.0 1.0
O5' A:G7 1.6 0.0 1.0
C3' A:G6 2.6 0.0 1.0
C5' A:G7 2.7 0.0 1.0
H3' A:G6 2.8 0.0 1.0
H5'' A:G7 2.8 0.0 1.0
H5' A:G7 2.9 0.0 1.0
HO2' A:G6 3.3 0.0 1.0
C2' A:G6 3.5 0.0 1.0
H2' A:G6 3.5 0.0 1.0
H8 A:G7 3.8 0.0 1.0
C4' A:G6 3.9 0.0 1.0
O2' A:G6 3.9 0.0 1.0
H5'' A:G6 3.9 0.0 1.0
H3' A:G7 3.9 0.0 1.0
C4' A:G7 4.0 0.0 1.0
H4' A:G6 4.1 0.0 1.0
C5' A:G6 4.4 0.0 1.0
O4' A:G7 4.4 0.0 1.0
C3' A:G7 4.5 0.0 1.0
O5' A:G6 4.7 0.0 1.0
H4' A:G7 4.8 0.0 1.0
C1' A:G6 4.8 0.0 1.0
C8 A:G7 4.8 0.0 1.0
OP2 A:G8 4.9 0.0 1.0
O4' A:G6 4.9 0.0 1.0

Phosphorus binding site 7 out of 17 in 1ajf

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Phosphorus binding site 7 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:G8 0.0 0.0 1.0
OP1 A:G8 1.5 0.0 1.0
OP2 A:G8 1.5 0.0 1.0
O3' A:G7 1.6 0.0 1.0
O5' A:G8 1.6 0.0 1.0
C5' A:G8 2.7 0.0 1.0
C3' A:G7 2.7 0.0 1.0
H5'' A:G8 2.7 0.0 1.0
H3' A:G7 2.7 0.0 1.0
HO2' A:G7 3.1 0.0 1.0
H5' A:G8 3.2 0.0 1.0
C2' A:G7 3.5 0.0 1.0
H2' A:G7 3.6 0.0 1.0
O2' A:G7 3.8 0.0 1.0
C4' A:G7 3.8 0.0 1.0
C4' A:G8 3.9 0.0 1.0
H5'' A:G7 4.0 0.0 1.0
H8 A:G8 4.0 0.0 1.0
O4' A:G8 4.0 0.0 1.0
H4' A:G7 4.0 0.0 1.0
H4' A:G8 4.3 0.0 1.0
C5' A:G7 4.4 0.0 1.0
O5' A:G7 4.7 0.0 1.0
C1' A:G7 4.9 0.0 1.0
O4' A:G7 4.9 0.0 1.0

Phosphorus binding site 8 out of 17 in 1ajf

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Phosphorus binding site 8 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average 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
O5' A:A9 1.6 0.0 1.0
O3' A:G8 1.6 0.0 1.0
C3' A:G8 2.7 0.0 1.0
C5' A:A9 2.7 0.0 1.0
H3' A:G8 2.7 0.0 1.0
H5' A:A9 2.9 0.0 1.0
H5'' A:A9 2.9 0.0 1.0
H8 A:A9 3.2 0.0 1.0
H5' A:G8 3.2 0.0 1.0
HO2' A:G8 3.5 0.0 1.0
C4' A:G8 3.5 0.0 1.0
H4' A:G8 3.7 0.0 1.0
C5' A:G8 3.8 0.0 1.0
C2' A:G8 3.8 0.0 1.0
H3' A:A9 4.0 0.0 1.0
C4' A:A9 4.0 0.0 1.0
H2' A:G8 4.1 0.0 1.0
H5'' A:G8 4.1 0.0 1.0
O2' A:G8 4.2 0.0 1.0
C8 A:A9 4.2 0.0 1.0
O4' A:A9 4.4 0.0 1.0
C3' A:A9 4.5 0.0 1.0
H4' A:A9 4.8 0.0 1.0
O4' A:G8 4.8 0.0 1.0
N7 A:A9 5.0 0.0 1.0
C1' A:G8 5.0 0.0 1.0

Phosphorus binding site 9 out of 17 in 1ajf

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Phosphorus binding site 9 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:A10 0.0 0.0 1.0
OP1 A:A10 1.5 0.0 1.0
OP2 A:A10 1.5 0.0 1.0
O3' A:A9 1.6 0.0 1.0
O5' A:A10 1.6 0.0 1.0
C5' A:A10 2.6 0.0 1.0
C3' A:A9 2.7 0.0 1.0
H5'' A:A10 2.7 0.0 1.0
H3' A:A9 2.8 0.0 1.0
HO2' A:A9 2.9 0.0 1.0
H5' A:A10 3.2 0.0 1.0
C2' A:A9 3.4 0.0 1.0
H2' A:A9 3.4 0.0 1.0
O2' A:A9 3.6 0.0 1.0
H8 A:A10 3.8 0.0 1.0
C4' A:A10 3.8 0.0 1.0
C4' A:A9 3.9 0.0 1.0
C6 A:G8 3.9 0.0 1.0
O4' A:A10 3.9 0.0 1.0
C5 A:G8 4.0 0.0 1.0
H4' A:A9 4.0 0.0 1.0
N1 A:G8 4.1 0.0 1.0
H5'' A:A9 4.2 0.0 1.0
C4 A:G8 4.2 0.0 1.0
O6 A:G8 4.3 0.0 1.0
H4' A:A10 4.3 0.0 1.0
C2 A:G8 4.4 0.0 1.0
H2' A:G8 4.4 0.0 1.0
N7 A:G8 4.5 0.0 1.0
H1 A:G8 4.5 0.0 1.0
N3 A:G8 4.5 0.0 1.0
H3' A:G8 4.6 0.0 1.0
C5' A:A9 4.6 0.0 1.0
C1' A:A9 4.8 0.0 1.0
N9 A:G8 4.8 0.0 1.0
C8 A:A10 4.9 0.0 1.0
C8 A:G8 4.9 0.0 1.0
O4' A:A9 5.0 0.0 1.0
O5' A:A9 5.0 0.0 1.0

Phosphorus binding site 10 out of 17 in 1ajf

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Phosphorus binding site 10 out of 17 in the Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Solution Structure of the P5B Stem Loop From A Group I Intron Complexed with Cobalt (III) Hexammine, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:0.0
occ:1.00
P A:A11 0.0 0.0 1.0
OP1 A:A11 1.5 0.0 1.0
OP2 A:A11 1.5 0.0 1.0
O3' A:A10 1.6 0.0 1.0
O5' A:A11 1.6 0.0 1.0
C3' A:A10 2.6 0.0 1.0
C5' A:A11 2.7 0.0 1.0
H3' A:A10 2.7 0.0 1.0
H5' A:A11 2.8 0.0 1.0
H21 A:G8 2.8 0.0 1.0
H5'' A:A11 3.0 0.0 1.0
H8 A:A11 3.1 0.0 1.0
HO2' A:A10 3.3 0.0 1.0
C2' A:A10 3.6 0.0 1.0
H2' A:A10 3.7 0.0 1.0
N2 A:G8 3.7 0.0 1.0
H5' A:A10 3.8 0.0 1.0
C4' A:A10 3.8 0.0 1.0
H5 A:C12 3.8 0.0 1.0
C4' A:A11 4.0 0.0 1.0
O2' A:A10 4.0 0.0 1.0
H4' A:A10 4.0 0.0 1.0
H42 A:C12 4.0 0.0 1.0
H1 A:G8 4.1 0.0 1.0
H3' A:A11 4.1 0.0 1.0
H22 A:G8 4.1 0.0 1.0
C8 A:A11 4.2 0.0 1.0
C5' A:A10 4.2 0.0 1.0
O4' A:A11 4.3 0.0 1.0
C5 A:C12 4.4 0.0 1.0
H5'' A:A10 4.4 0.0 1.0
N4 A:C12 4.5 0.0 1.0
C3' A:A11 4.6 0.0 1.0
C2 A:G8 4.7 0.0 1.0
C4 A:C12 4.8 0.0 1.0
H4' A:A11 4.8 0.0 1.0
N1 A:G8 4.8 0.0 1.0
C1' A:A10 4.9 0.0 1.0
N7 A:A11 4.9 0.0 1.0
O4' A:A10 4.9 0.0 1.0

Reference:

J.S.Kieft, I.Tinoco Jr.. Solution Structure of A Metal-Binding Site in the Major Groove of Rna Complexed with Cobalt (III) Hexammine. Structure V. 5 713 1997.
ISSN: ISSN 0969-2126
PubMed: 9195889
DOI: 10.1016/S0969-2126(97)00225-6
Page generated: Fri Sep 25 13:01:36 2020

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