Phosphorus in PDB 1afx: Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures

Phosphorus Binding Sites:

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

Binding sites:

The binding sites of Phosphorus atom in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures (pdb code 1afx). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 11 binding sites of Phosphorus where determined in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures, PDB code: 1afx:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 11 in 1afx

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Phosphorus binding site 1 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.6
occ:1.00
P A:G2 0.0 0.6 1.0
OP1 A:G2 1.5 0.6 1.0
OP2 A:G2 1.5 0.8 1.0
O3' A:G1 1.6 0.6 1.0
O5' A:G2 1.6 0.5 1.0
H5' A:G2 2.6 0.4 1.0
C3' A:G1 2.6 0.6 1.0
C5' A:G2 2.6 0.4 1.0
H3' A:G1 2.8 0.5 1.0
H4' A:G1 2.9 0.8 1.0
H5'' A:G2 3.2 0.5 1.0
C4' A:G1 3.2 0.7 1.0
HO2' A:G1 3.4 0.7 1.0
H5'' A:G1 3.5 0.7 1.0
C4' A:G2 3.8 0.3 1.0
C5' A:G1 3.9 0.7 1.0
C2' A:G1 3.9 0.5 1.0
O4' A:G2 4.0 0.3 1.0
H8 A:G2 4.1 0.5 1.0
O2' A:G1 4.1 0.6 1.0
H3' A:G2 4.3 0.4 1.0
H5' A:G1 4.4 0.8 1.0
O4' A:G1 4.5 0.7 1.0
H2' A:G1 4.5 0.5 1.0
H4' A:G2 4.6 0.3 1.0
C3' A:G2 4.7 0.3 1.0
C1' A:G1 4.9 0.6 1.0

Phosphorus binding site 2 out of 11 in 1afx

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Phosphorus binding site 2 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.4
occ:1.00
P A:U3 0.0 0.4 1.0
OP1 A:U3 1.5 0.6 1.0
OP2 A:U3 1.5 0.5 1.0
O5' A:U3 1.6 0.4 1.0
O3' A:G2 1.6 0.4 1.0
HO2' A:G2 2.5 0.5 1.0
C5' A:U3 2.6 0.4 1.0
C3' A:G2 2.7 0.3 1.0
H5'' A:U3 2.8 0.4 1.0
H3' A:G2 3.0 0.4 1.0
H5' A:U3 3.0 0.4 1.0
H6 A:U3 3.1 0.3 1.0
C2' A:G2 3.2 0.3 1.0
H2' A:G2 3.2 0.3 1.0
O2' A:G2 3.2 0.3 1.0
H3' A:U3 3.6 0.3 1.0
OP2 A:G4 3.8 0.4 1.0
C4' A:U3 4.0 0.4 1.0
C4' A:G2 4.0 0.3 1.0
H5 A:U3 4.0 0.3 1.0
C6 A:U3 4.1 0.3 1.0
H4' A:G2 4.1 0.3 1.0
H8 A:G4 4.2 0.3 1.0
H5'' A:G2 4.2 0.5 1.0
C3' A:U3 4.3 0.3 1.0
C5 A:U3 4.5 0.3 1.0
H3 A:U5 4.5 0.5 1.0
O4' A:U3 4.5 0.3 1.0
C1' A:G2 4.6 0.3 1.0
C5' A:G2 4.7 0.4 1.0
H4' A:U3 4.8 0.4 1.0
N7 A:G4 4.9 0.3 1.0
C8 A:G4 5.0 0.3 1.0
O4' A:G2 5.0 0.3 1.0

Phosphorus binding site 3 out of 11 in 1afx

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Phosphorus binding site 3 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.4
occ:1.00
P A:G4 0.0 0.4 1.0
OP1 A:G4 1.5 0.4 1.0
OP2 A:G4 1.5 0.4 1.0
O5' A:G4 1.6 0.3 1.0
O3' A:U3 1.6 0.4 1.0
H5' A:G4 2.6 0.3 1.0
C5' A:G4 2.6 0.3 1.0
C3' A:U3 2.7 0.3 1.0
H3' A:U3 2.7 0.3 1.0
H5'' A:G4 3.3 0.3 1.0
O4 A:U5 3.4 0.5 1.0
HO2' A:U3 3.5 0.5 1.0
H5'' A:U3 3.6 0.4 1.0
O4' A:G4 3.6 0.3 1.0
C2' A:U3 3.7 0.3 1.0
C4' A:G4 3.7 0.3 1.0
C4' A:U3 3.8 0.4 1.0
H8 A:G4 3.8 0.3 1.0
H2' A:U3 3.8 0.3 1.0
C4 A:U5 3.8 0.5 1.0
H4' A:U3 3.9 0.4 1.0
C5' A:U3 4.1 0.4 1.0
O2' A:U3 4.1 0.4 1.0
H5 A:U5 4.3 0.5 1.0
O5' A:U3 4.3 0.4 1.0
C5 A:U5 4.3 0.4 1.0
H4' A:G4 4.4 0.4 1.0
N3 A:U5 4.6 0.5 1.0
H3' A:G4 4.6 0.3 1.0
OP1 A:U3 4.6 0.6 1.0
H3 A:U5 4.7 0.5 1.0
C8 A:G4 4.7 0.3 1.0
C3' A:G4 4.8 0.3 1.0
C1' A:G4 5.0 0.3 1.0
O4' A:U3 5.0 0.3 1.0
C1' A:U3 5.0 0.3 1.0

Phosphorus binding site 4 out of 11 in 1afx

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Phosphorus binding site 4 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.3
occ:1.00
P A:U5 0.0 0.3 1.0
OP1 A:U5 1.5 0.5 1.0
OP2 A:U5 1.5 0.6 1.0
O3' A:G4 1.6 0.3 1.0
O5' A:U5 1.6 0.3 1.0
C3' A:G4 2.6 0.3 1.0
C5' A:U5 2.7 0.4 1.0
H3' A:G4 2.7 0.3 1.0
H5' A:U5 2.8 0.4 1.0
H5'' A:U5 3.0 0.5 1.0
H6 A:U5 3.1 0.4 1.0
HO2' A:G4 3.2 0.8 1.0
C2' A:G4 3.6 0.3 1.0
H5'' A:G4 3.6 0.3 1.0
H2' A:G4 3.7 0.4 1.0
O2' A:G4 3.8 0.4 1.0
C4' A:G4 3.8 0.3 1.0
H3' A:U5 3.9 0.4 1.0
C4' A:U5 4.0 0.3 1.0
C6 A:U5 4.0 0.3 1.0
H4' A:G4 4.1 0.4 1.0
H5 A:U5 4.1 0.5 1.0
H1 A:G6 4.2 0.8 1.0
C5' A:G4 4.3 0.3 1.0
OP2 A:G6 4.3 0.7 1.0
O4' A:U5 4.4 0.3 1.0
N1 A:G6 4.4 0.7 1.0
C5 A:U5 4.5 0.4 1.0
C3' A:U5 4.5 0.4 1.0
H21 A:G6 4.6 1.0 1.0
C2 A:G6 4.7 0.7 1.0
N2 A:G6 4.8 0.9 1.0
H4' A:U5 4.8 0.4 1.0
C1' A:G4 4.9 0.3 1.0
O4' A:G4 5.0 0.3 1.0
C6 A:G6 5.0 0.6 1.0
N1 A:U5 5.0 0.3 1.0

Phosphorus binding site 5 out of 11 in 1afx

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Phosphorus binding site 5 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.6
occ:1.00
P A:G6 0.0 0.6 1.0
OP2 A:G6 1.5 0.7 1.0
OP1 A:G6 1.5 0.7 1.0
O3' A:U5 1.6 0.5 1.0
O5' A:G6 1.6 0.6 1.0
C5' A:G6 2.6 0.6 1.0
H5' A:G6 2.6 0.6 1.0
C3' A:U5 2.7 0.4 1.0
H3' A:U5 2.7 0.4 1.0
H22 A:G6 2.8 0.9 1.0
H5'' A:U5 3.1 0.5 1.0
H62 A:A7 3.1 0.7 1.0
N3 A:G6 3.2 0.6 1.0
N7 A:A7 3.3 0.5 1.0
O4' A:G6 3.3 0.5 1.0
H4' A:U5 3.4 0.4 1.0
H5'' A:G6 3.5 0.7 1.0
C4' A:U5 3.5 0.3 1.0
N2 A:G6 3.5 0.9 1.0
HO2' A:U5 3.5 0.6 1.0
C4' A:G6 3.6 0.5 1.0
C2 A:G6 3.7 0.7 1.0
C5' A:U5 3.7 0.4 1.0
C2' A:U5 3.9 0.3 1.0
N6 A:A7 4.1 0.8 1.0
O2' A:U5 4.2 0.4 1.0
H4' A:G6 4.2 0.5 1.0
C8 A:A7 4.2 0.4 1.0
C4 A:G6 4.2 0.6 1.0
H8 A:A7 4.3 0.4 1.0
C5 A:A7 4.3 0.5 1.0
H2' A:U5 4.3 0.4 1.0
H21 A:G6 4.3 1.0 1.0
O5' A:U5 4.4 0.3 1.0
H2 A:A8 4.5 0.4 1.0
H3' A:G6 4.5 0.7 1.0
C1' A:G6 4.6 0.5 1.0
C6 A:A7 4.6 0.6 1.0
N1 A:A8 4.6 0.4 1.0
H5' A:U5 4.7 0.4 1.0
C3' A:G6 4.7 0.7 1.0
N9 A:G6 4.7 0.5 1.0
H61 A:A7 4.8 0.9 1.0
O4' A:U5 4.8 0.3 1.0
N1 A:G6 4.9 0.7 1.0
C2 A:A8 4.9 0.4 1.0
H6 A:U5 5.0 0.4 1.0

Phosphorus binding site 6 out of 11 in 1afx

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Phosphorus binding site 6 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.6
occ:1.00
P A:A7 0.0 0.6 1.0
OP1 A:A7 1.5 0.5 1.0
OP2 A:A7 1.5 0.7 1.0
O5' A:A7 1.6 0.6 1.0
O3' A:G6 1.6 0.7 1.0
HO2' A:G6 2.3 0.7 1.0
H4' A:G6 2.4 0.5 1.0
C5' A:A7 2.7 0.5 1.0
C3' A:G6 2.7 0.7 1.0
H5'' A:A7 2.8 0.5 1.0
C4' A:G6 3.0 0.5 1.0
O2' A:G6 3.2 0.7 1.0
O4' A:A7 3.3 0.4 1.0
C4' A:A7 3.4 0.5 1.0
C2' A:G6 3.5 0.7 1.0
H5' A:A7 3.5 0.6 1.0
H3' A:G6 3.6 0.7 1.0
H4' A:A7 3.7 0.5 1.0
H5'' A:G6 3.8 0.7 1.0
C5' A:G6 3.9 0.6 1.0
O4' A:G6 4.1 0.5 1.0
H5' A:G6 4.2 0.6 1.0
N9 A:A7 4.2 0.3 1.0
C1' A:G6 4.3 0.5 1.0
H2' A:G6 4.3 0.8 1.0
C1' A:A7 4.3 0.3 1.0
H8 A:A7 4.3 0.4 1.0
C8 A:A7 4.4 0.4 1.0
H1' A:G6 4.5 0.5 1.0
C4 A:A7 4.7 0.4 1.0
C3' A:A7 4.8 0.5 1.0
N7 A:A7 4.9 0.5 1.0
H2' A:A7 5.0 0.4 1.0

Phosphorus binding site 7 out of 11 in 1afx

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Phosphorus binding site 7 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.5
occ:1.00
P A:A8 0.0 0.5 1.0
OP2 A:A8 1.5 0.5 1.0
OP1 A:A8 1.5 0.6 1.0
O5' A:A8 1.6 0.4 1.0
O3' A:A7 1.6 0.5 1.0
HO2' A:A7 2.6 0.5 1.0
C5' A:A8 2.6 0.3 1.0
C3' A:A7 2.7 0.5 1.0
H5'' A:A8 2.8 0.4 1.0
H1' A:A7 2.9 0.3 1.0
H4' A:A7 3.0 0.5 1.0
H5' A:A8 3.0 0.3 1.0
C4' A:A7 3.2 0.5 1.0
O4' A:A7 3.2 0.4 1.0
O2' A:A7 3.2 0.4 1.0
C2' A:A7 3.3 0.4 1.0
C1' A:A7 3.3 0.3 1.0
H3' A:A7 3.6 0.5 1.0
H2' A:A8 3.7 0.4 1.0
H3' A:A8 3.8 0.4 1.0
C4' A:A8 4.0 0.3 1.0
C3' A:A8 4.3 0.3 1.0
H2' A:A7 4.3 0.4 1.0
C2' A:A8 4.5 0.3 1.0
O4' A:A8 4.5 0.3 1.0
C5' A:A7 4.7 0.5 1.0
N9 A:A7 4.7 0.3 1.0
H4' A:A8 4.8 0.3 1.0
C1' A:A8 5.0 0.3 1.0
H5' A:A7 5.0 0.6 1.0

Phosphorus binding site 8 out of 11 in 1afx

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Phosphorus binding site 8 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.4
occ:1.00
P A:C9 0.0 0.4 1.0
OP1 A:C9 1.5 0.5 1.0
OP2 A:C9 1.5 0.5 1.0
O5' A:C9 1.6 0.4 1.0
O3' A:A8 1.6 0.4 1.0
HO2' A:A8 2.3 0.5 1.0
O2' A:A8 2.6 0.4 1.0
C5' A:C9 2.6 0.4 1.0
C3' A:A8 2.7 0.3 1.0
H5' A:C9 2.7 0.4 1.0
H3' A:A8 3.0 0.4 1.0
H5'' A:C9 3.1 0.5 1.0
C2' A:A8 3.2 0.3 1.0
H1' A:A8 3.8 0.3 1.0
C4' A:C9 3.9 0.4 1.0
C4' A:A8 4.0 0.3 1.0
H2' A:A8 4.0 0.4 1.0
H4' A:A8 4.0 0.3 1.0
C1' A:A8 4.1 0.3 1.0
H3' A:C9 4.1 0.4 1.0
H6 A:C9 4.1 0.4 1.0
O4' A:C9 4.3 0.4 1.0
O4' A:A8 4.5 0.3 1.0
C3' A:C9 4.6 0.3 1.0
H4' A:C9 4.7 0.4 1.0

Phosphorus binding site 9 out of 11 in 1afx

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Phosphorus binding site 9 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.4
occ:1.00
P A:A10 0.0 0.4 1.0
OP2 A:A10 1.5 0.4 1.0
OP1 A:A10 1.5 0.5 1.0
O5' A:A10 1.6 0.4 1.0
O3' A:C9 1.6 0.4 1.0
HO2' A:C9 2.4 0.4 1.0
C5' A:A10 2.7 0.4 1.0
C3' A:C9 2.7 0.3 1.0
H5' A:A10 2.9 0.5 1.0
H5'' A:A10 2.9 0.5 1.0
H3' A:C9 3.0 0.4 1.0
H8 A:A10 3.1 0.4 1.0
O2' A:C9 3.1 0.4 1.0
C2' A:C9 3.1 0.3 1.0
H2' A:C9 3.1 0.3 1.0
H3' A:A10 3.9 0.3 1.0
C4' A:C9 4.0 0.4 1.0
C4' A:A10 4.0 0.4 1.0
H4' A:C9 4.1 0.4 1.0
C8 A:A10 4.1 0.3 1.0
OP2 A:C11 4.2 0.4 1.0
H5 A:C11 4.3 0.3 1.0
H5'' A:C9 4.4 0.5 1.0
O4' A:A10 4.5 0.4 1.0
C3' A:A10 4.5 0.3 1.0
C1' A:C9 4.6 0.3 1.0
C5' A:C9 4.7 0.4 1.0
N7 A:A10 4.7 0.3 1.0
H4' A:A10 4.8 0.5 1.0
O4' A:C9 4.9 0.4 1.0

Phosphorus binding site 10 out of 11 in 1afx

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Phosphorus binding site 10 out of 11 in the Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Ugaa Eukaryotic Ribosomal Rna Tetraloop, uc(Nmr), 13 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:0.3
occ:1.00
P A:C11 0.0 0.3 1.0
OP1 A:C11 1.5 0.4 1.0
OP2 A:C11 1.5 0.4 1.0
O5' A:C11 1.6 0.3 1.0
O3' A:A10 1.6 0.4 1.0
H5' A:C11 2.6 0.4 1.0
C3' A:A10 2.6 0.3 1.0
H3' A:A10 2.6 0.3 1.0
C5' A:C11 2.6 0.4 1.0
H6 A:C11 3.0 0.3 1.0
H5'' A:C11 3.3 0.5 1.0
H5'' A:A10 3.3 0.5 1.0
HO2' A:A10 3.5 0.6 1.0
C4' A:A10 3.7 0.4 1.0
O4' A:C11 3.7 0.3 1.0
C4' A:C11 3.7 0.4 1.0
C2' A:A10 3.8 0.3 1.0
H4' A:A10 3.9 0.5 1.0
H2' A:A10 3.9 0.3 1.0
C5' A:A10 3.9 0.4 1.0
C6 A:C11 4.1 0.2 1.0
O2' A:A10 4.2 0.4 1.0
H3' A:C11 4.3 0.3 1.0
O5' A:A10 4.4 0.4 1.0
H4' A:C11 4.5 0.4 1.0
H5 A:C11 4.6 0.3 1.0
C3' A:C11 4.7 0.4 1.0
C5 A:C11 4.8 0.3 1.0
C1' A:C11 4.9 0.3 1.0
H5' A:A10 4.9 0.5 1.0
O4' A:A10 4.9 0.4 1.0
N1 A:C11 5.0 0.2 1.0
C1' A:A10 5.0 0.4 1.0

Reference:

S.E.Butcher, F.H.Allain, J.Feigon. Solution Structure of the Loop B Domain From the Hairpin Ribozyme. Nat.Struct.Biol. V. 6 212 1999.
ISSN: ISSN 1072-8368
PubMed: 10074938
DOI: 10.1038/6651
Page generated: Fri Sep 25 12:48:44 2020

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