Phosphorus in PDB 1al5: A-Tract Rna Dodecamer, uc(Nmr), 12 Structures

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures (pdb code 1al5). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures, PDB code: 1al5:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 1al5

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Phosphorus binding site 1 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:G2 0.0 0.0 1.0
OP1 A:G2 1.5 0.0 1.0
OP2 A:G2 1.5 0.0 1.0
O5' A:G2 1.6 0.0 1.0
O3' A:C1 1.6 0.0 1.0
C5' A:G2 2.6 0.0 1.0
C3' A:C1 2.6 0.0 1.0
H3' A:C1 2.8 0.0 1.0
H5' A:G2 2.9 0.0 1.0
H5'' A:G2 2.9 0.0 1.0
HO2' A:C1 3.2 0.0 1.0
H2' A:C1 3.4 0.0 1.0
C2' A:C1 3.4 0.0 1.0
O2' A:C1 3.8 0.0 1.0
C4' A:C1 4.0 0.0 1.0
C4' A:G2 4.0 0.0 1.0
H8 A:G2 4.0 0.0 1.0
H3' A:G2 4.1 0.0 1.0
H5'' A:C1 4.1 0.0 1.0
H4' A:C1 4.2 0.0 1.0
O4' A:G2 4.3 0.0 1.0
C5' A:C1 4.5 0.0 1.0
C3' A:G2 4.6 0.0 1.0
H4' A:G2 4.8 0.0 1.0
C1' A:C1 4.8 0.0 1.0
O5' A:C1 4.8 0.0 1.0
O4' A:C1 5.0 0.0 1.0

Phosphorus binding site 2 out of 22 in 1al5

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Phosphorus binding site 2 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 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 A-Tract Rna Dodecamer, uc(Nmr), 12 Structures 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
O5' A:C3 1.6 0.0 1.0
O3' A:G2 1.6 0.0 1.0
C3' A:G2 2.6 0.0 1.0
C5' A:C3 2.6 0.0 1.0
H3' A:G2 2.8 0.0 1.0
H5' A:C3 2.9 0.0 1.0
H5'' A:C3 2.9 0.0 1.0
H2' A:G2 3.4 0.0 1.0
C2' A:G2 3.4 0.0 1.0
O2' A:G2 3.7 0.0 1.0
H6 A:C3 3.8 0.0 1.0
C4' A:G2 4.0 0.0 1.0
C4' A:C3 4.0 0.0 1.0
HO2' A:G2 4.1 0.0 1.0
H3' A:C3 4.1 0.0 1.0
H5'' A:G2 4.1 0.0 1.0
H4' A:G2 4.2 0.0 1.0
O4' A:C3 4.3 0.0 1.0
C5' A:G2 4.6 0.0 1.0
C3' A:C3 4.6 0.0 1.0
H4' A:C3 4.8 0.0 1.0
C1' A:G2 4.8 0.0 1.0
C6 A:C3 4.8 0.0 1.0
O5' A:G2 5.0 0.0 1.0
O4' A:G2 5.0 0.0 1.0

Phosphorus binding site 3 out of 22 in 1al5

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Phosphorus binding site 3 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures 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
OP2 A:A4 1.5 0.0 1.0
OP1 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
C5' A:A4 2.6 0.0 1.0
C3' A:C3 2.6 0.0 1.0
H3' A:C3 2.8 0.0 1.0
H5' A:A4 2.9 0.0 1.0
H5'' A:A4 2.9 0.0 1.0
HO2' A:C3 3.2 0.0 1.0
H2' A:C3 3.4 0.0 1.0
C2' A:C3 3.4 0.0 1.0
O2' A:C3 3.8 0.0 1.0
H8 A:A4 4.0 0.0 1.0
C4' A:C3 4.0 0.0 1.0
C4' A:A4 4.0 0.0 1.0
H3' A:A4 4.1 0.0 1.0
H5'' A:C3 4.1 0.0 1.0
H4' A:C3 4.2 0.0 1.0
O4' A:A4 4.3 0.0 1.0
C5' A:C3 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 5.0 0.0 1.0
C8 A:A4 5.0 0.0 1.0

Phosphorus binding site 4 out of 22 in 1al5

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Phosphorus binding site 4 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures 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:A4 1.6 0.0 1.0
C5' A:A5 2.6 0.0 1.0
C3' A:A4 2.7 0.0 1.0
H3' A:A4 2.8 0.0 1.0
H5' A:A5 2.8 0.0 1.0
H5'' A:A5 3.0 0.0 1.0
H2' A:A4 3.3 0.0 1.0
C2' A:A4 3.4 0.0 1.0
O2' A:A4 3.7 0.0 1.0
H8 A:A5 3.8 0.0 1.0
C4' A:A5 4.0 0.0 1.0
C4' A:A4 4.0 0.0 1.0
H3' A:A5 4.2 0.0 1.0
H5'' A:A4 4.2 0.0 1.0
H4' A:A4 4.2 0.0 1.0
O4' A:A5 4.3 0.0 1.0
HO2' A:A4 4.4 0.0 1.0
C5' A:A4 4.6 0.0 1.0
C3' A:A5 4.6 0.0 1.0
C1' A:A4 4.8 0.0 1.0
H4' A:A5 4.8 0.0 1.0
C8 A:A5 4.9 0.0 1.0
O5' A:A4 5.0 0.0 1.0
O4' A:A4 5.0 0.0 1.0

Phosphorus binding site 5 out of 22 in 1al5

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Phosphorus binding site 5 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures 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
O5' A:A6 1.6 0.0 1.0
O3' A:A5 1.6 0.0 1.0
C5' A:A6 2.6 0.0 1.0
C3' A:A5 2.7 0.0 1.0
H3' A:A5 2.8 0.0 1.0
H5' A:A6 2.8 0.0 1.0
H5'' A:A6 3.0 0.0 1.0
H2' A:A5 3.3 0.0 1.0
C2' A:A5 3.4 0.0 1.0
O2' A:A5 3.7 0.0 1.0
H8 A:A6 3.7 0.0 1.0
C4' A:A6 4.0 0.0 1.0
C4' A:A5 4.0 0.0 1.0
H5'' A:A5 4.2 0.0 1.0
H3' A:A6 4.2 0.0 1.0
H4' A:A5 4.2 0.0 1.0
O4' A:A6 4.3 0.0 1.0
HO2' A:A5 4.4 0.0 1.0
C5' A:A5 4.6 0.0 1.0
C3' A:A6 4.6 0.0 1.0
H4' A:A6 4.8 0.0 1.0
C1' A:A5 4.8 0.0 1.0
C8 A:A6 4.8 0.0 1.0
O4' A:A5 5.0 0.0 1.0

Phosphorus binding site 6 out of 22 in 1al5

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Phosphorus binding site 6 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures 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
OP2 A:U7 1.5 0.0 1.0
OP1 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
H3' A:A6 2.8 0.0 1.0
H5' A:U7 2.9 0.0 1.0
H5'' A:U7 3.0 0.0 1.0
HO2' A:A6 3.2 0.0 1.0
H2' A:A6 3.4 0.0 1.0
C2' A:A6 3.4 0.0 1.0
H6 A:U7 3.7 0.0 1.0
O2' A:A6 3.8 0.0 1.0
C4' A:U7 4.0 0.0 1.0
C4' A:A6 4.0 0.0 1.0
H5'' A:A6 4.1 0.0 1.0
H3' A:U7 4.1 0.0 1.0
H4' A:A6 4.2 0.0 1.0
O4' A:U7 4.3 0.0 1.0
C5' A:A6 4.5 0.0 1.0
C3' A:U7 4.6 0.0 1.0
C6 A:U7 4.7 0.0 1.0
H4' A:U7 4.8 0.0 1.0
C1' A:A6 4.8 0.0 1.0
O4' A:A6 5.0 0.0 1.0

Phosphorus binding site 7 out of 22 in 1al5

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Phosphorus binding site 7 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:U8 0.0 0.0 1.0
OP1 A:U8 1.5 0.0 1.0
OP2 A:U8 1.5 0.0 1.0
O5' A:U8 1.6 0.0 1.0
O3' A:U7 1.6 0.0 1.0
C5' A:U8 2.6 0.0 1.0
C3' A:U7 2.7 0.0 1.0
H3' A:U7 2.8 0.0 1.0
H5' A:U8 2.9 0.0 1.0
H5'' A:U8 2.9 0.0 1.0
H2' A:U7 3.4 0.0 1.0
C2' A:U7 3.4 0.0 1.0
H6 A:U8 3.7 0.0 1.0
O2' A:U7 3.8 0.0 1.0
C4' A:U8 4.0 0.0 1.0
C4' A:U7 4.0 0.0 1.0
H3' A:U8 4.0 0.0 1.0
H5'' A:U7 4.0 0.0 1.0
H4' A:U7 4.2 0.0 1.0
O4' A:U8 4.3 0.0 1.0
HO2' A:U7 4.5 0.0 1.0
C5' A:U7 4.5 0.0 1.0
C3' A:U8 4.5 0.0 1.0
H4' A:U8 4.8 0.0 1.0
C1' A:U7 4.8 0.0 1.0
C6 A:U8 4.8 0.0 1.0
O4' A:U7 5.0 0.0 1.0

Phosphorus binding site 8 out of 22 in 1al5

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Phosphorus binding site 8 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:U9 0.0 0.0 1.0
OP2 A:U9 1.5 0.0 1.0
OP1 A:U9 1.5 0.0 1.0
O5' A:U9 1.6 0.0 1.0
O3' A:U8 1.6 0.0 1.0
C5' A:U9 2.6 0.0 1.0
C3' A:U8 2.7 0.0 1.0
H3' A:U8 2.8 0.0 1.0
H5' A:U9 2.9 0.0 1.0
H5'' A:U9 3.0 0.0 1.0
H2' A:U8 3.3 0.0 1.0
C2' A:U8 3.4 0.0 1.0
O2' A:U8 3.7 0.0 1.0
H6 A:U9 3.7 0.0 1.0
C4' A:U9 4.0 0.0 1.0
C4' A:U8 4.0 0.0 1.0
H3' A:U9 4.1 0.0 1.0
H5'' A:U8 4.1 0.0 1.0
H4' A:U8 4.2 0.0 1.0
O4' A:U9 4.3 0.0 1.0
HO2' A:U8 4.4 0.0 1.0
C5' A:U8 4.6 0.0 1.0
C3' A:U9 4.6 0.0 1.0
C6 A:U9 4.8 0.0 1.0
H4' A:U9 4.8 0.0 1.0
C1' A:U8 4.8 0.0 1.0
O5' A:U8 5.0 0.0 1.0
O4' A:U8 5.0 0.0 1.0

Phosphorus binding site 9 out of 22 in 1al5

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Phosphorus binding site 9 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures 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
OP2 A:G10 1.5 0.0 1.0
OP1 A:G10 1.5 0.0 1.0
O5' A:G10 1.6 0.0 1.0
O3' A:U9 1.6 0.0 1.0
C5' A:G10 2.6 0.0 1.0
C3' A:U9 2.6 0.0 1.0
H3' A:U9 2.8 0.0 1.0
H5' A:G10 2.9 0.0 1.0
H5'' A:G10 2.9 0.0 1.0
H2' A:U9 3.4 0.0 1.0
C2' A:U9 3.4 0.0 1.0
O2' A:U9 3.8 0.0 1.0
C4' A:G10 4.0 0.0 1.0
C4' A:U9 4.0 0.0 1.0
H8 A:G10 4.0 0.0 1.0
H3' A:G10 4.0 0.0 1.0
H5'' A:U9 4.1 0.0 1.0
H4' A:U9 4.2 0.0 1.0
O4' A:G10 4.3 0.0 1.0
HO2' A:U9 4.5 0.0 1.0
C5' A:U9 4.5 0.0 1.0
C3' A:G10 4.5 0.0 1.0
H4' A:G10 4.8 0.0 1.0
C1' A:U9 4.8 0.0 1.0
O5' A:U9 4.9 0.0 1.0
O4' A:U9 5.0 0.0 1.0

Phosphorus binding site 10 out of 22 in 1al5

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Phosphorus binding site 10 out of 22 in the A-Tract Rna Dodecamer, uc(Nmr), 12 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of A-Tract Rna Dodecamer, uc(Nmr), 12 Structures 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
OP2 A:C11 1.5 0.0 1.0
OP1 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
C5' A:C11 2.6 0.0 1.0
C3' A:G10 2.6 0.0 1.0
H3' A:G10 2.8 0.0 1.0
H5' A:C11 2.9 0.0 1.0
H5'' A:C11 2.9 0.0 1.0
H2' A:G10 3.4 0.0 1.0
C2' A:G10 3.4 0.0 1.0
O2' A:G10 3.7 0.0 1.0
H6 A:C11 3.7 0.0 1.0
C4' A:C11 4.0 0.0 1.0
C4' A:G10 4.0 0.0 1.0
H3' A:C11 4.0 0.0 1.0
H5'' A:G10 4.1 0.0 1.0
H4' A:G10 4.2 0.0 1.0
O4' A:C11 4.3 0.0 1.0
HO2' A:G10 4.4 0.0 1.0
C3' A:C11 4.5 0.0 1.0
C5' A:G10 4.6 0.0 1.0
H4' A:C11 4.8 0.0 1.0
C1' A:G10 4.8 0.0 1.0
C6 A:C11 4.8 0.0 1.0
O5' A:G10 4.9 0.0 1.0
O4' A:G10 5.0 0.0 1.0

Reference:

M.R.Conte, G.L.Conn, T.Brown, A.N.Lane. Conformational Properties and Thermodynamics of the Rna Duplex R(Cgcaaauuugcg)2: Comparison with the Dna Analogue D(Cgcaaatttgcg)2. Nucleic Acids Res. V. 25 2627 1997.
ISSN: ISSN 0305-1048
PubMed: 9185574
DOI: 10.1093/NAR/25.13.2627
Page generated: Fri Sep 25 13:12:38 2020

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