Phosphorus in PDB 148d: Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)

Phosphorus Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Phosphorus atom in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) (pdb code 148d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 14 binding sites of Phosphorus where determined in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg), PDB code: 148d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 14 in 148d

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Phosphorus binding site 1 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:DG2 0.0 0.0 1.0
OP2 A:DG2 1.5 0.0 1.0
OP1 A:DG2 1.5 0.0 1.0
O3' A:DG1 1.6 0.0 1.0
O5' A:DG2 1.6 0.0 1.0
C3' A:DG1 2.6 0.0 1.0
C5' A:DG2 2.7 0.0 1.0
H3' A:DG1 2.7 0.0 1.0
H5' A:DG2 2.8 0.0 1.0
H5'' A:DG2 3.0 0.0 1.0
H2'' A:DG1 3.3 0.0 1.0
C2' A:DG1 3.5 0.0 1.0
H4' A:DG1 3.8 0.0 1.0
C4' A:DG1 3.9 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
H1' A:DG1 4.0 0.0 1.0
H3' A:DG2 4.0 0.0 1.0
H2' A:DG1 4.3 0.0 1.0
C1' A:DG1 4.3 0.0 1.0
O4' A:DG2 4.4 0.0 1.0
C3' A:DG2 4.6 0.0 1.0
OP2 A:DT4 4.6 0.0 1.0
O4' A:DG1 4.7 0.0 1.0
H5'' A:DG1 4.7 0.0 1.0
H2' A:DG2 4.7 0.0 1.0
H4' A:DG2 4.8 0.0 1.0
C5' A:DG1 4.9 0.0 1.0

Phosphorus binding site 2 out of 14 in 148d

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Phosphorus binding site 2 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:DT3 0.0 0.0 1.0
OP1 A:DT3 1.5 0.0 1.0
OP2 A:DT3 1.5 0.0 1.0
O5' A:DT3 1.6 0.0 1.0
O3' A:DG2 1.6 0.0 1.0
C5' A:DT3 2.7 0.0 1.0
C3' A:DG2 2.7 0.0 1.0
H6 A:DT3 2.8 0.0 1.0
H5'' A:DT3 2.8 0.0 1.0
H2'' A:DG2 2.9 0.0 1.0
H5' A:DT3 3.1 0.0 1.0
C2' A:DG2 3.2 0.0 1.0
H3' A:DG2 3.4 0.0 1.0
H71 A:DT3 3.4 0.0 1.0
H1' A:DG2 3.4 0.0 1.0
H73 A:DT3 3.4 0.0 1.0
H4' A:DG2 3.5 0.0 1.0
C4' A:DG2 3.8 0.0 1.0
C6 A:DT3 3.8 0.0 1.0
H3' A:DT3 3.8 0.0 1.0
C7 A:DT3 3.8 0.0 1.0
C1' A:DG2 3.8 0.0 1.0
C4' A:DT3 4.0 0.0 1.0
H2' A:DG2 4.1 0.0 1.0
H2' A:DT3 4.2 0.0 1.0
C5 A:DT3 4.3 0.0 1.0
C3' A:DT3 4.4 0.0 1.0
H72 A:DT4 4.4 0.0 1.0
O4' A:DG2 4.5 0.0 1.0
O4' A:DT3 4.6 0.0 1.0
C2' A:DT3 4.7 0.0 1.0
H4' A:DT3 4.8 0.0 1.0
H72 A:DT3 4.8 0.0 1.0
N1 A:DT3 4.8 0.0 1.0
H5'' A:DG2 4.9 0.0 1.0
C1' A:DT3 5.0 0.0 1.0
C5' A:DG2 5.0 0.0 1.0

Phosphorus binding site 3 out of 14 in 148d

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Phosphorus binding site 3 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:DT4 0.0 0.0 1.0
OP1 A:DT4 1.5 0.0 1.0
OP2 A:DT4 1.5 0.0 1.0
O3' A:DT3 1.6 0.0 1.0
O5' A:DT4 1.6 0.0 1.0
C3' A:DT3 2.7 0.0 1.0
H3' A:DT3 2.7 0.0 1.0
C5' A:DT4 2.7 0.0 1.0
H5'' A:DT4 2.8 0.0 1.0
H5' A:DT4 3.0 0.0 1.0
H2'' A:DT3 3.1 0.0 1.0
C2' A:DT3 3.4 0.0 1.0
H3' A:DT4 3.9 0.0 1.0
H2' A:DT3 3.9 0.0 1.0
H2' A:DG2 4.0 0.0 1.0
C4' A:DT3 4.0 0.0 1.0
H4' A:DT3 4.0 0.0 1.0
C4' A:DT4 4.0 0.0 1.0
H3' A:DG2 4.3 0.0 1.0
C3' A:DT4 4.5 0.0 1.0
H2'' A:DG2 4.7 0.0 1.0
C1' A:DT3 4.7 0.0 1.0
H8 A:DG2 4.7 0.0 1.0
C2' A:DG2 4.7 0.0 1.0
O4' A:DT4 4.7 0.0 1.0
H5'' A:DT3 4.8 0.0 1.0
H1' A:DT3 4.8 0.0 1.0
H6 A:DT4 4.8 0.0 1.0
H2' A:DT4 4.8 0.0 1.0
O4' A:DT3 4.8 0.0 1.0
H4' A:DT4 4.9 0.0 1.0
C5' A:DT3 4.9 0.0 1.0

Phosphorus binding site 4 out of 14 in 148d

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Phosphorus binding site 4 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:DG5 0.0 0.0 1.0
OP1 A:DG5 1.5 0.0 1.0
OP2 A:DG5 1.5 0.0 1.0
O3' A:DT4 1.6 0.0 1.0
O5' A:DG5 1.6 0.0 1.0
C3' A:DT4 2.7 0.0 1.0
C5' A:DG5 2.7 0.0 1.0
H5'' A:DG5 2.8 0.0 1.0
H3' A:DT4 3.0 0.0 1.0
H5' A:DG5 3.1 0.0 1.0
H4' A:DT4 3.4 0.0 1.0
C4' A:DT4 3.5 0.0 1.0
H5'' A:DT4 3.6 0.0 1.0
C2' A:DT4 3.9 0.0 1.0
C4' A:DG5 4.0 0.0 1.0
H2'' A:DT4 4.0 0.0 1.0
C5' A:DT4 4.1 0.0 1.0
O4' A:DG5 4.3 0.0 1.0
H4' A:DG5 4.4 0.0 1.0
H1' A:DT4 4.5 0.0 1.0
H2' A:DT4 4.6 0.0 1.0
C1' A:DT4 4.7 0.0 1.0
O4' A:DT4 4.7 0.0 1.0
N3 A:DG5 4.9 0.0 1.0
O5' A:DT4 4.9 0.0 1.0
H5' A:DT4 4.9 0.0 1.0

Phosphorus binding site 5 out of 14 in 148d

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Phosphorus binding site 5 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:DG6 0.0 0.0 1.0
OP2 A:DG6 1.5 0.0 1.0
OP1 A:DG6 1.5 0.0 1.0
O3' A:DG5 1.6 0.0 1.0
O5' A:DG6 1.6 0.0 1.0
C5' A:DG6 2.7 0.0 1.0
C3' A:DG5 2.7 0.0 1.0
H2'' A:DG5 2.9 0.0 1.0
H3' A:DG5 2.9 0.0 1.0
H5'' A:DG6 2.9 0.0 1.0
H5' A:DG6 3.0 0.0 1.0
H1' A:DG5 3.3 0.0 1.0
C2' A:DG5 3.3 0.0 1.0
C1' A:DG5 3.8 0.0 1.0
H4' A:DG5 3.9 0.0 1.0
C4' A:DG5 3.9 0.0 1.0
C4' A:DG6 4.0 0.0 1.0
H2' A:DG6 4.1 0.0 1.0
H3' A:DG6 4.2 0.0 1.0
H2' A:DG5 4.3 0.0 1.0
O4' A:DG5 4.4 0.0 1.0
C3' A:DG6 4.5 0.0 1.0
O4' A:DG6 4.6 0.0 1.0
H8 A:DG6 4.8 0.0 1.0
H4' A:DG6 4.8 0.0 1.0
C2' A:DG6 5.0 0.0 1.0

Phosphorus binding site 6 out of 14 in 148d

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Phosphorus binding site 6 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:DT7 0.0 0.0 1.0
OP1 A:DT7 1.5 0.0 1.0
OP2 A:DT7 1.5 0.0 1.0
O5' A:DT7 1.6 0.0 1.0
O3' A:DG6 1.6 0.0 1.0
C5' A:DT7 2.6 0.0 1.0
C3' A:DG6 2.7 0.0 1.0
H6 A:DT7 2.7 0.0 1.0
H5'' A:DT7 2.7 0.0 1.0
H3' A:DG6 2.8 0.0 1.0
H4' A:DG6 2.9 0.0 1.0
H5' A:DT7 3.1 0.0 1.0
C4' A:DG6 3.3 0.0 1.0
H73 A:DT7 3.4 0.0 1.0
H2' A:DT7 3.5 0.0 1.0
H71 A:DT7 3.7 0.0 1.0
C6 A:DT7 3.7 0.0 1.0
H5'' A:DG6 3.7 0.0 1.0
C4' A:DT7 3.9 0.0 1.0
C7 A:DT7 3.9 0.0 1.0
C2' A:DG6 4.0 0.0 1.0
H3' A:DT7 4.1 0.0 1.0
C5' A:DG6 4.1 0.0 1.0
H1' A:DG6 4.2 0.0 1.0
C5 A:DT7 4.3 0.0 1.0
C2' A:DT7 4.4 0.0 1.0
H2'' A:DG6 4.4 0.0 1.0
O4' A:DT7 4.4 0.0 1.0
C3' A:DT7 4.4 0.0 1.0
O4' A:DG6 4.5 0.0 1.0
C1' A:DG6 4.5 0.0 1.0
H2' A:DG6 4.6 0.0 1.0
N1 A:DT7 4.7 0.0 1.0
H4' A:DT7 4.7 0.0 1.0
C1' A:DT7 4.8 0.0 1.0
H72 A:DT7 4.9 0.0 1.0
H5' A:DG6 4.9 0.0 1.0

Phosphorus binding site 7 out of 14 in 148d

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Phosphorus binding site 7 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:DG8 0.0 0.0 1.0
OP2 A:DG8 1.5 0.0 1.0
OP1 A:DG8 1.5 0.0 1.0
O3' A:DT7 1.6 0.0 1.0
O5' A:DG8 1.6 0.0 1.0
C3' A:DT7 2.7 0.0 1.0
C5' A:DG8 2.7 0.0 1.0
H3' A:DT7 2.8 0.0 1.0
H5'' A:DG8 2.9 0.0 1.0
H5' A:DG8 3.3 0.0 1.0
H4' A:DT7 3.6 0.0 1.0
H2'' A:DT7 3.7 0.0 1.0
C2' A:DT7 3.7 0.0 1.0
C4' A:DT7 3.8 0.0 1.0
H8 A:DG8 3.9 0.0 1.0
H2' A:DG8 3.9 0.0 1.0
C4' A:DG8 3.9 0.0 1.0
H3' A:DG8 4.1 0.0 1.0
H1' A:DT7 4.4 0.0 1.0
H2' A:DT7 4.4 0.0 1.0
C1' A:DT7 4.5 0.0 1.0
C3' A:DG8 4.5 0.0 1.0
C8 A:DG8 4.5 0.0 1.0
H2'' A:DG6 4.5 0.0 1.0
O4' A:DG8 4.6 0.0 1.0
O4' A:DT7 4.6 0.0 1.0
C2' A:DG8 4.8 0.0 1.0
H4' A:DG8 4.8 0.0 1.0
H5'' A:DT7 4.9 0.0 1.0
C5' A:DT7 5.0 0.0 1.0

Phosphorus binding site 8 out of 14 in 148d

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Phosphorus binding site 8 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:DT9 0.0 0.0 1.0
OP1 A:DT9 1.5 0.0 1.0
OP2 A:DT9 1.5 0.0 1.0
O5' A:DT9 1.6 0.0 1.0
O3' A:DG8 1.6 0.0 1.0
C3' A:DG8 2.6 0.0 1.0
H3' A:DG8 2.6 0.0 1.0
C5' A:DT9 2.8 0.0 1.0
H4' A:DG8 2.8 0.0 1.0
H5'' A:DT9 3.1 0.0 1.0
H5' A:DT9 3.1 0.0 1.0
H6 A:DT9 3.1 0.0 1.0
C4' A:DG8 3.3 0.0 1.0
H73 A:DT9 3.4 0.0 1.0
H5'' A:DG8 3.5 0.0 1.0
H2' A:DT9 3.8 0.0 1.0
C2' A:DG8 3.9 0.0 1.0
C5' A:DG8 3.9 0.0 1.0
C6 A:DT9 4.0 0.0 1.0
C4' A:DT9 4.0 0.0 1.0
C7 A:DT9 4.2 0.0 1.0
H72 A:DT9 4.3 0.0 1.0
H2'' A:DG8 4.3 0.0 1.0
O4' A:DT9 4.3 0.0 1.0
H5' A:DG8 4.4 0.0 1.0
O4' A:DG8 4.4 0.0 1.0
C5 A:DT9 4.5 0.0 1.0
H2' A:DG8 4.6 0.0 1.0
C1' A:DG8 4.6 0.0 1.0
C2' A:DT9 4.7 0.0 1.0
C3' A:DT9 4.8 0.0 1.0
H3' A:DT9 4.8 0.0 1.0
H1' A:DG8 4.8 0.0 1.0
N1 A:DT9 4.9 0.0 1.0
H4' A:DT9 4.9 0.0 1.0
C1' A:DT9 4.9 0.0 1.0

Phosphorus binding site 9 out of 14 in 148d

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Phosphorus binding site 9 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:DG10 0.0 0.0 1.0
OP1 A:DG10 1.5 0.0 1.0
OP2 A:DG10 1.5 0.0 1.0
O5' A:DG10 1.6 0.0 1.0
O3' A:DT9 1.6 0.0 1.0
H3' A:DT9 2.5 0.0 1.0
C5' A:DG10 2.7 0.0 1.0
C3' A:DT9 2.7 0.0 1.0
H5' A:DG10 2.8 0.0 1.0
H5'' A:DG10 2.8 0.0 1.0
H4' A:DT9 3.4 0.0 1.0
C4' A:DT9 3.6 0.0 1.0
C2' A:DT9 3.9 0.0 1.0
C4' A:DG10 4.0 0.0 1.0
H2'' A:DT9 4.1 0.0 1.0
H4' A:DG10 4.2 0.0 1.0
O4' A:DG10 4.5 0.0 1.0
O4' A:DT9 4.6 0.0 1.0
H2' A:DT9 4.7 0.0 1.0
C1' A:DT9 4.7 0.0 1.0
H1' A:DT9 4.7 0.0 1.0
C5' A:DT9 4.7 0.0 1.0
H5'' A:DT9 4.7 0.0 1.0

Phosphorus binding site 10 out of 14 in 148d

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Phosphorus binding site 10 out of 14 in the Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Three-Dimensional Solution Structure of the Thrombin Binding Dna Aptamer D(Ggttggtgtggttgg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:0.0
occ:1.00
P A:DG11 0.0 0.0 1.0
OP2 A:DG11 1.5 0.0 1.0
OP1 A:DG11 1.5 0.0 1.0
O5' A:DG11 1.6 0.0 1.0
O3' A:DG10 1.6 0.0 1.0
C5' A:DG11 2.7 0.0 1.0
C3' A:DG10 2.7 0.0 1.0
H2'' A:DG10 2.7 0.0 1.0
H3' A:DG10 2.8 0.0 1.0
H5' A:DG11 2.9 0.0 1.0
H5'' A:DG11 3.0 0.0 1.0
C2' A:DG10 3.2 0.0 1.0
H1' A:DG10 3.8 0.0 1.0
H4' A:DG10 4.0 0.0 1.0
C4' A:DG10 4.0 0.0 1.0
C4' A:DG11 4.1 0.0 1.0
C1' A:DG10 4.1 0.0 1.0
H2' A:DG10 4.1 0.0 1.0
H3' A:DG11 4.3 0.0 1.0
H8 A:DG11 4.5 0.0 1.0
O4' A:DG11 4.5 0.0 1.0
OP2 A:DT13 4.6 0.0 1.0
O4' A:DG10 4.7 0.0 1.0
C3' A:DG11 4.8 0.0 1.0
H2' A:DG11 4.8 0.0 1.0
H4' A:DG11 4.8 0.0 1.0

Reference:

P.Schultze, R.F.Macaya, J.Feigon. Three-Dimensional Solution Structure of the Thrombin-Binding Dna Aptamer D(Ggttggtgtggttgg). J.Mol.Biol. V. 235 1532 1994.
ISSN: ISSN 0022-2836
PubMed: 8107090
DOI: 10.1006/JMBI.1994.1105
Page generated: Fri Sep 25 11:30:05 2020

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