Phosphorus in PDB 156d: Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)

Phosphorus Binding Sites:

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

Binding sites:

The binding sites of Phosphorus atom in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) (pdb code 156d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg), PDB code: 156d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 156d

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Phosphorus binding site 1 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) 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
OP1 A:DG2 1.5 0.0 1.0
OP2 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 2.6 0.0 1.0
H2'' A:DG1 2.9 0.0 1.0
H5'' A:DG2 2.9 0.0 1.0
H5' A:DG2 2.9 0.0 1.0
H3' A:DG1 2.9 0.0 1.0
C2' A:DG1 3.1 0.0 1.0
H1' A:DG1 3.8 0.0 1.0
H3' A:DG2 3.9 0.0 1.0
H2' A:DG1 3.9 0.0 1.0
C4' A:DG1 4.0 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
C1' A:DG1 4.0 0.0 1.0
H4' A:DG1 4.2 0.0 1.0
H2' A:DG2 4.4 0.0 1.0
O4' A:DG2 4.4 0.0 1.0
C3' A:DG2 4.5 0.0 1.0
H8 A:DG2 4.6 0.0 1.0
O4' A:DG1 4.6 0.0 1.0
H4' A:DG2 4.8 0.0 1.0
C2' A:DG2 4.9 0.0 1.0

Phosphorus binding site 2 out of 22 in 156d

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Phosphorus binding site 2 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:DG3 0.0 0.0 1.0
OP1 A:DG3 1.5 0.0 1.0
OP2 A:DG3 1.5 0.0 1.0
O5' A:DG3 1.6 0.0 1.0
O3' A:DG2 1.6 0.0 1.0
C5' A:DG3 2.6 0.0 1.0
C3' A:DG2 2.7 0.0 1.0
H5' A:DG3 2.7 0.0 1.0
H2'' A:DG2 2.9 0.0 1.0
H5'' A:DG3 2.9 0.0 1.0
H3' A:DG2 2.9 0.0 1.0
C2' A:DG2 3.3 0.0 1.0
H3' A:DG3 3.9 0.0 1.0
H2' A:DG2 4.0 0.0 1.0
C4' A:DG3 4.0 0.0 1.0
H1' A:DG2 4.0 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
H4' A:DG2 4.1 0.0 1.0
C1' A:DG2 4.3 0.0 1.0
H22 A:DG3 4.4 0.0 1.0
C3' A:DG3 4.5 0.0 1.0
H4' A:DG3 4.6 0.0 1.0
H5'' A:DG2 4.7 0.0 1.0
O4' A:DG2 4.9 0.0 1.0
C5' A:DG2 5.0 0.0 1.0

Phosphorus binding site 3 out of 22 in 156d

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Phosphorus binding site 3 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:DG4 0.0 0.0 1.0
OP2 A:DG4 1.5 0.0 1.0
OP1 A:DG4 1.5 0.0 1.0
O5' A:DG4 1.6 0.0 1.0
O3' A:DG3 1.6 0.0 1.0
C5' A:DG4 2.7 0.0 1.0
C3' A:DG3 2.7 0.0 1.0
H5' A:DG4 2.8 0.0 1.0
H2'' A:DG3 2.8 0.0 1.0
H3' A:DG3 2.8 0.0 1.0
H5'' A:DG4 3.1 0.0 1.0
C2' A:DG3 3.3 0.0 1.0
H4' A:DG3 3.7 0.0 1.0
C4' A:DG4 3.9 0.0 1.0
H1' A:DG3 3.9 0.0 1.0
C4' A:DG3 4.0 0.0 1.0
H3' A:DG4 4.0 0.0 1.0
H2' A:DG3 4.1 0.0 1.0
C1' A:DG3 4.2 0.0 1.0
O4' A:DG4 4.3 0.0 1.0
H2' A:DG4 4.3 0.0 1.0
C3' A:DG4 4.5 0.0 1.0
H8 A:DG4 4.7 0.0 1.0
O4' A:DG3 4.8 0.0 1.0
H4' A:DG4 4.8 0.0 1.0
C2' A:DG4 4.9 0.0 1.0

Phosphorus binding site 4 out of 22 in 156d

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Phosphorus binding site 4 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:DT5 0.0 0.0 1.0
OP2 A:DT5 1.5 0.0 1.0
OP1 A:DT5 1.5 0.0 1.0
O5' A:DT5 1.6 0.0 1.0
O3' A:DG4 1.6 0.0 1.0
C3' A:DG4 2.6 0.0 1.0
C5' A:DT5 2.7 0.0 1.0
H5'' A:DT5 2.8 0.0 1.0
H3' A:DG4 3.0 0.0 1.0
H2'' A:DG4 3.0 0.0 1.0
H5' A:DT5 3.1 0.0 1.0
C2' A:DG4 3.2 0.0 1.0
H4' A:DG4 3.7 0.0 1.0
H1' A:DG4 3.7 0.0 1.0
H3' A:DT5 3.8 0.0 1.0
C4' A:DG4 3.9 0.0 1.0
C4' A:DT5 4.0 0.0 1.0
H2' A:DG4 4.0 0.0 1.0
C1' A:DG4 4.2 0.0 1.0
O4' A:DT5 4.4 0.0 1.0
H6 A:DT5 4.5 0.0 1.0
C3' A:DT5 4.5 0.0 1.0
H2' A:DT5 4.5 0.0 1.0
O4' A:DG4 4.7 0.0 1.0
H5'' A:DG4 4.8 0.0 1.0
H4' A:DT5 4.8 0.0 1.0
C5' A:DG4 5.0 0.0 1.0

Phosphorus binding site 5 out of 22 in 156d

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Phosphorus binding site 5 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:DT6 0.0 0.0 1.0
OP1 A:DT6 1.5 0.0 1.0
OP2 A:DT6 1.5 0.0 1.0
O5' A:DT6 1.6 0.0 1.0
O3' A:DT5 1.6 0.0 1.0
C5' A:DT6 2.6 0.0 1.0
C3' A:DT5 2.6 0.0 1.0
H5' A:DT6 2.7 0.0 1.0
H2'' A:DT5 2.8 0.0 1.0
H3' A:DT5 3.0 0.0 1.0
H5'' A:DT6 3.1 0.0 1.0
C2' A:DT5 3.3 0.0 1.0
H3' A:DT6 3.8 0.0 1.0
H4' A:DT5 3.9 0.0 1.0
C4' A:DT6 3.9 0.0 1.0
H2' A:DT5 3.9 0.0 1.0
C4' A:DT5 3.9 0.0 1.0
O4' A:DT6 4.3 0.0 1.0
C3' A:DT6 4.4 0.0 1.0
H5'' A:DT5 4.5 0.0 1.0
C1' A:DT5 4.5 0.0 1.0
H73 A:DT7 4.6 0.0 1.0
H1' A:DT5 4.7 0.0 1.0
H4' A:DT6 4.7 0.0 1.0
C5' A:DT5 4.8 0.0 1.0
H2' A:DT6 4.8 0.0 1.0
H71 A:DT7 4.9 0.0 1.0
O4' A:DT5 4.9 0.0 1.0
H6 A:DT6 5.0 0.0 1.0

Phosphorus binding site 6 out of 22 in 156d

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Phosphorus binding site 6 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) 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
OP2 A:DT7 1.5 0.0 1.0
OP1 A:DT7 1.5 0.0 1.0
O5' A:DT7 1.6 0.0 1.0
O3' A:DT6 1.6 0.0 1.0
H5' A:DT7 2.6 0.0 1.0
C5' A:DT7 2.6 0.0 1.0
C3' A:DT6 2.7 0.0 1.0
H2'' A:DT6 2.7 0.0 1.0
H5'' A:DT7 3.1 0.0 1.0
C2' A:DT6 3.1 0.0 1.0
H73 A:DT8 3.2 0.0 1.0
H3' A:DT6 3.2 0.0 1.0
H2' A:DT6 3.6 0.0 1.0
H4' A:DT6 3.7 0.0 1.0
H71 A:DT8 3.7 0.0 1.0
H3' A:DT7 3.8 0.0 1.0
H2' A:DT7 3.9 0.0 1.0
C7 A:DT8 3.9 0.0 1.0
C4' A:DT7 3.9 0.0 1.0
C4' A:DT6 3.9 0.0 1.0
H72 A:DT8 4.2 0.0 1.0
H1' A:DT6 4.2 0.0 1.0
C1' A:DT6 4.2 0.0 1.0
O4' A:DT7 4.3 0.0 1.0
H5'' A:DT6 4.3 0.0 1.0
C3' A:DT7 4.4 0.0 1.0
C2' A:DT7 4.6 0.0 1.0
H6 A:DT7 4.6 0.0 1.0
H4' A:DT7 4.7 0.0 1.0
O4' A:DT6 4.7 0.0 1.0
C5' A:DT6 4.8 0.0 1.0

Phosphorus binding site 7 out of 22 in 156d

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Phosphorus binding site 7 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:DT8 0.0 0.0 1.0
OP1 A:DT8 1.5 0.0 1.0
OP2 A:DT8 1.5 0.0 1.0
O5' A:DT8 1.6 0.0 1.0
O3' A:DT7 1.6 0.0 1.0
C5' A:DT8 2.6 0.0 1.0
C3' A:DT7 2.7 0.0 1.0
H5' A:DT8 2.7 0.0 1.0
H3' A:DT7 2.8 0.0 1.0
H5'' A:DT8 3.1 0.0 1.0
H6 A:DT8 3.6 0.0 1.0
H4' A:DT7 3.7 0.0 1.0
C4' A:DT7 3.7 0.0 1.0
H2'' A:DT7 3.7 0.0 1.0
C2' A:DT7 3.8 0.0 1.0
C4' A:DT8 3.9 0.0 1.0
H5'' A:DT7 4.1 0.0 1.0
O4' A:DT8 4.2 0.0 1.0
H3' A:DT8 4.3 0.0 1.0
H2' A:DT8 4.4 0.0 1.0
C5' A:DT7 4.5 0.0 1.0
H72 A:DT8 4.5 0.0 1.0
H4' A:DT8 4.6 0.0 1.0
C3' A:DT8 4.6 0.0 1.0
C6 A:DT8 4.6 0.0 1.0
H1' A:DT7 4.6 0.0 1.0
H2' A:DT7 4.7 0.0 1.0
C1' A:DT7 4.7 0.0 1.0
O4' A:DT7 4.8 0.0 1.0
H73 A:DT8 4.8 0.0 1.0
H8 A:DG9 4.9 0.0 1.0
C2' A:DT8 4.9 0.0 1.0
O5' A:DT7 4.9 0.0 1.0
O4' A:DG9 5.0 0.0 1.0

Phosphorus binding site 8 out of 22 in 156d

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Phosphorus binding site 8 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:DG9 0.0 0.0 1.0
OP2 A:DG9 1.5 0.0 1.0
OP1 A:DG9 1.5 0.0 1.0
O5' A:DG9 1.6 0.0 1.0
O3' A:DT8 1.6 0.0 1.0
H3' A:DT8 2.6 0.0 1.0
C3' A:DT8 2.6 0.0 1.0
C5' A:DG9 2.7 0.0 1.0
H5'' A:DG9 2.9 0.0 1.0
H5' A:DG9 3.1 0.0 1.0
H2'' A:DT8 3.6 0.0 1.0
C2' A:DT8 3.6 0.0 1.0
H4' A:DT8 3.8 0.0 1.0
C4' A:DT8 3.8 0.0 1.0
C4' A:DG9 3.9 0.0 1.0
H22 A:DG9 4.0 0.0 1.0
O4' A:DG9 4.2 0.0 1.0
H4' A:DG9 4.2 0.0 1.0
H5'' A:DT8 4.2 0.0 1.0
H2' A:DT8 4.3 0.0 1.0
C5' A:DT8 4.6 0.0 1.0
N3 A:DG9 4.6 0.0 1.0
N2 A:DG9 4.6 0.0 1.0
C1' A:DT8 4.7 0.0 1.0
H1' A:DT8 4.7 0.0 1.0
O4' A:DT8 4.9 0.0 1.0

Phosphorus binding site 9 out of 22 in 156d

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Phosphorus binding site 9 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) 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:DG9 1.6 0.0 1.0
H2'' A:DG9 2.6 0.0 1.0
C5' A:DG10 2.7 0.0 1.0
C3' A:DG9 2.7 0.0 1.0
H5' A:DG10 2.8 0.0 1.0
H5'' A:DG10 3.1 0.0 1.0
H3' A:DG9 3.1 0.0 1.0
C2' A:DG9 3.2 0.0 1.0
H1' A:DG9 3.9 0.0 1.0
H3' A:DG10 4.0 0.0 1.0
C4' A:DG9 4.0 0.0 1.0
C4' A:DG10 4.0 0.0 1.0
H2' A:DG9 4.1 0.0 1.0
C1' A:DG9 4.1 0.0 1.0
H4' A:DG9 4.1 0.0 1.0
O4' A:DG10 4.4 0.0 1.0
H2' A:DG10 4.5 0.0 1.0
C3' A:DG10 4.6 0.0 1.0
O4' A:DG9 4.7 0.0 1.0
H8 A:DG10 4.9 0.0 1.0
H4' A:DG10 4.9 0.0 1.0

Phosphorus binding site 10 out of 22 in 156d

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Phosphorus binding site 10 out of 22 in the Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg) 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
OP1 A:DG11 1.5 0.0 1.0
OP2 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 2.6 0.0 1.0
C3' A:DG10 2.7 0.0 1.0
H2'' A:DG10 2.9 0.0 1.0
H5' A:DG11 3.0 0.0 1.0
H3' A:DG10 3.0 0.0 1.0
H5'' A:DG11 3.1 0.0 1.0
C2' A:DG10 3.3 0.0 1.0
H1' A:DG10 3.9 0.0 1.0
H3' A:DG11 4.0 0.0 1.0
C4' A:DG11 4.0 0.0 1.0
C4' A:DG10 4.1 0.0 1.0
H22 A:DG11 4.1 0.0 1.0
H2' A:DG10 4.1 0.0 1.0
H4' A:DG11 4.2 0.0 1.0
H4' A:DG10 4.2 0.0 1.0
C1' A:DG10 4.3 0.0 1.0
H5'' A:DG10 4.6 0.0 1.0
C3' A:DG11 4.6 0.0 1.0
O4' A:DG10 4.9 0.0 1.0
C5' A:DG10 5.0 0.0 1.0

Reference:

P.Schultze, F.W.Smith, J.Feigon. Refined Solution Structure of the Dimeric Quadruplex Formed From the Oxytricha Telomeric Oligonucleotide D(Ggggttttgggg). Structure V. 2 221 1994.
ISSN: ISSN 0969-2126
PubMed: 8069635
DOI: 10.1016/S0969-2126(00)00023-X
Page generated: Fri Sep 25 11:32:56 2020

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