Phosphorus in PDB 139d: Solution Structure of A Parallel-Stranded G-Quadruplex Dna

Phosphorus Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Phosphorus atom in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna (pdb code 139d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 24 binding sites of Phosphorus where determined in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna, PDB code: 139d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 24 in 139d

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Phosphorus binding site 1 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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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 A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.1
occ:1.00
P A:DT2 0.0 0.1 1.0
OP1 A:DT2 1.5 0.1 1.0
OP2 A:DT2 1.5 0.1 1.0
O3' A:DT1 1.6 0.1 1.0
O5' A:DT2 1.6 0.1 1.0
C3' A:DT1 2.7 0.1 1.0
C5' A:DT2 2.7 0.1 1.0
H5' A:DT2 2.8 0.2 1.0
H3' A:DT1 2.8 0.1 1.0
H2'' A:DT1 2.8 0.1 1.0
H5'' A:DT2 3.0 0.2 1.0
C2' A:DT1 3.2 0.1 1.0
H1' A:DT1 3.8 0.2 1.0
H2' A:DT1 4.0 0.1 1.0
C4' A:DT2 4.0 0.1 1.0
C1' A:DT1 4.0 0.1 1.0
C4' A:DT1 4.1 0.1 1.0
H4' A:DT1 4.1 0.2 1.0
H6 A:DT2 4.2 0.1 1.0
H2' A:DT2 4.2 0.1 1.0
O4' A:DT2 4.3 0.1 1.0
H3' A:DT2 4.5 0.1 1.0
O4' A:DT1 4.7 0.1 1.0
C3' A:DT2 4.7 0.1 1.0
H4' A:DT2 4.8 0.1 1.0
C2' A:DT2 4.9 0.1 1.0

Phosphorus binding site 2 out of 24 in 139d

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Phosphorus binding site 2 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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A full contact list of Phosphorus with other atoms in the P binding site number 2 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.1
occ:1.00
P A:DG3 0.0 0.1 1.0
OP2 A:DG3 1.5 0.1 1.0
OP1 A:DG3 1.5 0.2 1.0
O5' A:DG3 1.6 0.1 1.0
O3' A:DT2 1.6 0.1 1.0
C5' A:DG3 2.7 0.1 1.0
C3' A:DT2 2.7 0.1 1.0
H3' A:DT2 2.8 0.1 1.0
H5' A:DG3 2.8 0.1 1.0
H5'' A:DG3 3.1 0.1 1.0
H2'' A:DT2 3.2 0.1 1.0
C2' A:DT2 3.5 0.1 1.0
C4' A:DG3 4.0 0.1 1.0
C4' A:DT2 4.0 0.1 1.0
H4' A:DT2 4.0 0.1 1.0
H1' A:DT2 4.1 0.1 1.0
H8 A:DG3 4.2 0.1 1.0
H2' A:DG3 4.2 0.1 1.0
H2' A:DT2 4.2 0.1 1.0
O4' A:DG3 4.2 0.1 1.0
C1' A:DT2 4.4 0.1 1.0
H3' A:DG3 4.5 0.1 1.0
C3' A:DG3 4.7 0.1 1.0
H4' A:DG3 4.7 0.2 1.0
O4' A:DT2 4.8 0.1 1.0
H5'' A:DT2 4.8 0.2 1.0
C2' A:DG3 4.9 0.1 1.0

Phosphorus binding site 3 out of 24 in 139d

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Phosphorus binding site 3 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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A full contact list of Phosphorus with other atoms in the P binding site number 3 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.1
occ:1.00
P A:DG4 0.0 0.1 1.0
OP2 A:DG4 1.5 0.1 1.0
OP1 A:DG4 1.5 0.1 1.0
O5' A:DG4 1.6 0.1 1.0
O3' A:DG3 1.6 0.1 1.0
C5' A:DG4 2.7 0.1 1.0
C3' A:DG3 2.7 0.1 1.0
H5' A:DG4 2.8 0.1 1.0
H3' A:DG3 2.8 0.1 1.0
H2'' A:DG3 3.0 0.1 1.0
H5'' A:DG4 3.1 0.2 1.0
C2' A:DG3 3.3 0.1 1.0
H8 A:DG4 3.7 0.1 1.0
H2' A:DG4 3.9 0.1 1.0
H1' A:DG3 3.9 0.1 1.0
C4' A:DG4 3.9 0.1 1.0
C4' A:DG3 4.0 0.1 1.0
H4' A:DG3 4.0 0.2 1.0
H2' A:DG3 4.2 0.1 1.0
C1' A:DG3 4.2 0.1 1.0
O4' A:DG4 4.2 0.2 1.0
H3' A:DG4 4.3 0.1 1.0
H5' B:DG6 4.4 0.1 1.0
C3' A:DG4 4.6 0.1 1.0
C2' A:DG4 4.7 0.1 1.0
H4' A:DG4 4.7 0.2 1.0
O4' A:DG3 4.7 0.1 1.0
C8 A:DG4 4.8 0.1 1.0

Phosphorus binding site 4 out of 24 in 139d

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Phosphorus binding site 4 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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A full contact list of Phosphorus with other atoms in the P binding site number 4 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.2
occ:1.00
P A:DG5 0.0 0.2 1.0
OP2 A:DG5 1.5 0.3 1.0
OP1 A:DG5 1.5 0.4 1.0
O3' A:DG4 1.6 0.2 1.0
O5' A:DG5 1.6 0.1 1.0
C5' A:DG5 2.7 0.1 1.0
C3' A:DG4 2.7 0.1 1.0
H5'' A:DG5 2.8 0.2 1.0
H2'' A:DG4 2.9 0.1 1.0
H2' A:DG5 3.0 0.1 1.0
H3' A:DG4 3.1 0.1 1.0
H8 A:DG5 3.2 0.1 1.0
C2' A:DG4 3.2 0.1 1.0
H5' A:DG5 3.3 0.1 1.0
H1' A:DG4 3.4 0.1 1.0
H3' A:DG5 3.6 0.1 1.0
C1' A:DG4 3.8 0.1 1.0
C4' A:DG5 3.9 0.1 1.0
C2' A:DG5 4.0 0.1 1.0
C4' A:DG4 4.0 0.1 1.0
H4' A:DG4 4.0 0.2 1.0
C3' A:DG5 4.1 0.1 1.0
H2' A:DG4 4.2 0.1 1.0
C8 A:DG5 4.2 0.1 1.0
O4' A:DG5 4.5 0.1 1.0
O4' A:DG4 4.5 0.2 1.0
H4' A:DG5 4.7 0.1 1.0
H2'' A:DG5 4.7 0.1 1.0
C1' A:DG5 4.8 0.1 1.0
N9 A:DG5 4.9 0.1 1.0

Phosphorus binding site 5 out of 24 in 139d

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Phosphorus binding site 5 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.1
occ:1.00
P A:DG6 0.0 0.1 1.0
OP1 A:DG6 1.5 0.2 1.0
OP2 A:DG6 1.5 0.2 1.0
O5' A:DG6 1.6 0.2 1.0
O3' A:DG5 1.6 0.1 1.0
C5' A:DG6 2.7 0.2 1.0
C3' A:DG5 2.7 0.1 1.0
H3' A:DG5 2.9 0.1 1.0
H5'' A:DG6 2.9 0.2 1.0
H5' A:DG6 3.0 0.2 1.0
H2'' A:DG5 3.1 0.1 1.0
C2' A:DG5 3.4 0.1 1.0
H2' A:DG6 3.6 0.2 1.0
H1' A:DG5 3.8 0.1 1.0
C4' A:DG6 4.0 0.2 1.0
C4' A:DG5 4.0 0.1 1.0
C1' A:DG5 4.1 0.1 1.0
H4' A:DG5 4.1 0.1 1.0
H2' A:DG5 4.2 0.1 1.0
H3' A:DG6 4.2 0.2 1.0
O4' A:DG6 4.3 0.2 1.0
C2' A:DG6 4.5 0.2 1.0
C3' A:DG6 4.5 0.2 1.0
O4' A:DG5 4.6 0.1 1.0
H8 A:DG6 4.7 0.2 1.0
H4' A:DG6 4.7 0.2 1.0

Phosphorus binding site 6 out of 24 in 139d

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Phosphorus binding site 6 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.2
occ:1.00
P A:DT7 0.0 0.2 1.0
OP1 A:DT7 1.5 0.2 1.0
OP2 A:DT7 1.5 0.2 1.0
O5' A:DT7 1.6 0.1 1.0
O3' A:DG6 1.6 0.2 1.0
C3' A:DG6 2.7 0.2 1.0
C5' A:DT7 2.7 0.1 1.0
H5' A:DT7 2.9 0.2 1.0
H2'' A:DG6 2.9 0.2 1.0
H3' A:DG6 3.0 0.2 1.0
H5'' A:DT7 3.2 0.1 1.0
C2' A:DG6 3.3 0.2 1.0
H1' A:DG6 3.5 0.2 1.0
H6 A:DT7 3.5 0.1 1.0
C1' A:DG6 4.0 0.1 1.0
C4' A:DT7 4.0 0.1 1.0
C4' A:DG6 4.1 0.2 1.0
O4' A:DT7 4.1 0.1 1.0
H71 A:DT7 4.2 0.2 1.0
H4' A:DG6 4.2 0.2 1.0
H2' A:DG6 4.3 0.2 1.0
C6 A:DT7 4.4 0.1 1.0
H2' A:DT7 4.5 0.2 1.0
O4' A:DG6 4.7 0.2 1.0
H4' A:DT7 4.7 0.1 1.0
C7 A:DT7 4.9 0.1 1.0
H72 A:DT7 5.0 0.2 1.0

Phosphorus binding site 7 out of 24 in 139d

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Phosphorus binding site 7 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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A full contact list of Phosphorus with other atoms in the P binding site number 7 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P2

b:0.1
occ:1.00
P B:DT2 0.0 0.1 1.0
OP1 B:DT2 1.5 0.1 1.0
OP2 B:DT2 1.5 0.1 1.0
O5' B:DT2 1.6 0.1 1.0
O3' B:DT1 1.6 0.1 1.0
C3' B:DT1 2.7 0.1 1.0
C5' B:DT2 2.7 0.1 1.0
H5' B:DT2 2.8 0.1 1.0
H2'' B:DT1 2.8 0.1 1.0
H3' B:DT1 2.9 0.2 1.0
H5'' B:DT2 3.0 0.1 1.0
C2' B:DT1 3.2 0.1 1.0
H1' B:DT1 3.9 0.1 1.0
H2' B:DT1 4.0 0.2 1.0
C4' B:DT2 4.0 0.1 1.0
C4' B:DT1 4.1 0.1 1.0
C1' B:DT1 4.1 0.1 1.0
H4' B:DT1 4.1 0.2 1.0
H2' B:DT2 4.2 0.1 1.0
H6 B:DT2 4.2 0.1 1.0
O4' B:DT2 4.3 0.1 1.0
H3' B:DT2 4.4 0.1 1.0
O4' B:DT1 4.7 0.2 1.0
C3' B:DT2 4.7 0.1 1.0
H4' B:DT2 4.8 0.1 1.0
C2' B:DT2 4.9 0.1 1.0
H72 B:DT2 5.0 0.2 1.0

Phosphorus binding site 8 out of 24 in 139d

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Phosphorus binding site 8 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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A full contact list of Phosphorus with other atoms in the P binding site number 8 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P3

b:0.1
occ:1.00
P B:DG3 0.0 0.1 1.0
OP2 B:DG3 1.5 0.1 1.0
OP1 B:DG3 1.5 0.2 1.0
O5' B:DG3 1.6 0.1 1.0
O3' B:DT2 1.6 0.1 1.0
C5' B:DG3 2.7 0.1 1.0
C3' B:DT2 2.7 0.1 1.0
H5' B:DG3 2.8 0.1 1.0
H3' B:DT2 2.8 0.1 1.0
H5'' B:DG3 3.1 0.2 1.0
H2'' B:DT2 3.2 0.1 1.0
C2' B:DT2 3.5 0.1 1.0
C4' B:DG3 4.0 0.1 1.0
C4' B:DT2 4.0 0.1 1.0
H4' B:DT2 4.0 0.1 1.0
H1' B:DT2 4.1 0.1 1.0
H8 B:DG3 4.2 0.1 1.0
O4' B:DG3 4.2 0.1 1.0
H2' B:DG3 4.2 0.1 1.0
H2' B:DT2 4.3 0.1 1.0
C1' B:DT2 4.3 0.1 1.0
H3' B:DG3 4.5 0.2 1.0
C3' B:DG3 4.7 0.1 1.0
H4' B:DG3 4.7 0.2 1.0
O4' B:DT2 4.8 0.1 1.0
H5'' B:DT2 4.8 0.1 1.0
C2' B:DG3 4.9 0.1 1.0

Phosphorus binding site 9 out of 24 in 139d

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Phosphorus binding site 9 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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A full contact list of Phosphorus with other atoms in the P binding site number 9 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P4

b:0.1
occ:1.00
P B:DG4 0.0 0.1 1.0
OP1 B:DG4 1.5 0.1 1.0
OP2 B:DG4 1.5 0.2 1.0
O5' B:DG4 1.6 0.1 1.0
O3' B:DG3 1.6 0.2 1.0
C5' B:DG4 2.7 0.1 1.0
C3' B:DG3 2.7 0.1 1.0
H3' B:DG3 2.8 0.2 1.0
H5' B:DG4 2.8 0.1 1.0
H2'' B:DG3 3.0 0.1 1.0
H5'' B:DG4 3.1 0.1 1.0
C2' B:DG3 3.3 0.1 1.0
H8 B:DG4 3.8 0.1 1.0
H2' B:DG4 3.9 0.1 1.0
H1' B:DG3 3.9 0.1 1.0
C4' B:DG4 3.9 0.1 1.0
C4' B:DG3 4.0 0.1 1.0
H4' B:DG3 4.1 0.2 1.0
H2' B:DG3 4.1 0.1 1.0
C1' B:DG3 4.2 0.1 1.0
O4' B:DG4 4.2 0.2 1.0
H5' C:DG6 4.3 0.1 1.0
H3' B:DG4 4.3 0.1 1.0
C3' B:DG4 4.6 0.1 1.0
C2' B:DG4 4.7 0.1 1.0
H4' B:DG4 4.7 0.1 1.0
O4' B:DG3 4.7 0.1 1.0
C8 B:DG4 4.8 0.1 1.0

Phosphorus binding site 10 out of 24 in 139d

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Phosphorus binding site 10 out of 24 in the Solution Structure of A Parallel-Stranded G-Quadruplex Dna


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A full contact list of Phosphorus with other atoms in the P binding site number 10 of Solution Structure of A Parallel-Stranded G-Quadruplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P5

b:0.2
occ:1.00
P B:DG5 0.0 0.2 1.0
OP1 B:DG5 1.5 0.3 1.0
OP2 B:DG5 1.5 0.3 1.0
O5' B:DG5 1.6 0.2 1.0
O3' B:DG4 1.6 0.1 1.0
C5' B:DG5 2.7 0.1 1.0
C3' B:DG4 2.7 0.1 1.0
H5'' B:DG5 2.8 0.1 1.0
H2'' B:DG4 2.9 0.1 1.0
H2' B:DG5 3.0 0.1 1.0
H3' B:DG4 3.1 0.1 1.0
H8 B:DG5 3.2 0.1 1.0
C2' B:DG4 3.2 0.1 1.0
H5' B:DG5 3.3 0.2 1.0
H1' B:DG4 3.4 0.1 1.0
H3' B:DG5 3.6 0.1 1.0
C1' B:DG4 3.8 0.1 1.0
C4' B:DG5 3.9 0.2 1.0
C2' B:DG5 4.0 0.1 1.0
C4' B:DG4 4.0 0.1 1.0
H4' B:DG4 4.0 0.1 1.0
C3' B:DG5 4.1 0.2 1.0
H2' B:DG4 4.2 0.1 1.0
C8 B:DG5 4.2 0.1 1.0
O4' B:DG5 4.5 0.2 1.0
O4' B:DG4 4.5 0.2 1.0
H4' B:DG5 4.7 0.2 1.0
H2'' B:DG5 4.7 0.2 1.0
C1' B:DG5 4.8 0.1 1.0
N9 B:DG5 4.9 0.1 1.0

Reference:

Y.Wang, D.J.Patel. Solution Structure of A Parallel-Stranded G-Quadruplex Dna. J.Mol.Biol. V. 234 1171 1993.
ISSN: ISSN 0022-2836
PubMed: 8263919
DOI: 10.1006/JMBI.1993.1668
Page generated: Fri Sep 25 11:23:24 2020

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