Phosphorus in PDB 1aff: Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures

Phosphorus Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Phosphorus atom in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures (pdb code 1aff). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 12 binding sites of Phosphorus where determined in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures, PDB code: 1aff:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 12 in 1aff

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Phosphorus binding site 1 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.9
occ:1.00
 P A:DA2 0.0 0.9 1.0
OP2 A:DA2 1.5 1.0 1.0
OP1 A:DA2 1.5 1.1 1.0
O3' A:DT1 1.6 0.7 1.0
O5' A:DA2 1.6 0.8 1.0
C3' A:DT1 2.6 0.7 1.0
C5' A:DA2 2.7 0.8 1.0
H4' A:DT1 2.8 0.9 1.0
H5' A:DA2 2.8 0.8 1.0
H3' A:DT1 3.0 0.8 1.0
H2'' A:DT1 3.2 0.6 1.0
HO5' A:DT1 3.2 1.1 1.0
C4' A:DT1 3.2 0.8 1.0
H5'' A:DA2 3.3 0.9 1.0
H8 A:DA2 3.5 0.6 1.0
C2' A:DT1 3.8 0.6 1.0
O4' A:DA2 3.8 0.5 1.0
C4' A:DA2 3.9 0.6 1.0
O5' A:DT1 4.0 1.1 1.0
O4' A:DT1 4.1 0.9 1.0
H2' A:DA2 4.1 0.6 1.0
C8 A:DA2 4.2 0.5 1.0
C5' A:DT1 4.3 0.9 1.0
H3' A:DA2 4.3 0.6 1.0
H2' A:DT1 4.4 0.7 1.0
C3' A:DA2 4.6 0.5 1.0
N9 A:DA2 4.7 0.4 1.0
C1' A:DT1 4.7 0.8 1.0
C1' A:DA2 4.7 0.4 1.0
C2' A:DA2 4.8 0.5 1.0
H4' A:DA2 4.8 0.7 1.0
H5' A:DT1 4.9 0.8 1.0
H5'' A:DT1 5.0 1.0 1.0

Phosphorus binding site 2 out of 12 in 1aff

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Phosphorus binding site 2 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.5
occ:1.00
 P A:DG3 0.0 0.5 1.0
OP2 A:DG3 1.5 0.7 1.0
OP1 A:DG3 1.5 1.2 1.0
O5' A:DG3 1.6 0.8 1.0
O3' A:DA2 1.6 0.5 1.0
H22 A:DG3 2.1 0.5 1.0
H5' A:DG3 2.5 0.7 1.0
C5' A:DG3 2.6 0.7 1.0
C3' A:DA2 2.7 0.5 1.0
H2'' A:DA2 2.8 0.4 1.0
H1' A:DA2 2.8 0.4 1.0
N2 A:DG3 3.0 0.3 1.0
C2' A:DA2 3.1 0.5 1.0
H5'' A:DG3 3.1 1.2 1.0
H2' A:DG3 3.2 0.5 1.0
N3 A:DG3 3.2 0.3 1.0
H4' A:DA2 3.2 0.7 1.0
C1' A:DA2 3.3 0.4 1.0
C2 A:DG3 3.5 0.3 1.0
C4' A:DA2 3.5 0.6 1.0
H3' A:DA2 3.6 0.6 1.0
H21 A:DG3 3.8 0.4 1.0
C4' A:DG3 3.8 0.6 1.0
O4' A:DA2 3.9 0.5 1.0
H3' A:DG3 4.1 0.8 1.0
H2' A:DA2 4.1 0.6 1.0
C2' A:DG3 4.2 0.5 1.0
OP1 C:DG3 4.2 1.1 1.0
C3' A:DG3 4.4 0.6 1.0
O4' A:DG3 4.4 0.6 1.0
C4 A:DG3 4.4 0.3 1.0
H61 B:DA2 4.6 0.8 1.0
N9 A:DA2 4.6 0.4 1.0
H4' A:DG3 4.6 0.7 1.0
N1 A:DG3 4.7 0.3 1.0
H2'' A:DG3 4.8 0.6 1.0
C1' A:DG3 4.9 0.5 1.0
H2' C:DG3 4.9 0.6 1.0
H1 A:DG3 4.9 0.3 1.0
C5' A:DA2 5.0 0.8 1.0

Phosphorus binding site 3 out of 12 in 1aff

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Phosphorus binding site 3 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.7
occ:1.00
 P A:DG4 0.0 0.7 1.0
OP2 A:DG4 1.5 0.8 1.0
OP1 A:DG4 1.5 0.8 1.0
O3' A:DG3 1.6 0.7 1.0
O5' A:DG4 1.6 1.1 1.0
C5' A:DG4 2.6 0.7 1.0
C3' A:DG3 2.7 0.6 1.0
H5'' A:DG4 2.9 0.8 1.0
H5' A:DG4 2.9 1.1 1.0
H3' A:DG3 3.0 0.8 1.0
H2'' A:DG3 3.2 0.6 1.0
C2' A:DG3 3.4 0.5 1.0
H1' A:DG3 3.5 0.6 1.0
C1' A:DG3 3.9 0.5 1.0
C4' A:DG3 4.0 0.6 1.0
C4' A:DG4 4.0 0.7 1.0
H4' A:DG3 4.1 0.7 1.0
H4' A:DG4 4.1 0.8 1.0
H2' A:DG3 4.3 0.5 1.0
O4' A:DG3 4.4 0.6 1.0
O4' A:DG4 4.5 0.6 1.0
H8 A:DG4 4.9 0.6 1.0

Phosphorus binding site 4 out of 12 in 1aff

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Phosphorus binding site 4 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P2

b:0.6
occ:1.00
 P B:DA2 0.0 0.6 1.0
OP1 B:DA2 1.5 0.9 1.0
OP2 B:DA2 1.5 0.8 1.0
O5' B:DA2 1.6 0.5 1.0
O3' B:DT1 1.6 0.6 1.0
C5' B:DA2 2.6 0.5 1.0
H5' B:DA2 2.7 0.5 1.0
C3' B:DT1 2.7 0.5 1.0
H3' B:DT1 2.8 0.5 1.0
H5'' B:DA2 2.9 0.6 1.0
H2'' B:DT1 3.0 0.5 1.0
C2' B:DT1 3.2 0.6 1.0
H2' B:DT1 3.7 0.7 1.0
C4' B:DA2 4.0 0.4 1.0
C4' B:DT1 4.1 0.4 1.0
H4' B:DT1 4.1 0.5 1.0
O4' B:DA2 4.3 0.4 1.0
H2' B:DA2 4.5 0.4 1.0
C1' B:DT1 4.5 0.4 1.0
H4' B:DA2 4.7 0.4 1.0
H1' B:DT1 4.8 0.4 1.0
H3' B:DA2 4.8 0.6 1.0
O4' B:DT1 4.9 0.4 1.0
C3' B:DA2 5.0 0.5 1.0

Phosphorus binding site 5 out of 12 in 1aff

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Phosphorus binding site 5 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P3

b:0.8
occ:1.00
 P B:DG3 0.0 0.8 1.0
OP1 B:DG3 1.5 1.2 1.0
OP2 B:DG3 1.5 1.2 1.0
O3' B:DA2 1.6 0.6 1.0
O5' B:DG3 1.6 0.6 1.0
C5' B:DG3 2.7 0.5 1.0
H5'' B:DG3 2.8 0.6 1.0
C3' B:DA2 2.8 0.5 1.0
H3' B:DA2 3.0 0.6 1.0
H5' B:DG3 3.1 0.5 1.0
H22 B:DG3 3.4 0.4 1.0
H1' B:DA2 3.8 0.6 1.0
C2' B:DA2 3.9 0.5 1.0
H4' B:DA2 3.9 0.4 1.0
H2'' B:DA2 3.9 0.6 1.0
C4' B:DA2 3.9 0.4 1.0
C4' B:DG3 4.1 0.6 1.0
N2 B:DG3 4.1 0.3 1.0
H4' B:DG3 4.3 0.6 1.0
C1' B:DA2 4.4 0.4 1.0
H3' B:DG3 4.5 0.7 1.0
N3 B:DG3 4.5 0.3 1.0
H21 B:DG3 4.7 0.3 1.0
C2 B:DG3 4.7 0.2 1.0
O4' B:DA2 4.8 0.4 1.0
H2' B:DA2 4.9 0.4 1.0
H5'' B:DA2 4.9 0.6 1.0
C3' B:DG3 4.9 0.6 1.0

Phosphorus binding site 6 out of 12 in 1aff

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Phosphorus binding site 6 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P4

b:0.8
occ:1.00
 P B:DG4 0.0 0.8 1.0
OP1 B:DG4 1.5 0.9 1.0
OP2 B:DG4 1.5 1.1 1.0
O5' B:DG4 1.6 0.7 1.0
O3' B:DG3 1.6 0.8 1.0
C5' B:DG4 2.6 0.6 1.0
H5' B:DG4 2.7 0.6 1.0
C3' B:DG3 2.8 0.6 1.0
H5'' B:DG4 3.0 0.6 1.0
H2'' B:DG3 3.1 0.5 1.0
H4' B:DG3 3.3 0.6 1.0
C2' B:DG3 3.3 0.5 1.0
H1' B:DG3 3.4 0.5 1.0
C4' B:DG3 3.5 0.6 1.0
H3' B:DG3 3.6 0.7 1.0
O4' B:DG3 3.6 0.5 1.0
C1' B:DG3 3.6 0.4 1.0
C4' B:DG4 4.0 0.5 1.0
O4' B:DG4 4.2 0.5 1.0
H2' B:DG4 4.3 0.5 1.0
H2' B:DG3 4.4 0.5 1.0
H3' B:DG4 4.5 0.6 1.0
H4' B:DG4 4.7 0.5 1.0
C3' B:DG4 4.8 0.5 1.0
C5' B:DG3 5.0 0.5 1.0

Phosphorus binding site 7 out of 12 in 1aff

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Phosphorus binding site 7 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P2

b:0.8
occ:1.00
 P C:DA2 0.0 0.8 1.0
OP2 C:DA2 1.5 0.9 1.0
OP1 C:DA2 1.5 1.0 1.0
O3' C:DT1 1.6 0.6 1.0
O5' C:DA2 1.6 0.8 1.0
C3' C:DT1 2.6 0.7 1.0
C5' C:DA2 2.8 0.8 1.0
H4' C:DT1 2.8 0.8 1.0
H3' C:DT1 2.8 0.7 1.0
H5' C:DA2 2.9 0.8 1.0
HO5' C:DT1 3.2 1.1 1.0
C4' C:DT1 3.2 0.8 1.0
H5'' C:DA2 3.4 0.9 1.0
H8 C:DA2 3.5 0.5 1.0
O4' C:DA2 3.8 0.4 1.0
C4' C:DA2 3.8 0.6 1.0
H2' C:DA2 3.9 0.6 1.0
H2'' C:DT1 3.9 0.6 1.0
C2' C:DT1 3.9 0.6 1.0
O5' C:DT1 4.0 1.0 1.0
C8 C:DA2 4.1 0.4 1.0
O4' C:DT1 4.1 0.8 1.0
C5' C:DT1 4.3 0.9 1.0
C2' C:DA2 4.5 0.5 1.0
C1' C:DA2 4.5 0.3 1.0
H3' C:DA2 4.5 0.7 1.0
N9 C:DA2 4.6 0.3 1.0
H2' C:DT1 4.6 0.6 1.0
C3' C:DA2 4.6 0.5 1.0
H4' C:DA2 4.7 0.6 1.0
C1' C:DT1 4.7 0.7 1.0
H5'' C:DT1 4.9 1.1 1.0
H5' C:DT1 5.0 0.9 1.0

Phosphorus binding site 8 out of 12 in 1aff

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Phosphorus binding site 8 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P3

b:0.5
occ:1.00
 P C:DG3 0.0 0.5 1.0
OP2 C:DG3 1.5 0.7 1.0
OP1 C:DG3 1.5 1.1 1.0
O5' C:DG3 1.6 0.8 1.0
O3' C:DA2 1.6 0.5 1.0
H22 C:DG3 2.2 0.5 1.0
C5' C:DG3 2.6 0.8 1.0
H1' C:DA2 2.6 0.4 1.0
H5' C:DG3 2.7 0.8 1.0
C3' C:DA2 2.8 0.5 1.0
N2 C:DG3 3.1 0.4 1.0
H2'' C:DA2 3.1 0.6 1.0
N3 C:DG3 3.2 0.3 1.0
H5'' C:DG3 3.2 1.2 1.0
C2' C:DA2 3.2 0.5 1.0
C1' C:DA2 3.3 0.3 1.0
H4' C:DA2 3.4 0.6 1.0
H2' C:DG3 3.5 0.6 1.0
C4' C:DA2 3.5 0.6 1.0
C2 C:DG3 3.6 0.3 1.0
H3' C:DA2 3.6 0.7 1.0
C4' C:DG3 3.8 0.6 1.0
O4' C:DA2 3.9 0.4 1.0
H21 C:DG3 3.9 0.4 1.0
H3' C:DG3 4.1 0.7 1.0
OP1 A:DG3 4.2 1.2 1.0
H2' C:DA2 4.3 0.6 1.0
C2' C:DG3 4.3 0.5 1.0
O4' C:DG3 4.3 0.5 1.0
C3' C:DG3 4.4 0.6 1.0
C4 C:DG3 4.4 0.3 1.0
H4' C:DG3 4.6 0.6 1.0
N9 C:DA2 4.6 0.3 1.0
H61 D:DA2 4.7 0.9 1.0
C1' C:DG3 4.8 0.4 1.0
N1 C:DG3 4.9 0.3 1.0
N3 C:DA2 4.9 0.3 1.0
N6 D:DA2 5.0 0.8 1.0

Phosphorus binding site 9 out of 12 in 1aff

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Phosphorus binding site 9 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P4

b:0.6
occ:1.00
 P C:DG4 0.0 0.6 1.0
OP2 C:DG4 1.5 0.7 1.0
OP1 C:DG4 1.5 0.7 1.0
O3' C:DG3 1.6 0.6 1.0
O5' C:DG4 1.6 0.9 1.0
C5' C:DG4 2.6 0.6 1.0
C3' C:DG3 2.7 0.6 1.0
H5'' C:DG4 2.9 0.7 1.0
H2'' C:DG3 2.9 0.5 1.0
H5' C:DG4 2.9 1.0 1.0
H3' C:DG3 3.0 0.7 1.0
C2' C:DG3 3.3 0.5 1.0
H1' C:DG3 3.6 0.4 1.0
C1' C:DG3 3.9 0.4 1.0
C4' C:DG3 4.0 0.6 1.0
C4' C:DG4 4.0 0.6 1.0
H4' C:DG3 4.1 0.6 1.0
H4' C:DG4 4.1 0.7 1.0
H2' C:DG3 4.2 0.6 1.0
O4' C:DG3 4.4 0.5 1.0
O4' C:DG4 4.5 0.6 1.0
H8 C:DG4 4.9 0.5 1.0
H2' C:DG4 4.9 0.6 1.0

Phosphorus binding site 10 out of 12 in 1aff

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Phosphorus binding site 10 out of 12 in the Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Dna Quadruplex Containing Gggg Tetrads and (T.A).A Triads, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
D:P2

b:0.6
occ:1.00
 P D:DA2 0.0 0.6 1.0
OP1 D:DA2 1.5 0.9 1.0
OP2 D:DA2 1.5 0.8 1.0
O5' D:DA2 1.6 0.5 1.0
O3' D:DT1 1.6 0.6 1.0
C5' D:DA2 2.6 0.5 1.0
H5' D:DA2 2.6 0.5 1.0
C3' D:DT1 2.7 0.4 1.0
H2'' D:DT1 2.8 0.5 1.0
H3' D:DT1 2.9 0.5 1.0
H5'' D:DA2 2.9 0.5 1.0
C2' D:DT1 3.2 0.5 1.0
H2' D:DT1 3.7 0.6 1.0
C4' D:DA2 4.0 0.5 1.0
C4' D:DT1 4.1 0.4 1.0
O4' D:DA2 4.1 0.4 1.0
H4' D:DT1 4.3 0.4 1.0
C1' D:DT1 4.5 0.4 1.0
H1' D:DT1 4.7 0.4 1.0
H4' D:DA2 4.7 0.5 1.0
H2' D:DA2 4.8 0.5 1.0
O4' D:DT1 4.9 0.4 1.0
H3' D:DA2 4.9 0.6 1.0
C3' D:DA2 5.0 0.5 1.0

Reference:

A.Kettani, S.Bouaziz, W.Wang, R.A.Jones, D.J.Patel. Bombyx Mori Single Repeat Telomeric Dna Sequence Forms A G-Quadruplex Capped By Base Triads. Nat.Struct.Biol. V. 4 382 1997.
ISSN: ISSN 1072-8368
PubMed: 9145109
DOI: 10.1038/NSB0597-382
Page generated: Fri Sep 25 12:47:06 2020

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