Phosphorus in PDB 1ac3: Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures

Phosphorus Binding Sites:

Pages:

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

Binding sites:

The binding sites of Phosphorus atom in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures (pdb code 1ac3). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 21 binding sites of Phosphorus where determined in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures, PDB code: 1ac3:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 21 in 1ac3

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Phosphorus binding site 1 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures 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:DC1 1.6 0.0 1.0
O5' A:DG2 1.6 0.0 1.0
C3' A:DC1 2.6 0.0 1.0
C5' A:DG2 2.7 0.0 1.0
H3' A:DC1 2.7 0.0 1.0
H5' A:DG2 2.9 0.0 1.0
H5'' A:DG2 3.0 0.0 1.0
C2' A:DC1 3.7 0.0 1.0
H2'' A:DC1 3.7 0.0 1.0
H5'' A:DC1 3.7 0.0 1.0
C4' A:DC1 3.8 0.0 1.0
H3' A:DG2 3.9 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
H4' A:DC1 4.0 0.0 1.0
H2' A:DC1 4.0 0.0 1.0
C5' A:DC1 4.2 0.0 1.0
O4' A:DG2 4.3 0.0 1.0
C3' A:DG2 4.5 0.0 1.0
O5' A:DC1 4.7 0.0 1.0
H4' A:DG2 4.8 0.0 1.0
O4' A:DC1 4.9 0.0 1.0
C1' A:DC1 4.9 0.0 1.0

Phosphorus binding site 2 out of 21 in 1ac3

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Phosphorus binding site 2 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:DC3 0.0 0.0 1.0
OP2 A:DC3 1.5 0.0 1.0
OP1 A:DC3 1.5 0.0 1.0
O5' A:DC3 1.6 0.0 1.0
O3' A:DG2 1.6 0.0 1.0
C5' A:DC3 2.7 0.0 1.0
C3' A:DG2 2.7 0.0 1.0
H5' A:DC3 2.9 0.0 1.0
H2'' A:DG2 2.9 0.0 1.0
H3' A:DG2 2.9 0.0 1.0
H5'' A:DC3 3.0 0.0 1.0
C2' A:DG2 3.3 0.0 1.0
H2' A:DG2 3.9 0.0 1.0
H3' A:DC3 3.9 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
C4' A:DC3 4.0 0.0 1.0
H4' A:DG2 4.0 0.0 1.0
O4' A:DC3 4.3 0.0 1.0
H1' A:DG2 4.3 0.0 1.0
C1' A:DG2 4.4 0.0 1.0
C3' A:DC3 4.5 0.0 1.0
H6 A:DC3 4.7 0.0 1.0
H5'' A:DG2 4.7 0.0 1.0
H4' A:DC3 4.8 0.0 1.0
O4' A:DG2 4.9 0.0 1.0
C5' A:DG2 4.9 0.0 1.0

Phosphorus binding site 3 out of 21 in 1ac3

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Phosphorus binding site 3 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures 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
OP1 A:DG4 1.5 0.0 1.0
OP2 A:DG4 1.5 0.0 1.0
O5' A:DG4 1.6 0.0 1.0
O3' A:DC3 1.6 0.0 1.0
C5' A:DG4 2.6 0.0 1.0
C3' A:DC3 2.7 0.0 1.0
H3' A:DC3 2.8 0.0 1.0
H5' A:DG4 2.9 0.0 1.0
H5'' A:DG4 2.9 0.0 1.0
H2'' A:DC3 3.1 0.0 1.0
C2' A:DC3 3.3 0.0 1.0
H2' A:DC3 3.7 0.0 1.0
H3' A:DG4 4.0 0.0 1.0
C4' A:DC3 4.0 0.0 1.0
C4' A:DG4 4.0 0.0 1.0
H4' A:DC3 4.1 0.0 1.0
O4' A:DG4 4.4 0.0 1.0
H5'' A:DC3 4.4 0.0 1.0
C3' A:DG4 4.5 0.0 1.0
C1' A:DC3 4.7 0.0 1.0
C5' A:DC3 4.7 0.0 1.0
H4' A:DG4 4.8 0.0 1.0
H1' A:DC3 4.8 0.0 1.0
O4' A:DC3 4.9 0.0 1.0

Phosphorus binding site 4 out of 21 in 1ac3

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Phosphorus binding site 4 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures 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
OP1 A:DT5 1.5 0.0 1.0
OP2 A:DT5 1.5 0.0 1.0
O3' A:DG4 1.6 0.0 1.0
O5' A:DT5 1.6 0.0 1.0
C5' A:DT5 2.7 0.0 1.0
C3' A:DG4 2.7 0.0 1.0
H5' A:DT5 2.9 0.0 1.0
H3' A:DG4 2.9 0.0 1.0
H5'' A:DT5 3.0 0.0 1.0
H2'' A:DG4 3.0 0.0 1.0
C2' A:DG4 3.3 0.0 1.0
H2' A:DG4 3.7 0.0 1.0
C4' A:DT5 4.0 0.0 1.0
C4' A:DG4 4.0 0.0 1.0
H3' A:DT5 4.0 0.0 1.0
H4' A:DG4 4.1 0.0 1.0
O4' A:DT5 4.3 0.0 1.0
H5'' A:DG4 4.5 0.0 1.0
C3' A:DT5 4.6 0.0 1.0
C1' A:DG4 4.6 0.0 1.0
H6 A:DT5 4.7 0.0 1.0
H1' A:DG4 4.8 0.0 1.0
H4' A:DT5 4.8 0.0 1.0
C5' A:DG4 4.8 0.0 1.0
O4' A:DG4 4.9 0.0 1.0

Phosphorus binding site 5 out of 21 in 1ac3

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Phosphorus binding site 5 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:TSP6 0.0 0.0 1.0
OP2 A:TSP6 1.5 0.0 1.0
OP1 A:TSP6 1.5 0.0 1.0
O5' A:TSP6 1.6 0.0 1.0
O3' A:DT5 1.6 0.0 1.0
C5' A:TSP6 2.7 0.0 1.0
C3' A:DT5 2.7 0.0 1.0
H5' A:TSP6 2.8 0.0 1.0
H3' A:DT5 2.9 0.0 1.0
H2'' A:DT5 3.0 0.0 1.0
H5'' A:TSP6 3.1 0.0 1.0
C2' A:DT5 3.3 0.0 1.0
H2' A:DT5 3.8 0.0 1.0
C4' A:TSP6 3.9 0.0 1.0
C4' A:DT5 4.0 0.0 1.0
H4' A:DT5 4.1 0.0 1.0
O4' A:TSP6 4.1 0.0 1.0
H3' A:TSP6 4.2 0.0 1.0
H6 A:TSP6 4.3 0.0 1.0
H5'' A:DT5 4.5 0.0 1.0
C1' A:DT5 4.6 0.0 1.0
H1' A:DT5 4.7 0.0 1.0
C3' A:TSP6 4.7 0.0 1.0
H4' A:TSP6 4.7 0.0 1.0
C5' A:DT5 4.8 0.0 1.0
O4' A:DT5 4.9 0.0 1.0

Phosphorus binding site 6 out of 21 in 1ac3

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Phosphorus binding site 6 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures 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:TCP7 1.6 0.0 1.0
C5' A:DT8 2.7 0.0 1.0
C3' A:TCP7 2.7 0.0 1.0
H5'' A:DT8 2.9 0.0 1.0
H3' A:TCP7 2.9 0.0 1.0
H5' A:DT8 3.0 0.0 1.0
H2'' A:TCP7 3.0 0.0 1.0
C2' A:TCP7 3.3 0.0 1.0
H2' A:TCP7 3.7 0.0 1.0
H3' A:DT8 3.8 0.0 1.0
C4' A:DT8 3.9 0.0 1.0
C4' A:TCP7 4.0 0.0 1.0
H4' A:TCP7 4.0 0.0 1.0
H6 A:DT8 4.1 0.0 1.0
O4' A:DT8 4.2 0.0 1.0
H5'' A:TCP7 4.4 0.0 1.0
C3' A:DT8 4.4 0.0 1.0
C1' A:TCP7 4.6 0.0 1.0
C5' A:TCP7 4.8 0.0 1.0
H4' A:DT8 4.8 0.0 1.0
H1' A:TCP7 4.8 0.0 1.0
O4' A:TCP7 4.9 0.0 1.0
H72 A:DT8 5.0 0.0 1.0

Phosphorus binding site 7 out of 21 in 1ac3

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Phosphorus binding site 7 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures 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
OP1 A:DG9 1.5 0.0 1.0
OP2 A:DG9 1.5 0.0 1.0
O3' A:DT8 1.6 0.0 1.0
O5' A:DG9 1.6 0.0 1.0
C5' A:DG9 2.7 0.0 1.0
C3' A:DT8 2.7 0.0 1.0
H3' A:DT8 2.8 0.0 1.0
H5' A:DG9 2.9 0.0 1.0
H5'' A:DG9 3.0 0.0 1.0
H2'' A:DT8 3.1 0.0 1.0
C2' A:DT8 3.4 0.0 1.0
H2' A:DT8 3.8 0.0 1.0
H3' A:DG9 3.9 0.0 1.0
C4' A:DT8 4.0 0.0 1.0
C4' A:DG9 4.0 0.0 1.0
H4' A:DT8 4.1 0.0 1.0
O4' A:DG9 4.4 0.0 1.0
H5'' A:DT8 4.4 0.0 1.0
C3' A:DG9 4.5 0.0 1.0
C1' A:DT8 4.7 0.0 1.0
H4' A:DG9 4.8 0.0 1.0
C5' A:DT8 4.8 0.0 1.0
H1' A:DT8 4.8 0.0 1.0
O4' A:DT8 4.9 0.0 1.0

Phosphorus binding site 8 out of 21 in 1ac3

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Phosphorus binding site 8 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:DC10 0.0 0.0 1.0
OP1 A:DC10 1.5 0.0 1.0
OP2 A:DC10 1.5 0.0 1.0
O3' A:DG9 1.6 0.0 1.0
O5' A:DC10 1.6 0.0 1.0
C5' A:DC10 2.7 0.0 1.0
C3' A:DG9 2.7 0.0 1.0
H5' A:DC10 2.9 0.0 1.0
H3' A:DG9 2.9 0.0 1.0
H5'' A:DC10 3.0 0.0 1.0
H2'' A:DG9 3.0 0.0 1.0
C2' A:DG9 3.3 0.0 1.0
H2' A:DG9 3.8 0.0 1.0
C4' A:DC10 4.0 0.0 1.0
C4' A:DG9 4.0 0.0 1.0
H3' A:DC10 4.0 0.0 1.0
H4' A:DG9 4.0 0.0 1.0
O4' A:DC10 4.3 0.0 1.0
H6 A:DC10 4.5 0.0 1.0
H5'' A:DG9 4.5 0.0 1.0
C1' A:DG9 4.5 0.0 1.0
C3' A:DC10 4.5 0.0 1.0
H1' A:DG9 4.6 0.0 1.0
H4' A:DC10 4.8 0.0 1.0
C5' A:DG9 4.8 0.0 1.0
O4' A:DG9 4.9 0.0 1.0

Phosphorus binding site 9 out of 21 in 1ac3

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Phosphorus binding site 9 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures 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
O3' A:DC10 1.6 0.0 1.0
O5' A:DG11 1.6 0.0 1.0
C5' A:DG11 2.7 0.0 1.0
C3' A:DC10 2.7 0.0 1.0
H3' A:DC10 2.9 0.0 1.0
H5' A:DG11 2.9 0.0 1.0
H5'' A:DG11 3.0 0.0 1.0
H2'' A:DC10 3.1 0.0 1.0
C2' A:DC10 3.4 0.0 1.0
H2' A:DC10 3.9 0.0 1.0
C4' A:DC10 4.0 0.0 1.0
C4' A:DG11 4.0 0.0 1.0
H3' A:DG11 4.0 0.0 1.0
H4' A:DC10 4.0 0.0 1.0
O4' A:DG11 4.3 0.0 1.0
H5'' A:DC10 4.5 0.0 1.0
C3' A:DG11 4.5 0.0 1.0
C1' A:DC10 4.6 0.0 1.0
H1' A:DC10 4.6 0.0 1.0
H4' A:DG11 4.8 0.0 1.0
C5' A:DC10 4.8 0.0 1.0
H8 A:DG11 4.9 0.0 1.0
O4' A:DC10 4.9 0.0 1.0

Phosphorus binding site 10 out of 21 in 1ac3

Go back to Phosphorus Binding Sites List in 1ac3
Phosphorus binding site 10 out of 21 in the Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, 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 Solution Structure of An Rna-Dna Hybrid Duplex Containing A 3'- Thioformacetal Linker and An Rna A-Tract, uc(Nmr), 8 Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P12

b:0.0
occ:1.00
P A:DC12 0.0 0.0 1.0
OP2 A:DC12 1.5 0.0 1.0
OP1 A:DC12 1.5 0.0 1.0
O5' A:DC12 1.6 0.0 1.0
O3' A:DG11 1.6 0.0 1.0
C5' A:DC12 2.7 0.0 1.0
C3' A:DG11 2.7 0.0 1.0
H5' A:DC12 2.8 0.0 1.0
H3' A:DG11 2.9 0.0 1.0
H2'' A:DG11 3.0 0.0 1.0
H5'' A:DC12 3.0 0.0 1.0
C2' A:DG11 3.3 0.0 1.0
H2' A:DG11 3.8 0.0 1.0
C4' A:DC12 3.9 0.0 1.0
C4' A:DG11 4.0 0.0 1.0
H3' A:DC12 4.0 0.0 1.0
H4' A:DG11 4.0 0.0 1.0
O4' A:DC12 4.3 0.0 1.0
C1' A:DG11 4.5 0.0 1.0
H6 A:DC12 4.5 0.0 1.0
H5'' A:DG11 4.5 0.0 1.0
C3' A:DC12 4.5 0.0 1.0
H1' A:DG11 4.6 0.0 1.0
H4' A:DC12 4.8 0.0 1.0
C5' A:DG11 4.8 0.0 1.0
O4' A:DG11 4.9 0.0 1.0

Reference:

C.W.Cross, J.S.Rice, X.Gao. Solution Structure of An Rna X Dna Hybrid Duplex Containing A 3'-Thioformacetal Linker and An Rna A-Tract. Biochemistry V. 36 4096 1997.
ISSN: ISSN 0006-2960
PubMed: 9100003
DOI: 10.1021/BI962382K
Page generated: Fri Sep 25 12:42:43 2020

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