Phosphorus in PDB 104d: Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in

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 Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in (pdb code 104d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in, PDB code: 104d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 104d

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Phosphorus binding site 1 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:G2 0.0 0.0 1.0
OP2 A:G2 1.5 0.0 1.0
OP1 A:G2 1.5 0.0 1.0
O5' A:G2 1.6 0.0 1.0
O3' A:C1 1.6 0.0 1.0
C3' A:C1 2.7 0.0 1.0
C5' A:G2 2.7 0.0 1.0
H3' A:C1 2.9 0.0 1.0
H5' A:G2 2.9 0.0 1.0
H5'' A:G2 2.9 0.0 1.0
C2' A:C1 3.2 0.0 1.0
H2' A:C1 3.2 0.0 1.0
O2' A:C1 3.3 0.0 1.0
H8 A:G2 3.9 0.0 1.0
HO2' A:C1 3.9 0.0 1.0
C4' A:G2 4.0 0.0 1.0
C4' A:C1 4.0 0.0 1.0
H3' A:G2 4.1 0.0 1.0
H4' A:C1 4.2 0.0 1.0
H5'' A:C1 4.5 0.0 1.0
O4' A:G2 4.5 0.0 1.0
C3' A:G2 4.6 0.0 1.0
C1' A:C1 4.6 0.0 1.0
C5' A:C1 4.8 0.0 1.0
H4' A:G2 4.8 0.0 1.0
C8 A:G2 4.9 0.0 1.0
O4' A:C1 5.0 0.0 1.0

Phosphorus binding site 2 out of 22 in 104d

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Phosphorus binding site 2 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:C3 0.0 0.0 1.0
OP1 A:C3 1.5 0.0 1.0
OP2 A:C3 1.5 0.0 1.0
O3' A:G2 1.6 0.0 1.0
O5' A:C3 1.6 0.0 1.0
C3' A:G2 2.6 0.0 1.0
C5' A:C3 2.7 0.0 1.0
H3' A:G2 2.9 0.0 1.0
H5'' A:C3 2.9 0.0 1.0
H5' A:C3 3.0 0.0 1.0
HO2' A:G2 3.2 0.0 1.0
C2' A:G2 3.4 0.0 1.0
H2' A:G2 3.4 0.0 1.0
H6 A:C3 3.7 0.0 1.0
O2' A:G2 3.8 0.0 1.0
C4' A:C3 4.0 0.0 1.0
C4' A:G2 4.0 0.0 1.0
H3' A:C3 4.0 0.0 1.0
H5'' A:G2 4.1 0.0 1.0
H4' A:G2 4.2 0.0 1.0
O4' A:C3 4.5 0.0 1.0
C3' A:C3 4.5 0.0 1.0
C5' A:G2 4.6 0.0 1.0
C1' A:G2 4.7 0.0 1.0
C6 A:C3 4.7 0.0 1.0
H4' A:C3 4.8 0.0 1.0
O5' A:G2 4.9 0.0 1.0
O4' A:G2 5.0 0.0 1.0

Phosphorus binding site 3 out of 22 in 104d

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Phosphorus binding site 3 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:G4 0.0 0.0 1.0
OP2 A:G4 1.5 0.0 1.0
OP1 A:G4 1.5 0.0 1.0
O5' A:G4 1.6 0.0 1.0
O3' A:C3 1.6 0.0 1.0
C3' A:C3 2.6 0.0 1.0
C5' A:G4 2.7 0.0 1.0
H3' A:C3 2.8 0.0 1.0
H5'' A:G4 2.9 0.0 1.0
H5' A:G4 2.9 0.0 1.0
H2' A:C3 3.3 0.0 1.0
C2' A:C3 3.4 0.0 1.0
HO2' A:C3 3.4 0.0 1.0
O2' A:C3 4.0 0.0 1.0
C4' A:G4 4.0 0.0 1.0
C4' A:C3 4.0 0.0 1.0
H3' A:G4 4.0 0.0 1.0
H8 A:G4 4.0 0.0 1.0
H5'' A:C3 4.1 0.0 1.0
H4' A:C3 4.3 0.0 1.0
O4' A:G4 4.5 0.0 1.0
C3' A:G4 4.5 0.0 1.0
C5' A:C3 4.5 0.0 1.0
C1' A:C3 4.7 0.0 1.0
O5' A:C3 4.7 0.0 1.0
H4' A:G4 4.8 0.0 1.0
O4' A:C3 5.0 0.0 1.0

Phosphorus binding site 4 out of 22 in 104d

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Phosphorus binding site 4 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in 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
O5' A:DT5 1.6 0.0 1.0
O3' A:G4 1.6 0.0 1.0
C3' A:G4 2.7 0.0 1.0
C5' A:DT5 2.7 0.0 1.0
H3' A:G4 2.9 0.0 1.0
H5'' A:DT5 2.9 0.0 1.0
H5' A:DT5 3.0 0.0 1.0
HO2' A:G4 3.1 0.0 1.0
C2' A:G4 3.4 0.0 1.0
H6 A:DT5 3.5 0.0 1.0
H2' A:G4 3.5 0.0 1.0
H3' A:DT5 3.7 0.0 1.0
O2' A:G4 3.8 0.0 1.0
H72 A:DT5 3.9 0.0 1.0
C4' A:DT5 3.9 0.0 1.0
C4' A:G4 4.0 0.0 1.0
H5'' A:G4 4.1 0.0 1.0
H4' A:G4 4.2 0.0 1.0
O4' A:DT5 4.3 0.0 1.0
C3' A:DT5 4.4 0.0 1.0
C5' A:G4 4.5 0.0 1.0
C6 A:DT5 4.5 0.0 1.0
C1' A:G4 4.7 0.0 1.0
H4' A:DT5 4.8 0.0 1.0
O5' A:G4 4.8 0.0 1.0
C7 A:DT5 4.9 0.0 1.0
O4' A:G4 5.0 0.0 1.0

Phosphorus binding site 5 out of 22 in 104d

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Phosphorus binding site 5 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:DA6 0.0 0.0 1.0
OP1 A:DA6 1.5 0.0 1.0
OP2 A:DA6 1.5 0.0 1.0
O5' A:DA6 1.6 0.0 1.0
O3' A:DT5 1.6 0.0 1.0
C5' A:DA6 2.7 0.0 1.0
C3' A:DT5 2.7 0.0 1.0
H5' A:DA6 2.9 0.0 1.0
H5'' A:DA6 3.0 0.0 1.0
H3' A:DT5 3.0 0.0 1.0
H2'' A:DT5 3.0 0.0 1.0
C2' A:DT5 3.2 0.0 1.0
H2' A:DT5 3.4 0.0 1.0
H8 A:DA6 3.5 0.0 1.0
C4' A:DA6 4.0 0.0 1.0
C4' A:DT5 4.0 0.0 1.0
H4' A:DT5 4.1 0.0 1.0
H3' A:DA6 4.1 0.0 1.0
O4' A:DA6 4.2 0.0 1.0
H5'' A:DT5 4.4 0.0 1.0
C8 A:DA6 4.5 0.0 1.0
C3' A:DA6 4.6 0.0 1.0
C1' A:DT5 4.6 0.0 1.0
H2' A:DA6 4.7 0.0 1.0
C5' A:DT5 4.8 0.0 1.0
H4' A:DA6 4.8 0.0 1.0
O4' A:DT5 5.0 0.0 1.0

Phosphorus binding site 6 out of 22 in 104d

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Phosphorus binding site 6 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in 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:DA6 1.6 0.0 1.0
C5' A:DT7 2.7 0.0 1.0
C3' A:DA6 2.7 0.0 1.0
H5' A:DT7 2.8 0.0 1.0
H3' A:DA6 2.9 0.0 1.0
H2'' A:DA6 3.0 0.0 1.0
H5'' A:DT7 3.0 0.0 1.0
C2' A:DA6 3.3 0.0 1.0
H6 A:DT7 3.8 0.0 1.0
H2' A:DA6 3.9 0.0 1.0
C4' A:DT7 4.0 0.0 1.0
C4' A:DA6 4.0 0.0 1.0
H4' A:DA6 4.1 0.0 1.0
O4' A:DT7 4.1 0.0 1.0
H2' A:DT7 4.4 0.0 1.0
H71 A:DT7 4.4 0.0 1.0
C1' A:DA6 4.6 0.0 1.0
C6 A:DT7 4.7 0.0 1.0
H5'' A:DA6 4.7 0.0 1.0
H3' A:DT7 4.7 0.0 1.0
H4' A:DT7 4.7 0.0 1.0
H1' A:DA6 4.7 0.0 1.0
C3' A:DT7 4.8 0.0 1.0
O4' A:DA6 4.9 0.0 1.0
C5' A:DA6 4.9 0.0 1.0
C2' A:DT7 5.0 0.0 1.0

Phosphorus binding site 7 out of 22 in 104d

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Phosphorus binding site 7 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:DA8 0.0 0.0 1.0
OP2 A:DA8 1.5 0.0 1.0
OP1 A:DA8 1.5 0.0 1.0
O5' A:DA8 1.6 0.0 1.0
O3' A:DT7 1.6 0.0 1.0
C5' A:DA8 2.7 0.0 1.0
C3' A:DT7 2.7 0.0 1.0
H3' A:DT7 2.9 0.0 1.0
H5'' A:DA8 2.9 0.0 1.0
H5' A:DA8 3.0 0.0 1.0
H2'' A:DT7 3.0 0.0 1.0
C2' A:DT7 3.3 0.0 1.0
H3' A:DA8 3.9 0.0 1.0
H1' A:DT7 3.9 0.0 1.0
C4' A:DT7 4.0 0.0 1.0
C4' A:DA8 4.0 0.0 1.0
H4' A:DT7 4.0 0.0 1.0
H2' A:DT7 4.1 0.0 1.0
C1' A:DT7 4.2 0.0 1.0
C3' A:DA8 4.4 0.0 1.0
O4' A:DA8 4.5 0.0 1.0
O4' A:DT7 4.7 0.0 1.0
H4' A:DA8 4.8 0.0 1.0
H5'' A:DT7 4.9 0.0 1.0
H8 A:DA8 4.9 0.0 1.0
H2' A:DA8 4.9 0.0 1.0

Phosphorus binding site 8 out of 22 in 104d

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Phosphorus binding site 8 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:DC9 0.0 0.0 1.0
OP2 A:DC9 1.5 0.0 1.0
OP1 A:DC9 1.5 0.0 1.0
O5' A:DC9 1.6 0.0 1.0
O3' A:DA8 1.6 0.0 1.0
C5' A:DC9 2.7 0.0 1.0
H2'' A:DA8 2.7 0.0 1.0
C3' A:DA8 2.7 0.0 1.0
H5' A:DC9 2.8 0.0 1.0
H5'' A:DC9 3.0 0.0 1.0
H3' A:DA8 3.0 0.0 1.0
C2' A:DA8 3.2 0.0 1.0
H2' A:DA8 3.9 0.0 1.0
H4' A:DA8 4.0 0.0 1.0
C4' A:DA8 4.0 0.0 1.0
C4' A:DC9 4.0 0.0 1.0
H1' A:DA8 4.1 0.0 1.0
H3' A:DC9 4.1 0.0 1.0
C1' A:DA8 4.3 0.0 1.0
O4' A:DC9 4.4 0.0 1.0
C3' A:DC9 4.6 0.0 1.0
H4' A:DC9 4.7 0.0 1.0
H5'' A:DA8 4.8 0.0 1.0
H6 A:DC9 4.8 0.0 1.0
O4' A:DA8 4.8 0.0 1.0
H2' A:DC9 5.0 0.0 1.0
C5' A:DA8 5.0 0.0 1.0

Phosphorus binding site 9 out of 22 in 104d

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Phosphorus binding site 9 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in 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:DC9 1.6 0.0 1.0
C5' A:DG10 2.7 0.0 1.0
C3' A:DC9 2.7 0.0 1.0
H2'' A:DC9 2.8 0.0 1.0
H5' A:DG10 2.9 0.0 1.0
H3' A:DC9 2.9 0.0 1.0
H5'' A:DG10 2.9 0.0 1.0
C2' A:DC9 3.3 0.0 1.0
H3' A:DG10 3.9 0.0 1.0
C4' A:DC9 4.0 0.0 1.0
H4' A:DC9 4.0 0.0 1.0
C4' A:DG10 4.0 0.0 1.0
H2' A:DC9 4.1 0.0 1.0
H1' A:DC9 4.3 0.0 1.0
C1' A:DC9 4.4 0.0 1.0
C3' A:DG10 4.5 0.0 1.0
H5'' A:DC9 4.5 0.0 1.0
O4' A:DG10 4.6 0.0 1.0
H2' A:DG10 4.6 0.0 1.0
H4' A:DG10 4.8 0.0 1.0
O4' A:DC9 4.8 0.0 1.0
C5' A:DC9 4.9 0.0 1.0

Phosphorus binding site 10 out of 22 in 104d

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Phosphorus binding site 10 out of 22 in the Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:0.0
occ:1.00
P A:DC11 0.0 0.0 1.0
OP2 A:DC11 1.5 0.0 1.0
OP1 A:DC11 1.5 0.0 1.0
O5' A:DC11 1.6 0.0 1.0
O3' A:DG10 1.6 0.0 1.0
C5' A:DC11 2.7 0.0 1.0
C3' A:DG10 2.7 0.0 1.0
H2'' A:DG10 2.7 0.0 1.0
H5'' A:DC11 2.9 0.0 1.0
H3' A:DG10 2.9 0.0 1.0
H5' A:DC11 2.9 0.0 1.0
C2' A:DG10 3.3 0.0 1.0
H1' A:DG10 3.9 0.0 1.0
C4' A:DG10 4.0 0.0 1.0
C4' A:DC11 4.0 0.0 1.0
H4' A:DG10 4.0 0.0 1.0
H2' A:DG10 4.1 0.0 1.0
H3' A:DC11 4.1 0.0 1.0
C1' A:DG10 4.2 0.0 1.0
H6 A:DC11 4.2 0.0 1.0
H2' A:DC11 4.4 0.0 1.0
O4' A:DC11 4.5 0.0 1.0
C3' A:DC11 4.6 0.0 1.0
H4' A:DC11 4.7 0.0 1.0
O4' A:DG10 4.8 0.0 1.0
H5'' A:DG10 4.9 0.0 1.0

Reference:

L.Zhu, M.Salazar, B.R.Reid. Dna Duplexes Flanked By Hybrid Duplexes: the Solution Structure of Chimeric Junctions in [R(Cgcg)D(Tatacgcg)]2. Biochemistry V. 34 2372 1995.
ISSN: ISSN 0006-2960
PubMed: 7857947
DOI: 10.1021/BI00007A033
Page generated: Fri Sep 25 11:03:54 2020

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