Phosphorus in PDB 124d: Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna

Phosphorus Binding Sites:

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Binding sites:

The binding sites of Phosphorus atom in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna (pdb code 124d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 14 binding sites of Phosphorus where determined in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna, PDB code: 124d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 14 in 124d

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Phosphorus binding site 1 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:DT2 0.0 0.0 1.0
OP1 A:DT2 1.5 0.0 1.0
OP2 A:DT2 1.5 0.0 1.0
O5' A:DT2 1.6 0.0 1.0
O3' A:DG1 1.6 0.0 1.0
C5' A:DT2 2.6 0.0 1.0
C3' A:DG1 2.7 0.0 1.0
H5'' A:DT2 2.9 0.0 1.0
H3' A:DG1 2.9 0.0 1.0
H2'' A:DG1 2.9 0.0 1.0
H5' A:DT2 2.9 0.0 1.0
C2' A:DG1 3.3 0.0 1.0
H3' A:DT2 3.8 0.0 1.0
H1' A:DG1 3.8 0.0 1.0
C4' A:DG1 4.0 0.0 1.0
C4' A:DT2 4.0 0.0 1.0
H4' A:DG1 4.0 0.0 1.0
H2' A:DG1 4.1 0.0 1.0
C1' A:DG1 4.1 0.0 1.0
C3' A:DT2 4.4 0.0 1.0
O4' A:DT2 4.5 0.0 1.0
H6 A:DT2 4.5 0.0 1.0
O4' A:DG1 4.7 0.0 1.0
H4' A:DT2 4.8 0.0 1.0
H5'' A:DG1 4.9 0.0 1.0

Phosphorus binding site 2 out of 14 in 124d

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Phosphorus binding site 2 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna 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
OP1 A:DC3 1.5 0.0 1.0
OP2 A:DC3 1.5 0.0 1.0
O5' A:DC3 1.6 0.0 1.0
O3' A:DT2 1.6 0.0 1.0
C5' A:DC3 2.7 0.0 1.0
C3' A:DT2 2.7 0.0 1.0
H5' A:DC3 2.9 0.0 1.0
H3' A:DT2 2.9 0.0 1.0
H5'' A:DC3 2.9 0.0 1.0
H2'' A:DT2 3.0 0.0 1.0
C2' A:DT2 3.3 0.0 1.0
H2' A:DT2 3.8 0.0 1.0
H3' A:DC3 3.9 0.0 1.0
C4' A:DT2 4.0 0.0 1.0
C4' A:DC3 4.0 0.0 1.0
H4' A:DT2 4.0 0.0 1.0
C3' A:DC3 4.5 0.0 1.0
O4' A:DC3 4.5 0.0 1.0
C1' A:DT2 4.5 0.0 1.0
H1' A:DT2 4.5 0.0 1.0
H5'' A:DT2 4.6 0.0 1.0
H4' A:DC3 4.7 0.0 1.0
H6 A:DC3 4.8 0.0 1.0
C5' A:DT2 4.9 0.0 1.0
O4' A:DT2 4.9 0.0 1.0

Phosphorus binding site 3 out of 14 in 124d

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Phosphorus binding site 3 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:DA4 0.0 0.0 1.0
OP1 A:DA4 1.5 0.0 1.0
OP2 A:DA4 1.5 0.0 1.0
O5' A:DA4 1.6 0.0 1.0
O3' A:DC3 1.6 0.0 1.0
C5' A:DA4 2.7 0.0 1.0
C3' A:DC3 2.7 0.0 1.0
H2'' A:DC3 2.8 0.0 1.0
H5' A:DA4 2.9 0.0 1.0
H5'' A:DA4 2.9 0.0 1.0
H3' A:DC3 3.0 0.0 1.0
C2' A:DC3 3.2 0.0 1.0
H2' A:DC3 3.7 0.0 1.0
H3' A:DA4 3.9 0.0 1.0
C4' A:DC3 4.0 0.0 1.0
C4' A:DA4 4.0 0.0 1.0
H4' A:DC3 4.0 0.0 1.0
C3' A:DA4 4.5 0.0 1.0
C1' A:DC3 4.5 0.0 1.0
H1' A:DC3 4.5 0.0 1.0
O4' A:DA4 4.6 0.0 1.0
H5'' A:DC3 4.7 0.0 1.0
H4' A:DA4 4.7 0.0 1.0
H8 A:DA4 4.8 0.0 1.0
C5' A:DC3 4.9 0.0 1.0
O4' A:DC3 4.9 0.0 1.0

Phosphorus binding site 4 out of 14 in 124d

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Phosphorus binding site 4 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:DC5 0.0 0.0 1.0
OP1 A:DC5 1.5 0.0 1.0
OP2 A:DC5 1.5 0.0 1.0
O5' A:DC5 1.6 0.0 1.0
O3' A:DA4 1.6 0.0 1.0
C5' A:DC5 2.7 0.0 1.0
C3' A:DA4 2.7 0.0 1.0
H5' A:DC5 2.8 0.0 1.0
H2'' A:DA4 2.9 0.0 1.0
H3' A:DA4 2.9 0.0 1.0
H5'' A:DC5 3.0 0.0 1.0
C2' A:DA4 3.3 0.0 1.0
H2' A:DA4 3.9 0.0 1.0
C4' A:DC5 4.0 0.0 1.0
C4' A:DA4 4.0 0.0 1.0
H3' A:DC5 4.0 0.0 1.0
H4' A:DA4 4.0 0.0 1.0
H1' A:DA4 4.4 0.0 1.0
O4' A:DC5 4.4 0.0 1.0
C1' A:DA4 4.5 0.0 1.0
C3' A:DC5 4.6 0.0 1.0
H5'' A:DA4 4.7 0.0 1.0
H4' A:DC5 4.8 0.0 1.0
H6 A:DC5 4.8 0.0 1.0
O4' A:DA4 4.9 0.0 1.0
C5' A:DA4 4.9 0.0 1.0

Phosphorus binding site 5 out of 14 in 124d

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Phosphorus binding site 5 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna 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
OP2 A:DA6 1.5 0.0 1.0
OP1 A:DA6 1.5 0.0 1.0
O5' A:DA6 1.6 0.0 1.0
O3' A:DC5 1.6 0.0 1.0
C5' A:DA6 2.7 0.0 1.0
C3' A:DC5 2.7 0.0 1.0
H2'' A:DC5 2.9 0.0 1.0
H5' A:DA6 2.9 0.0 1.0
H3' A:DC5 2.9 0.0 1.0
H5'' A:DA6 2.9 0.0 1.0
C2' A:DC5 3.3 0.0 1.0
H2' A:DC5 3.7 0.0 1.0
H3' A:DA6 3.9 0.0 1.0
C4' A:DC5 4.0 0.0 1.0
C4' A:DA6 4.0 0.0 1.0
H4' A:DC5 4.1 0.0 1.0
C3' A:DA6 4.5 0.0 1.0
O4' A:DA6 4.5 0.0 1.0
H1' A:DC5 4.5 0.0 1.0
C1' A:DC5 4.5 0.0 1.0
H5'' A:DC5 4.6 0.0 1.0
H8 A:DA6 4.7 0.0 1.0
H4' A:DA6 4.7 0.0 1.0
C5' A:DC5 4.9 0.0 1.0
O4' A:DC5 4.9 0.0 1.0

Phosphorus binding site 6 out of 14 in 124d

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Phosphorus binding site 6 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna 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 2.9 0.0 1.0
H2'' A:DA6 2.9 0.0 1.0
H5'' A:DT7 2.9 0.0 1.0
H3' A:DA6 2.9 0.0 1.0
C2' A:DA6 3.3 0.0 1.0
H2' A:DA6 3.8 0.0 1.0
H3' A:DT7 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 4.0 0.0 1.0
H6 A:DT7 4.3 0.0 1.0
O4' A:DT7 4.4 0.0 1.0
C1' A:DA6 4.5 0.0 1.0
C3' A:DT7 4.5 0.0 1.0
H1' A:DA6 4.5 0.0 1.0
H2' A:DT7 4.7 0.0 1.0
H5'' A:DA6 4.7 0.0 1.0
H4' 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

Phosphorus binding site 7 out of 14 in 124d

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Phosphorus binding site 7 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:DG8 0.0 0.0 1.0
OP1 A:DG8 1.5 0.0 1.0
OP2 A:DG8 1.5 0.0 1.0
O5' A:DG8 1.6 0.0 1.0
O3' A:DT7 1.6 0.0 1.0
C5' A:DG8 2.7 0.0 1.0
C3' A:DT7 2.7 0.0 1.0
H5' A:DG8 2.9 0.0 1.0
H3' A:DT7 2.9 0.0 1.0
H2'' A:DT7 2.9 0.0 1.0
H5'' A:DG8 2.9 0.0 1.0
C2' A:DT7 3.3 0.0 1.0
H3' A:DG8 3.9 0.0 1.0
H2' A:DT7 4.0 0.0 1.0
C4' A:DT7 4.0 0.0 1.0
C4' A:DG8 4.0 0.0 1.0
H4' A:DT7 4.0 0.0 1.0
H1' A:DT7 4.2 0.0 1.0
C1' A:DT7 4.4 0.0 1.0
C3' A:DG8 4.5 0.0 1.0
O4' A:DG8 4.5 0.0 1.0
H5'' A:DT7 4.8 0.0 1.0
H4' A:DG8 4.8 0.0 1.0
O4' A:DT7 4.8 0.0 1.0
HO3' A:DG8 4.9 0.0 1.0
C5' A:DT7 4.9 0.0 1.0

Phosphorus binding site 8 out of 14 in 124d

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Phosphorus binding site 8 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:0.0
occ:1.00
P B:A10 0.0 0.0 1.0
OP2 B:A10 1.5 0.0 1.0
OP1 B:A10 1.5 0.0 1.0
O5' B:A10 1.6 0.0 1.0
O3' B:C9 1.6 0.0 1.0
C5' B:A10 2.6 0.0 1.0
C3' B:C9 2.6 0.0 1.0
H3' B:C9 2.8 0.0 1.0
H5' B:A10 2.9 0.0 1.0
H5'' B:A10 2.9 0.0 1.0
HO2' B:C9 3.4 0.0 1.0
H8 B:A10 3.4 0.0 1.0
C2' B:C9 3.6 0.0 1.0
H2' B:C9 3.6 0.0 1.0
HO5' B:C9 3.8 0.0 1.0
C4' B:C9 3.9 0.0 1.0
C4' B:A10 4.0 0.0 1.0
O2' B:C9 4.0 0.0 1.0
H5'' B:C9 4.0 0.0 1.0
H3' B:A10 4.0 0.0 1.0
H4' B:C9 4.2 0.0 1.0
C5' B:C9 4.3 0.0 1.0
O4' B:A10 4.4 0.0 1.0
O5' B:C9 4.5 0.0 1.0
C8 B:A10 4.5 0.0 1.0
C3' B:A10 4.5 0.0 1.0
H4' B:A10 4.7 0.0 1.0
C1' B:C9 4.9 0.0 1.0
O4' B:C9 5.0 0.0 1.0

Phosphorus binding site 9 out of 14 in 124d

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Phosphorus binding site 9 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:0.0
occ:1.00
P B:U11 0.0 0.0 1.0
OP1 B:U11 1.5 0.0 1.0
OP2 B:U11 1.5 0.0 1.0
O3' B:A10 1.6 0.0 1.0
O5' B:U11 1.6 0.0 1.0
C3' B:A10 2.6 0.0 1.0
C5' B:U11 2.7 0.0 1.0
H3' B:A10 2.8 0.0 1.0
H5' B:U11 2.9 0.0 1.0
H5'' B:U11 2.9 0.0 1.0
H2' B:A10 3.3 0.0 1.0
HO2' B:A10 3.4 0.0 1.0
C2' B:A10 3.4 0.0 1.0
H6 B:U11 3.7 0.0 1.0
O2' B:A10 3.9 0.0 1.0
C4' B:A10 4.0 0.0 1.0
C4' B:U11 4.0 0.0 1.0
H3' B:U11 4.0 0.0 1.0
H5'' B:A10 4.2 0.0 1.0
H4' B:A10 4.2 0.0 1.0
C3' B:U11 4.5 0.0 1.0
O4' B:U11 4.5 0.0 1.0
C5' B:A10 4.6 0.0 1.0
C6 B:U11 4.7 0.0 1.0
C1' B:A10 4.7 0.0 1.0
H4' B:U11 4.8 0.0 1.0
O5' B:A10 4.8 0.0 1.0
O4' B:A10 5.0 0.0 1.0

Phosphorus binding site 10 out of 14 in 124d

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Phosphorus binding site 10 out of 14 in the Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Structure of A Dna:Rna Hybrid Duplex: Why Rnase H Does Not Cleave Pure Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:0.0
occ:1.00
P B:G12 0.0 0.0 1.0
OP2 B:G12 1.5 0.0 1.0
OP1 B:G12 1.5 0.0 1.0
O5' B:G12 1.6 0.0 1.0
O3' B:U11 1.6 0.0 1.0
C3' B:U11 2.6 0.0 1.0
C5' B:G12 2.7 0.0 1.0
H3' B:U11 2.9 0.0 1.0
H5' B:G12 2.9 0.0 1.0
H5'' B:G12 2.9 0.0 1.0
H2' B:U11 3.2 0.0 1.0
HO2' B:U11 3.3 0.0 1.0
C2' B:U11 3.3 0.0 1.0
H8 B:G12 3.7 0.0 1.0
O2' B:U11 3.8 0.0 1.0
C4' B:G12 4.0 0.0 1.0
C4' B:U11 4.0 0.0 1.0
H3' B:G12 4.1 0.0 1.0
H4' B:U11 4.2 0.0 1.0
H5'' B:U11 4.3 0.0 1.0
O4' B:G12 4.5 0.0 1.0
C3' B:G12 4.5 0.0 1.0
C5' B:U11 4.6 0.0 1.0
C1' B:U11 4.7 0.0 1.0
C8 B:G12 4.7 0.0 1.0
H4' B:G12 4.8 0.0 1.0
O5' B:U11 4.8 0.0 1.0
O4' B:U11 5.0 0.0 1.0

Reference:

O.Y.Fedoroff, M.Salazar, B.R.Reid. Structure of A Dna:Rna Hybrid Duplex. Why Rnase H Does Not Cleave Pure Rna J.Mol.Biol. V. 233 509 1993.
ISSN: ISSN 0022-2836
PubMed: 8411159
DOI: 10.1006/JMBI.1993.1528
Page generated: Fri Sep 25 11:14:56 2020

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