Phosphorus in PDB 1agk: The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure

Phosphorus Binding Sites:

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Binding sites:

The binding sites of Phosphorus atom in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure (pdb code 1agk). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure, PDB code: 1agk:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1agk

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Phosphorus binding site 1 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:1.4
occ:1.00
P A:DG2 0.0 1.4 1.0
OP2 A:DG2 1.5 1.3 1.0
O5' A:DG2 1.6 1.3 1.0
OP1 A:DG2 1.6 2.4 1.0
O3' A:DC1 1.6 1.5 1.0
C3' A:DC1 2.5 1.5 1.0
H3' A:DC1 2.6 1.5 1.0
C5' A:DG2 2.6 1.4 1.0
H5'' A:DG2 2.6 1.7 1.0
H2'' A:DC1 2.9 1.2 1.0
H5' A:DG2 3.1 1.5 1.0
C2' A:DC1 3.2 1.3 1.0
H3' A:DG2 3.5 1.1 1.0
H2' A:DC1 3.7 1.3 1.0
C4' A:DG2 3.9 1.2 1.0
C4' A:DC1 3.9 1.6 1.0
H4' A:DC1 4.0 1.7 1.0
H8 A:DG2 4.1 0.9 1.0
C3' A:DG2 4.2 1.1 1.0
H5'' A:DC1 4.3 2.2 1.0
O4' A:DG2 4.4 1.1 1.0
C1' A:DC1 4.5 1.4 1.0
H1' A:DC1 4.6 1.3 1.0
H2' A:DG2 4.6 0.9 1.0
C5' A:DC1 4.7 1.8 1.0
H4' A:DG2 4.7 1.2 1.0
O4' A:DC1 4.8 1.6 1.0
C2' A:DG2 4.9 0.9 1.0

Phosphorus binding site 2 out of 20 in 1agk

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Phosphorus binding site 2 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:1.0
occ:1.00
P A:DG3 0.0 1.0 1.0
OP2 A:DG3 1.5 1.9 1.0
OP1 A:DG3 1.5 1.5 1.0
O5' A:DG3 1.6 0.8 1.0
O3' A:DG2 1.6 1.1 1.0
H2'' A:DG2 2.5 0.9 1.0
C5' A:DG3 2.7 0.8 1.0
C3' A:DG2 2.7 1.1 1.0
H5'' A:DG3 2.8 0.8 1.0
H5' A:DG3 3.0 0.8 1.0
C2' A:DG2 3.0 0.9 1.0
H3' A:DG2 3.1 1.1 1.0
H2' A:DG2 3.7 0.9 1.0
H3' A:DG3 3.8 0.6 1.0
H8 A:DG3 3.8 0.5 1.0
C4' A:DG2 4.0 1.2 1.0
C4' A:DG3 4.0 0.6 1.0
H4' A:DG2 4.0 1.2 1.0
H1' A:DG2 4.2 0.9 1.0
C1' A:DG2 4.2 0.9 1.0
C3' A:DG3 4.4 0.6 1.0
O4' A:DG3 4.5 0.6 1.0
H2' A:DG3 4.5 0.5 1.0
O4' A:DG2 4.7 1.1 1.0
C8 A:DG3 4.8 0.5 1.0
H4' A:DG3 4.8 0.7 1.0
H5'' A:DG2 4.9 1.7 1.0
C2' A:DG3 5.0 0.5 1.0

Phosphorus binding site 3 out of 20 in 1agk

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Phosphorus binding site 3 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.8
occ:1.00
P A:DA4 0.0 0.8 1.0
OP2 A:DA4 1.5 1.8 1.0
OP1 A:DA4 1.5 1.4 1.0
O5' A:DA4 1.6 0.7 1.0
O3' A:DG3 1.6 0.7 1.0
H2'' A:DG3 2.5 0.6 1.0
C5' A:DA4 2.6 0.8 1.0
C3' A:DG3 2.7 0.6 1.0
H5' A:DA4 2.8 0.8 1.0
H5'' A:DA4 2.9 0.8 1.0
H3' A:DG3 3.0 0.6 1.0
C2' A:DG3 3.1 0.5 1.0
H8 A:DA4 3.7 0.6 1.0
H2' A:DG3 3.7 0.5 1.0
C4' A:DG3 4.0 0.6 1.0
C4' A:DA4 4.0 0.8 1.0
H4' A:DG3 4.0 0.7 1.0
H3' A:DA4 4.1 0.8 1.0
H1' A:DG3 4.2 0.5 1.0
C1' A:DG3 4.2 0.5 1.0
H2' A:DA4 4.3 0.7 1.0
O4' A:DA4 4.4 0.7 1.0
C3' A:DA4 4.5 0.8 1.0
C8 A:DA4 4.7 0.6 1.0
O4' A:DG3 4.7 0.6 1.0
H4' A:DA4 4.8 0.8 1.0
C2' A:DA4 4.9 0.7 1.0

Phosphorus binding site 4 out of 20 in 1agk

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Phosphorus binding site 4 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.9
occ:1.00
P A:DC5 0.0 0.9 1.0
OP1 A:DC5 1.5 1.4 1.0
OP2 A:DC5 1.5 1.7 1.0
O5' A:DC5 1.6 0.9 1.0
O3' A:DA4 1.6 0.8 1.0
H2'' A:DA4 2.5 0.7 1.0
C5' A:DC5 2.6 0.9 1.0
C3' A:DA4 2.7 0.8 1.0
H5'' A:DC5 2.7 1.0 1.0
H6 A:DC5 2.9 0.8 1.0
H3' A:DA4 3.0 0.8 1.0
C2' A:DA4 3.1 0.7 1.0
H5' A:DC5 3.1 1.0 1.0
H3' A:DC5 3.5 0.9 1.0
H2' A:DA4 3.8 0.7 1.0
C4' A:DC5 3.9 0.9 1.0
H1' A:DA4 3.9 0.7 1.0
H2' A:DC5 3.9 0.7 1.0
C4' A:DA4 4.0 0.8 1.0
C6 A:DC5 4.0 0.7 1.0
H4' A:DA4 4.1 0.8 1.0
C1' A:DA4 4.1 0.7 1.0
C3' A:DC5 4.1 0.8 1.0
H5 A:DC5 4.4 0.7 1.0
O4' A:DC5 4.5 0.8 1.0
C2' A:DC5 4.5 0.8 1.0
O4' A:DA4 4.6 0.7 1.0
C5 A:DC5 4.7 0.7 1.0
H4' A:DC5 4.7 0.9 1.0
C1' A:DC5 4.9 0.8 1.0
N1 A:DC5 4.9 0.7 1.0
HO' A:R6 5.0 0.7 1.0
H5'' A:DA4 5.0 0.8 1.0

Phosphorus binding site 5 out of 20 in 1agk

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Phosphorus binding site 5 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.8
occ:1.00
P A:R6 0.0 0.8 1.0
OP2 A:R6 1.5 1.0 1.0
OP1 A:R6 1.5 1.9 1.0
O3' A:DC5 1.6 0.9 1.0
O5' A:R6 1.6 0.8 1.0
H2'' A:DC5 2.6 0.7 1.0
C5' A:R6 2.7 0.9 1.0
C3' A:DC5 2.7 0.8 1.0
H5'' A:R6 2.8 1.2 1.0
H3' A:DC5 3.0 0.9 1.0
H5' A:R6 3.1 1.1 1.0
C2' A:DC5 3.1 0.8 1.0
H3' A:R6 3.6 0.7 1.0
H2' A:DC5 3.9 0.7 1.0
C4' A:DC5 4.0 0.9 1.0
C4' A:R6 4.0 0.7 1.0
H4' A:DC5 4.0 0.9 1.0
H8 A:R6 4.1 0.7 1.0
H1' A:DC5 4.2 0.8 1.0
C1' A:DC5 4.2 0.8 1.0
C3' A:R6 4.3 0.7 1.0
O4' A:R6 4.6 0.6 1.0
H2' A:R6 4.6 0.7 1.0
O4' A:DC5 4.7 0.8 1.0
H4' A:R6 4.8 0.7 1.0
C2' A:R6 5.0 0.6 1.0

Phosphorus binding site 6 out of 20 in 1agk

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Phosphorus binding site 6 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:1.2
occ:1.00
P A:DA7 0.0 1.2 1.0
OP1 A:DA7 1.5 2.0 1.0
OP2 A:DA7 1.5 2.3 1.0
O3' A:R6 1.6 0.7 1.0
O5' A:DA7 1.6 1.0 1.0
H2'' A:R6 2.5 0.6 1.0
C5' A:DA7 2.6 1.0 1.0
C3' A:R6 2.7 0.7 1.0
H5'' A:DA7 2.7 1.1 1.0
H5' A:DA7 3.0 1.1 1.0
C2' A:R6 3.1 0.6 1.0
H3' A:R6 3.1 0.7 1.0
H3' A:DA7 3.6 0.8 1.0
H2' A:R6 3.7 0.7 1.0
H8 A:DA7 3.8 0.5 1.0
C4' A:DA7 3.9 0.8 1.0
C4' A:R6 4.0 0.7 1.0
H4' A:R6 4.0 0.7 1.0
H1' A:R6 4.2 0.6 1.0
C1' A:R6 4.2 0.6 1.0
C3' A:DA7 4.3 0.7 1.0
O4' A:DA7 4.5 0.8 1.0
H2' A:DA7 4.6 0.6 1.0
C8 A:DA7 4.7 0.5 1.0
O4' A:R6 4.7 0.6 1.0
H4' A:DA7 4.7 0.9 1.0
C2' A:DA7 4.9 0.6 1.0

Phosphorus binding site 7 out of 20 in 1agk

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Phosphorus binding site 7 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.8
occ:1.00
P A:DG8 0.0 0.8 1.0
OP1 A:DG8 1.5 1.6 1.0
OP2 A:DG8 1.5 1.4 1.0
O5' A:DG8 1.6 0.7 1.0
O3' A:DA7 1.6 0.7 1.0
H2'' A:DA7 2.3 0.6 1.0
C5' A:DG8 2.6 0.8 1.0
C3' A:DA7 2.6 0.7 1.0
H5'' A:DG8 2.7 0.9 1.0
H5' A:DG8 2.9 0.8 1.0
C2' A:DA7 2.9 0.6 1.0
H3' A:DA7 3.0 0.8 1.0
H2' A:DA7 3.5 0.6 1.0
H8 A:DG8 3.6 0.5 1.0
H3' A:DG8 3.6 0.9 1.0
C4' A:DG8 3.9 0.8 1.0
C4' A:DA7 3.9 0.8 1.0
H4' A:DA7 3.9 0.9 1.0
C1' A:DA7 4.1 0.6 1.0
H1' A:DA7 4.1 0.7 1.0
C3' A:DG8 4.2 0.9 1.0
H2' A:DG8 4.4 0.7 1.0
O4' A:DG8 4.5 0.8 1.0
O4' A:DA7 4.6 0.8 1.0
C8 A:DG8 4.6 0.5 1.0
H4' A:DG8 4.7 0.9 1.0
C2' A:DG8 4.8 0.7 1.0
H5'' A:DA7 4.9 1.1 1.0
C5' A:DA7 5.0 1.0 1.0

Phosphorus binding site 8 out of 20 in 1agk

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Phosphorus binding site 8 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:1.1
occ:1.00
P A:DA9 0.0 1.1 1.0
OP1 A:DA9 1.5 2.0 1.0
OP2 A:DA9 1.5 1.7 1.0
O5' A:DA9 1.6 1.0 1.0
O3' A:DG8 1.6 1.0 1.0
H2'' A:DG8 2.4 0.8 1.0
C5' A:DA9 2.6 1.0 1.0
C3' A:DG8 2.7 0.9 1.0
H5'' A:DA9 2.8 1.1 1.0
H5' A:DA9 3.0 1.1 1.0
C2' A:DG8 3.0 0.7 1.0
H3' A:DG8 3.1 0.9 1.0
H2' A:DG8 3.7 0.7 1.0
H8 A:DA9 3.7 0.7 1.0
H3' A:DA9 3.8 0.9 1.0
C4' A:DG8 3.9 0.8 1.0
H4' A:DG8 4.0 0.9 1.0
C4' A:DA9 4.0 0.8 1.0
H1' A:DG8 4.1 0.7 1.0
C1' A:DG8 4.1 0.7 1.0
C3' A:DA9 4.4 0.8 1.0
O4' A:DA9 4.5 0.8 1.0
O4' A:DG8 4.6 0.8 1.0
H2' A:DA9 4.7 0.7 1.0
C8 A:DA9 4.7 0.6 1.0
H4' A:DA9 4.8 0.9 1.0

Phosphorus binding site 9 out of 20 in 1agk

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Phosphorus binding site 9 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:1.6
occ:1.00
P A:DA10 0.0 1.6 1.0
OP1 A:DA10 1.5 2.6 1.0
OP2 A:DA10 1.5 2.4 1.0
O5' A:DA10 1.6 1.3 1.0
O3' A:DA9 1.6 0.8 1.0
H2'' A:DA9 2.5 0.8 1.0
C5' A:DA10 2.7 1.4 1.0
C3' A:DA9 2.7 0.8 1.0
H5'' A:DA10 2.7 1.6 1.0
C2' A:DA9 3.0 0.7 1.0
H3' A:DA9 3.1 0.9 1.0
H3' A:DA10 3.2 1.2 1.0
H5' A:DA10 3.2 1.6 1.0
H2' A:DA9 3.7 0.7 1.0
C4' A:DA10 3.9 1.1 1.0
C4' A:DA9 4.0 0.8 1.0
C3' A:DA10 4.0 1.1 1.0
H4' A:DA9 4.0 0.9 1.0
H8 A:DA10 4.0 0.7 1.0
H1' A:DA9 4.2 0.7 1.0
C1' A:DA9 4.2 0.7 1.0
H2' A:DA10 4.5 0.9 1.0
O4' A:DA10 4.6 0.9 1.0
O4' A:DA9 4.7 0.8 1.0
H4' A:DA10 4.7 1.2 1.0
C2' A:DA10 4.8 0.9 1.0
C8 A:DA10 5.0 0.6 1.0

Phosphorus binding site 10 out of 20 in 1agk

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Phosphorus binding site 10 out of 20 in the The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Solution uc(Nmr) Structure of An (R)-A-(N6-Adenyl)-Styrene Oxide-RAS61 Oligodeoxynucleotide Modified at the Second Position of the Codon 61 Region, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:1.7
occ:1.00
P A:DG11 0.0 1.7 1.0
OP2 A:DG11 1.5 2.5 1.0
OP1 A:DG11 1.5 2.2 1.0
O5' A:DG11 1.6 1.5 1.0
O3' A:DA10 1.6 1.2 1.0
C5' A:DG11 2.6 1.5 1.0
C3' A:DA10 2.7 1.1 1.0
H2'' A:DA10 2.7 1.0 1.0
H5'' A:DG11 2.8 1.7 1.0
H5' A:DG11 2.9 1.5 1.0
H3' A:DA10 3.0 1.2 1.0
C2' A:DA10 3.1 0.9 1.0
H2' A:DA10 3.6 0.9 1.0
H3' A:DG11 3.8 1.6 1.0
H8 A:DG11 3.8 1.1 1.0
C4' A:DG11 4.0 1.4 1.0
C4' A:DA10 4.0 1.1 1.0
H4' A:DA10 4.0 1.2 1.0
C3' A:DG11 4.4 1.5 1.0
C1' A:DA10 4.5 0.8 1.0
O4' A:DG11 4.5 1.2 1.0
H1' A:DA10 4.6 0.8 1.0
H2' A:DG11 4.7 1.4 1.0
H4' A:DG11 4.8 1.4 1.0
C8 A:DG11 4.8 1.0 1.0
O4' A:DA10 4.8 0.9 1.0
H5'' A:DA10 4.9 1.6 1.0
C5' A:DA10 4.9 1.4 1.0

Reference:

B.Feng, L.Zhou, M.Passarelli, C.M.Harris, T.M.Harris, M.P.Stone. Major Groove (R)-Alpha-(N6-Adenyl)Styrene Oxide Adducts in An Oligodeoxynucleotide Containing the Human N-Ras Codon 61 Sequence: Conformations of the R(61,2) and R(61,3) Sequence Isomers From 1H uc(Nmr). Biochemistry V. 34 14021 1995.
ISSN: ISSN 0006-2960
PubMed: 7578000
DOI: 10.1021/BI00043A008
Page generated: Fri Sep 25 12:51:55 2020

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