Phosphorus in PDB 1af1: The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure (pdb code 1af1). 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure, PDB code: 1af1:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1af1

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Phosphorus binding site 1 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure


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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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:1.3
occ:1.00
P A:DG2 0.0 1.3 1.0
OP2 A:DG2 1.5 1.9 1.0
OP1 A:DG2 1.5 1.8 1.0
O5' A:DG2 1.6 1.2 1.0
O3' A:DG1 1.6 1.3 1.0
C5' A:DG2 2.6 0.9 1.0
H2'' A:DG1 2.6 1.0 1.0
C3' A:DG1 2.7 1.2 1.0
H5'' A:DG2 2.8 1.1 1.0
H5' A:DG2 2.9 1.0 1.0
H3' A:DG1 3.0 1.3 1.0
C2' A:DG1 3.1 1.0 1.0
H2' A:DG1 3.6 1.0 1.0
H8 A:DG2 3.7 0.8 1.0
H3' A:DG2 3.8 0.9 1.0
C4' A:DG1 4.0 1.3 1.0
C4' A:DG2 4.0 0.9 1.0
H4' A:DG1 4.0 1.3 1.0
C1' A:DG1 4.4 1.0 1.0
C3' A:DG2 4.4 0.9 1.0
O4' A:DG2 4.5 0.8 1.0
H2' A:DG2 4.5 0.8 1.0
H1' A:DG1 4.6 1.0 1.0
C8 A:DG2 4.8 0.8 1.0
H4' A:DG2 4.8 0.9 1.0
H5'' A:DG1 4.8 1.5 1.0
O4' A:DG1 4.8 1.2 1.0
C5' A:DG1 4.9 1.4 1.0
C2' A:DG2 5.0 0.8 1.0

Phosphorus binding site 2 out of 20 in 1af1

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Phosphorus binding site 2 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure


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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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:1.1
occ:1.00
P A:DC3 0.0 1.1 1.0
OP2 A:DC3 1.5 2.0 1.0
OP1 A:DC3 1.5 1.9 1.0
O3' A:DG2 1.6 0.9 1.0
O5' A:DC3 1.6 0.9 1.0
H2'' A:DG2 2.4 0.8 1.0
C5' A:DC3 2.7 0.9 1.0
C3' A:DG2 2.7 0.9 1.0
H5'' A:DC3 2.7 1.0 1.0
C2' A:DG2 3.0 0.8 1.0
H5' A:DC3 3.2 0.9 1.0
H3' A:DG2 3.2 0.9 1.0
H3' A:DC3 3.3 0.8 1.0
H6 A:DC3 3.6 0.7 1.0
H2' A:DG2 3.8 0.8 1.0
H1' A:DG2 3.8 0.7 1.0
H4' A:DG2 3.9 0.9 1.0
C4' A:DG2 3.9 0.9 1.0
C4' A:DC3 3.9 0.7 1.0
C1' A:DG2 4.0 0.7 1.0
C3' A:DC3 4.1 0.7 1.0
H2' A:DC3 4.3 0.6 1.0
O4' A:DG2 4.5 0.8 1.0
O4' A:DC3 4.6 0.6 1.0
C6 A:DC3 4.7 0.6 1.0
H4' A:DC3 4.7 0.8 1.0
C2' A:DC3 4.7 0.6 1.0

Phosphorus binding site 3 out of 20 in 1af1

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Phosphorus binding site 3 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.7
occ:1.00
P A:DA4 0.0 0.7 1.0
OP2 A:DA4 1.5 1.6 1.0
OP1 A:DA4 1.5 1.3 1.0
O5' A:DA4 1.6 0.7 1.0
O3' A:DC3 1.6 0.7 1.0
H2'' A:DC3 2.5 0.5 1.0
C5' A:DA4 2.6 0.7 1.0
C3' A:DC3 2.7 0.7 1.0
H5'' A:DA4 2.7 1.0 1.0
H3' A:DC3 3.0 0.8 1.0
C2' A:DC3 3.1 0.6 1.0
H5' A:DA4 3.1 0.8 1.0
H3' A:DA4 3.4 0.7 1.0
H2' A:DC3 3.7 0.6 1.0
C4' A:DA4 3.9 0.6 1.0
C4' A:DC3 4.0 0.7 1.0
H4' A:DC3 4.0 0.8 1.0
H8 A:DA4 4.1 0.5 1.0
C3' A:DA4 4.1 0.6 1.0
H2' A:DA4 4.1 0.6 1.0
C1' A:DC3 4.3 0.5 1.0
H1' A:DC3 4.3 0.5 1.0
O4' A:DA4 4.6 0.5 1.0
C2' A:DA4 4.6 0.5 1.0
H4' A:DA4 4.7 0.6 1.0
O4' A:DC3 4.7 0.6 1.0
H5'' A:DC3 4.9 1.0 1.0
C8 A:DA4 5.0 0.5 1.0
C5' A:DC3 5.0 0.9 1.0

Phosphorus binding site 4 out of 20 in 1af1

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Phosphorus binding site 4 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.7
occ:1.00
P A:DG5 0.0 0.7 1.0
OP1 A:DG5 1.5 1.1 1.0
OP2 A:DG5 1.5 1.7 1.0
O5' A:DG5 1.6 0.6 1.0
O3' A:DA4 1.6 0.6 1.0
H2'' A:DA4 2.5 0.5 1.0
C5' A:DG5 2.6 0.6 1.0
C3' A:DA4 2.7 0.6 1.0
H5'' A:DG5 2.8 0.6 1.0
H5' A:DG5 2.9 0.6 1.0
H3' A:DA4 3.0 0.7 1.0
C2' A:DA4 3.1 0.5 1.0
H3' A:DG5 3.7 0.6 1.0
H2' A:DA4 3.8 0.6 1.0
C4' A:DA4 4.0 0.6 1.0
C4' A:DG5 4.0 0.5 1.0
H4' A:DA4 4.0 0.6 1.0
H1' A:DA4 4.1 0.4 1.0
C1' A:DA4 4.2 0.5 1.0
C3' A:DG5 4.4 0.5 1.0
H8 A:DG5 4.5 0.5 1.0
O4' A:DG5 4.5 0.5 1.0
O4' A:DA4 4.7 0.5 1.0
H4' A:DG5 4.8 0.5 1.0
H2' A:DG5 4.9 0.5 1.0

Phosphorus binding site 5 out of 20 in 1af1

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Phosphorus binding site 5 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.6
occ:1.00
P A:GSR6 0.0 0.6 1.0
OP2 A:GSR6 1.5 1.6 1.0
OP1 A:GSR6 1.5 1.2 1.0
O5' A:GSR6 1.6 0.5 1.0
O3' A:DG5 1.6 0.6 1.0
H2'' A:DG5 2.6 0.5 1.0
C5' A:GSR6 2.6 0.5 1.0
C3' A:DG5 2.7 0.5 1.0
H5' A:GSR6 2.8 0.6 1.0
H5'' A:GSR6 2.9 0.6 1.0
H3' A:DG5 3.0 0.6 1.0
C2' A:DG5 3.1 0.5 1.0
H2' A:DG5 3.6 0.5 1.0
H3' A:GSR6 3.8 0.5 1.0
C4' A:GSR6 4.0 0.5 1.0
C4' A:DG5 4.0 0.5 1.0
H4' A:DG5 4.0 0.5 1.0
H8 A:GSR6 4.1 0.5 1.0
C1' A:DG5 4.3 0.5 1.0
H1' A:DG5 4.4 0.4 1.0
O4' A:GSR6 4.4 0.5 1.0
C3' A:GSR6 4.5 0.5 1.0
H4' A:GSR6 4.8 0.5 1.0
O4' A:DG5 4.8 0.5 1.0
H5'' A:DG5 4.8 0.6 1.0
C5' A:DG5 4.9 0.6 1.0

Phosphorus binding site 6 out of 20 in 1af1

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Phosphorus binding site 6 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.6
occ:1.00
P A:DT7 0.0 0.6 1.0
OP1 A:DT7 1.5 1.7 1.0
OP2 A:DT7 1.5 1.1 1.0
O5' A:DT7 1.6 0.5 1.0
O3' A:GSR6 1.6 0.5 1.0
C5' A:DT7 2.6 0.5 1.0
C3' A:GSR6 2.7 0.5 1.0
H5' A:DT7 2.8 0.5 1.0
H2'' A:GSR6 2.8 0.5 1.0
H3' A:GSR6 2.9 0.5 1.0
H5'' A:DT7 3.0 0.5 1.0
H6 A:DT7 3.2 0.5 1.0
H71 A:DT7 3.2 1.3 1.0
C2' A:GSR6 3.2 0.5 1.0
H2' A:GSR6 3.7 0.5 1.0
C4' A:DT7 4.0 0.5 1.0
H3' A:DT7 4.0 0.4 1.0
C4' A:GSR6 4.0 0.5 1.0
C6 A:DT7 4.0 0.5 1.0
H4' A:GSR6 4.0 0.5 1.0
C7 A:DT7 4.2 0.6 1.0
O4' A:DT7 4.3 0.5 1.0
C1' A:GSR6 4.5 0.5 1.0
C5 A:DT7 4.5 0.6 1.0
C3' A:DT7 4.5 0.5 1.0
H73 A:DT7 4.6 1.1 1.0
H5'' A:GSR6 4.6 0.6 1.0
H1' A:GSR6 4.6 0.5 1.0
H4' A:DT7 4.8 0.5 1.0
C5' A:GSR6 4.9 0.5 1.0
O4' A:GSR6 4.9 0.5 1.0
N1 A:DT7 4.9 0.6 1.0
H72 A:DT7 4.9 1.0 1.0

Phosphorus binding site 7 out of 20 in 1af1

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Phosphorus binding site 7 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.5
occ:1.00
P A:DG8 0.0 0.5 1.0
OP1 A:DG8 1.5 1.4 1.0
OP2 A:DG8 1.5 1.3 1.0
O3' A:DT7 1.6 0.5 1.0
O5' A:DG8 1.6 0.4 1.0
C5' A:DG8 2.6 0.5 1.0
C3' A:DT7 2.7 0.5 1.0
H5'' A:DG8 2.8 0.5 1.0
H3' A:DT7 2.8 0.4 1.0
H5' A:DG8 3.0 0.5 1.0
H2'' A:DT7 3.1 0.5 1.0
C2' A:DT7 3.3 0.5 1.0
H2' A:DT7 3.5 0.5 1.0
H3' A:DG8 3.6 0.5 1.0
H8 A:DG8 3.7 0.5 1.0
C4' A:DT7 4.0 0.5 1.0
C4' A:DG8 4.0 0.5 1.0
H4' A:DT7 4.0 0.5 1.0
C3' A:DG8 4.3 0.5 1.0
HM' A:GSR6 4.3 3.1 1.0
H5'' A:DT7 4.3 0.5 1.0
H2' A:DG8 4.5 0.5 1.0
O4' A:DG8 4.6 0.5 1.0
C8 A:DG8 4.7 0.5 1.0
C1' A:DT7 4.7 0.5 1.0
C5' A:DT7 4.7 0.5 1.0
H4' A:DG8 4.7 0.5 1.0
C2' A:DG8 4.9 0.5 1.0
O4' A:DT7 5.0 0.5 1.0

Phosphorus binding site 8 out of 20 in 1af1

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Phosphorus binding site 8 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:1.1
occ:1.00
P A:DG9 0.0 1.1 1.0
OP2 A:DG9 1.5 2.2 1.0
OP1 A:DG9 1.5 1.9 1.0
O5' A:DG9 1.6 1.0 1.0
O3' A:DG8 1.6 0.6 1.0
H2'' A:DG8 2.5 0.6 1.0
C5' A:DG9 2.6 1.0 1.0
C3' A:DG8 2.7 0.5 1.0
H5'' A:DG9 2.8 1.3 1.0
H5' A:DG9 3.0 1.3 1.0
C2' A:DG8 3.1 0.5 1.0
H3' A:DG8 3.1 0.5 1.0
H8 A:DG9 3.6 0.5 1.0
H3' A:DG9 3.7 0.8 1.0
H2' A:DG8 3.7 0.5 1.0
H4' A:DG8 3.9 0.5 1.0
C4' A:DG8 3.9 0.5 1.0
C4' A:DG9 3.9 0.9 1.0
H1' A:DG8 4.1 0.5 1.0
C1' A:DG8 4.2 0.5 1.0
H2' A:DG9 4.3 0.6 1.0
C3' A:DG9 4.3 0.8 1.0
O4' A:DG9 4.4 0.8 1.0
C8 A:DG9 4.6 0.5 1.0
O4' A:DG8 4.6 0.5 1.0
H4' A:DG9 4.8 0.9 1.0
C2' A:DG9 4.8 0.6 1.0

Phosphorus binding site 9 out of 20 in 1af1

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Phosphorus binding site 9 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.8
occ:1.00
P A:DT10 0.0 0.8 1.0
OP2 A:DT10 1.5 1.3 1.0
OP1 A:DT10 1.5 1.7 1.0
O5' A:DT10 1.6 0.8 1.0
O3' A:DG9 1.6 0.8 1.0
H2'' A:DG9 2.5 0.6 1.0
C5' A:DT10 2.6 1.1 1.0
C3' A:DG9 2.7 0.8 1.0
H5'' A:DT10 2.9 1.4 1.0
H5' A:DT10 2.9 1.6 1.0
H3' A:DG9 3.0 0.8 1.0
C2' A:DG9 3.0 0.6 1.0
H6 A:DT10 3.6 0.6 1.0
H2' A:DG9 3.7 0.6 1.0
H3' A:DT10 3.9 1.0 1.0
C4' A:DG9 4.0 0.9 1.0
C4' A:DT10 4.0 0.9 1.0
H4' A:DG9 4.0 0.9 1.0
H1' A:DG9 4.1 0.6 1.0
C1' A:DG9 4.2 0.6 1.0
O4' A:DT10 4.4 0.8 1.0
C3' A:DT10 4.5 0.9 1.0
H73 A:DT10 4.5 1.2 1.0
O4' A:DG9 4.7 0.8 1.0
C6 A:DT10 4.7 0.5 1.0
H72 A:DT10 4.7 1.0 1.0
H4' A:DT10 4.8 1.0 1.0
H5'' A:DG9 5.0 1.3 1.0

Phosphorus binding site 10 out of 20 in 1af1

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Phosphorus binding site 10 out of 20 in the The Solution uc(Nmr) Structure of An R-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, 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-Styrene Oxide Adduct at the N2 Position of Guanine of An 11 Base-Pair Oligonucleotide Sequence Coding For Amino Acids 11-13 of the Product of the N-Ras Protooncogene, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:1.2
occ:1.00
P A:DG11 0.0 1.2 1.0
OP2 A:DG11 1.5 1.5 1.0
OP1 A:DG11 1.5 2.0 1.0
O5' A:DG11 1.6 1.1 1.0
O3' A:DT10 1.6 1.0 1.0
C5' A:DG11 2.6 1.4 1.0
C3' A:DT10 2.7 0.9 1.0
H2'' A:DT10 2.8 0.8 1.0
H5' A:DG11 2.9 1.9 1.0
H5'' A:DG11 2.9 1.9 1.0
H3' A:DT10 2.9 1.0 1.0
C2' A:DT10 3.2 0.8 1.0
H2' A:DT10 3.6 0.8 1.0
H8 A:DG11 3.9 0.9 1.0
H3' A:DG11 3.9 1.4 1.0
C4' A:DT10 4.0 0.9 1.0
C4' A:DG11 4.0 1.2 1.0
H4' A:DT10 4.0 1.0 1.0
O4' A:DG11 4.4 1.0 1.0
C1' A:DT10 4.5 0.7 1.0
C3' A:DG11 4.5 1.3 1.0
H5'' A:DT10 4.6 1.4 1.0
H1' A:DT10 4.7 0.7 1.0
H4' A:DG11 4.8 1.3 1.0
O4' A:DT10 4.9 0.8 1.0
C5' A:DT10 4.9 1.1 1.0
C8 A:DG11 5.0 0.8 1.0

Reference:

I.S.Zegar, F.R.Setayesh, B.L.Decorte, C.M.Harris, T.M.Harris, M.P.Stone. Styrene Oxide Adducts in An Oligodeoxynucleotide Containing the Human N-Ras Codon 12 Sequence: Structural Refinement of the Minor Groove R(12,2)- and S(12,2)-Alpha-(N2-Guanyl) Stereoisomers From 1H uc(Nmr). Biochemistry V. 35 4334 1996.
ISSN: ISSN 0006-2960
PubMed: 8605182
DOI: 10.1021/BI952086S
Page generated: Fri Sep 25 12:47:05 2020

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