Phosphorus in PDB 1afz: Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure

Phosphorus Binding Sites:

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

Binding sites:

The binding sites of Phosphorus atom in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure (pdb code 1afz). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure, PDB code: 1afz:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1afz

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Phosphorus binding site 1 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.5
occ:1.00
P A:DG2 0.0 0.5 1.0
OP2 A:DG2 1.5 0.8 1.0
OP1 A:DG2 1.5 1.5 1.0
O5' A:DG2 1.6 0.4 1.0
O3' A:DG1 1.6 0.9 1.0
H2'' A:DG1 2.5 0.7 1.0
C5' A:DG2 2.6 0.4 1.0
C3' A:DG1 2.7 1.0 1.0
H5'' A:DG2 2.8 0.4 1.0
H5' A:DG2 3.0 0.6 1.0
H3' A:DG1 3.0 1.1 1.0
C2' A:DG1 3.1 0.8 1.0
H3' A:DG2 3.6 0.2 1.0
H2' A:DG1 3.7 0.9 1.0
H8 A:DG2 3.8 0.4 1.0
C4' A:DG1 4.0 1.1 1.0
C4' A:DG2 4.0 0.4 1.0
H4' A:DG1 4.0 1.1 1.0
C1' A:DG1 4.3 0.9 1.0
H1' A:DG1 4.3 0.8 1.0
C3' A:DG2 4.3 0.3 1.0
O4' A:DG2 4.5 0.4 1.0
O4' A:DG1 4.7 1.1 1.0
H4' A:DG2 4.8 0.5 1.0
H2' A:DG2 4.8 0.2 1.0
C8 A:DG2 4.8 0.4 1.0
H5'' A:DG1 4.9 1.4 1.0

Phosphorus binding site 2 out of 20 in 1afz

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Phosphorus binding site 2 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.4
occ:1.00
P A:DC3 0.0 0.4 1.0
OP2 A:DC3 1.5 1.2 1.0
OP1 A:DC3 1.5 1.5 1.0
O3' A:DG2 1.6 0.4 1.0
O5' A:DC3 1.6 0.4 1.0
H2'' A:DG2 2.6 0.3 1.0
C5' A:DC3 2.6 0.4 1.0
C3' A:DG2 2.7 0.3 1.0
H5'' A:DC3 2.8 0.5 1.0
H5' A:DC3 3.0 0.4 1.0
C2' A:DG2 3.1 0.2 1.0
H3' A:DG2 3.2 0.2 1.0
H6 A:DC3 3.7 0.3 1.0
H2' A:DG2 3.8 0.2 1.0
H3' A:DC3 3.8 0.5 1.0
H4' A:DG2 3.8 0.5 1.0
C4' A:DG2 3.9 0.4 1.0
C4' A:DC3 4.0 0.4 1.0
C1' A:DG2 4.3 0.3 1.0
H1' A:DG2 4.3 0.3 1.0
C3' A:DC3 4.4 0.5 1.0
O4' A:DC3 4.5 0.4 1.0
O4' A:DG2 4.7 0.4 1.0
C6 A:DC3 4.7 0.3 1.0
H4' A:DC3 4.8 0.5 1.0
H2' A:DC3 4.8 0.4 1.0
H5'' A:DG2 4.9 0.4 1.0
C5' A:DG2 5.0 0.4 1.0

Phosphorus binding site 3 out of 20 in 1afz

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Phosphorus binding site 3 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.6
occ:1.00
P A:DA4 0.0 0.6 1.0
OP2 A:DA4 1.5 1.8 1.0
OP1 A:DA4 1.5 0.8 1.0
O3' A:DC3 1.6 0.5 1.0
O5' A:DA4 1.6 0.5 1.0
C3' A:DC3 2.7 0.5 1.0
C5' A:DA4 2.7 0.5 1.0
H5'' A:DA4 2.7 0.6 1.0
H3' A:DC3 2.8 0.5 1.0
H2'' A:DC3 3.0 0.5 1.0
H5' A:DA4 3.2 0.5 1.0
C2' A:DC3 3.3 0.4 1.0
H8 A:DA4 3.3 0.5 1.0
H3' A:DA4 3.6 0.6 1.0
H2' A:DC3 3.8 0.4 1.0
C4' A:DA4 3.9 0.5 1.0
C4' A:DC3 4.0 0.4 1.0
H4' A:DC3 4.1 0.5 1.0
C3' A:DA4 4.3 0.5 1.0
C8 A:DA4 4.3 0.5 1.0
O4' A:DA4 4.6 0.5 1.0
C1' A:DC3 4.6 0.4 1.0
H5'' A:DC3 4.7 0.5 1.0
H4' A:DA4 4.7 0.5 1.0
H1' A:DC3 4.8 0.4 1.0
H2' A:DA4 4.8 0.5 1.0
C5' A:DC3 4.9 0.4 1.0
O4' A:DC3 4.9 0.4 1.0

Phosphorus binding site 4 out of 20 in 1afz

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Phosphorus binding site 4 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.6
occ:1.00
P A:DG5 0.0 0.6 1.0
OP2 A:DG5 1.5 1.5 1.0
OP1 A:DG5 1.5 0.7 1.0
O5' A:DG5 1.6 0.5 1.0
O3' A:DA4 1.6 0.5 1.0
H2'' A:DA4 2.5 0.5 1.0
C5' A:DG5 2.6 0.5 1.0
H5'' A:DG5 2.7 0.5 1.0
C3' A:DA4 2.8 0.5 1.0
C2' A:DA4 3.1 0.5 1.0
H5' A:DG5 3.1 0.5 1.0
H3' A:DA4 3.4 0.6 1.0
H3' A:DG5 3.6 0.6 1.0
H4' A:DA4 3.7 0.5 1.0
H2' A:DA4 3.8 0.5 1.0
C4' A:DA4 3.8 0.5 1.0
C4' A:DG5 3.9 0.5 1.0
H8 A:DG5 4.1 0.5 1.0
C1' A:DA4 4.2 0.5 1.0
H1' A:DA4 4.2 0.4 1.0
C3' A:DG5 4.3 0.6 1.0
O4' A:DA4 4.5 0.5 1.0
O4' A:DG5 4.6 0.5 1.0
H2' A:DG5 4.6 0.6 1.0
H4' A:DG5 4.7 0.5 1.0
C2' A:DG5 5.0 0.6 1.0
C8 A:DG5 5.0 0.5 1.0

Phosphorus binding site 5 out of 20 in 1afz

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Phosphorus binding site 5 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.5
occ:1.00
P A:DG6 0.0 0.5 1.0
OP2 A:DG6 1.5 1.4 1.0
OP1 A:DG6 1.5 1.0 1.0
O5' A:DG6 1.6 0.5 1.0
O3' A:DG5 1.6 0.6 1.0
H2'' A:DG5 2.5 0.6 1.0
C5' A:DG6 2.6 0.5 1.0
C3' A:DG5 2.7 0.6 1.0
H5'' A:DG6 2.8 0.4 1.0
H5' A:DG6 3.0 0.4 1.0
C2' A:DG5 3.0 0.6 1.0
H3' A:DG5 3.1 0.6 1.0
H8 A:DG6 3.5 0.6 1.0
H3' A:DG6 3.5 0.5 1.0
H2' A:DG5 3.7 0.6 1.0
H4' A:DG5 3.9 0.5 1.0
C4' A:DG6 3.9 0.5 1.0
C4' A:DG5 3.9 0.5 1.0
H1' A:DG5 4.1 0.5 1.0
C1' A:DG5 4.2 0.5 1.0
C3' A:DG6 4.2 0.5 1.0
H2' A:DG6 4.3 0.5 1.0
C8 A:DG6 4.5 0.6 1.0
O4' A:DG6 4.5 0.6 1.0
O4' A:DG5 4.7 0.5 1.0
C2' A:DG6 4.7 0.5 1.0
H4' A:DG6 4.7 0.5 1.0
H5'' A:DG5 4.9 0.5 1.0

Phosphorus binding site 6 out of 20 in 1afz

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Phosphorus binding site 6 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.5
occ:1.00
P A:DT7 0.0 0.5 1.0
OP1 A:DT7 1.5 1.7 1.0
OP2 A:DT7 1.5 0.9 1.0
O3' A:DG6 1.6 0.5 1.0
O5' A:DT7 1.6 0.5 1.0
H2'' A:DG6 2.5 0.5 1.0
C5' A:DT7 2.7 0.6 1.0
C3' A:DG6 2.7 0.5 1.0
H5'' A:DT7 2.9 0.5 1.0
H5' A:DT7 2.9 0.6 1.0
H3' A:DG6 3.0 0.5 1.0
C2' A:DG6 3.1 0.5 1.0
H6 A:DT7 3.6 0.5 1.0
H2' A:DG6 3.7 0.5 1.0
H3' A:DT7 3.8 0.5 1.0
C4' A:DG6 4.0 0.5 1.0
C4' A:DT7 4.0 0.6 1.0
H4' A:DG6 4.0 0.5 1.0
H72 A:DT7 4.0 0.4 1.0
C1' A:DG6 4.2 0.6 1.0
H1' A:DG6 4.3 0.6 1.0
C3' A:DT7 4.4 0.5 1.0
O4' A:DT7 4.4 0.6 1.0
C6 A:DT7 4.5 0.5 1.0
O4' A:DG6 4.7 0.6 1.0
H4' A:DT7 4.8 0.6 1.0
H2' A:DT7 4.8 0.4 1.0
C7 A:DT7 5.0 0.5 1.0
H5'' A:DG6 5.0 0.4 1.0

Phosphorus binding site 7 out of 20 in 1afz

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Phosphorus binding site 7 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.7
occ:1.00
P A:DG8 0.0 0.7 1.0
OP2 A:DG8 1.5 1.3 1.0
OP1 A:DG8 1.5 1.3 1.0
O5' A:DG8 1.6 0.6 1.0
O3' A:DT7 1.6 0.5 1.0
C5' A:DG8 2.6 0.7 1.0
H2'' A:DT7 2.7 0.5 1.0
C3' A:DT7 2.7 0.5 1.0
H5'' A:DG8 2.8 0.8 1.0
H5' A:DG8 3.0 0.8 1.0
H3' A:DT7 3.0 0.5 1.0
C2' A:DT7 3.1 0.5 1.0
H8 A:DG8 3.2 0.4 1.0
H2' A:DT7 3.7 0.4 1.0
H3' A:DG8 3.8 0.7 1.0
C4' A:DT7 4.0 0.6 1.0
C4' A:DG8 4.0 0.7 1.0
H4' A:DT7 4.0 0.6 1.0
C8 A:DG8 4.2 0.4 1.0
C3' A:DG8 4.4 0.7 1.0
C1' A:DT7 4.4 0.5 1.0
O4' A:DG8 4.5 0.6 1.0
H1' A:DT7 4.5 0.6 1.0
H2' A:DG8 4.7 0.5 1.0
H4' A:DG8 4.8 0.8 1.0
H5'' A:DT7 4.8 0.5 1.0
O4' A:DT7 4.8 0.6 1.0
N7 A:DG8 4.9 0.3 1.0
C5' A:DT7 4.9 0.6 1.0
C2' A:DG8 5.0 0.5 1.0
N9 A:DG8 5.0 0.4 1.0

Phosphorus binding site 8 out of 20 in 1afz

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Phosphorus binding site 8 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.5
occ:1.00
P A:DG9 0.0 0.5 1.0
OP1 A:DG9 1.5 1.3 1.0
OP2 A:DG9 1.5 0.6 1.0
O5' A:DG9 1.6 0.5 1.0
O3' A:DG8 1.6 0.7 1.0
H2'' A:DG8 2.5 0.5 1.0
C5' A:DG9 2.6 0.4 1.0
C3' A:DG8 2.7 0.7 1.0
H5'' A:DG9 2.7 0.5 1.0
C2' A:DG8 3.1 0.5 1.0
H5' A:DG9 3.1 0.5 1.0
H3' A:DG8 3.3 0.7 1.0
H3' A:DG9 3.4 0.4 1.0
H2' A:DG8 3.8 0.5 1.0
H4' A:DG8 3.8 0.8 1.0
C4' A:DG8 3.9 0.7 1.0
C4' A:DG9 3.9 0.3 1.0
H8 A:DG9 4.0 0.4 1.0
H1' A:DG8 4.1 0.5 1.0
C3' A:DG9 4.1 0.3 1.0
C1' A:DG8 4.1 0.5 1.0
H2' A:DG9 4.4 0.3 1.0
O4' A:DG8 4.5 0.6 1.0
O4' A:DG9 4.5 0.4 1.0
H4' A:DG9 4.7 0.3 1.0
C2' A:DG9 4.8 0.3 1.0
C8 A:DG9 5.0 0.3 1.0

Phosphorus binding site 9 out of 20 in 1afz

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Phosphorus binding site 9 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.4
occ:1.00
P A:DT10 0.0 0.4 1.0
OP2 A:DT10 1.5 1.3 1.0
OP1 A:DT10 1.5 1.4 1.0
O5' A:DT10 1.6 0.5 1.0
O3' A:DG9 1.6 0.3 1.0
H2'' A:DG9 2.5 0.3 1.0
C5' A:DT10 2.7 0.5 1.0
C3' A:DG9 2.7 0.3 1.0
H5'' A:DT10 2.9 0.6 1.0
H5' A:DT10 2.9 0.5 1.0
C2' A:DG9 3.0 0.3 1.0
H3' A:DG9 3.1 0.4 1.0
H3' A:DT10 3.7 0.7 1.0
H2' A:DG9 3.7 0.3 1.0
H6 A:DT10 3.7 0.5 1.0
C4' A:DG9 3.9 0.3 1.0
H4' A:DG9 4.0 0.3 1.0
C4' A:DT10 4.0 0.6 1.0
H1' A:DG9 4.1 0.3 1.0
C1' A:DG9 4.2 0.3 1.0
C3' A:DT10 4.4 0.7 1.0
H72 A:DT10 4.5 0.4 1.0
O4' A:DT10 4.5 0.6 1.0
O4' A:DG9 4.7 0.4 1.0
C6 A:DT10 4.7 0.5 1.0
H4' A:DT10 4.8 0.7 1.0
H5'' A:DG9 5.0 0.5 1.0
H71 A:DT10 5.0 0.5 1.0

Phosphorus binding site 10 out of 20 in 1afz

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Phosphorus binding site 10 out of 20 in the Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, 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 Solution uc(Nmr) Structure of An 11 Base-Pair Oligonucleotide From the Human N-Ras Protooncogene Encoding For Amino Acids 11-13 of P21, Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:1.0
occ:1.00
P A:DG11 0.0 1.0 1.0
OP1 A:DG11 1.5 1.0 1.0
OP2 A:DG11 1.5 2.1 1.0
O3' A:DT10 1.6 0.9 1.0
O5' A:DG11 1.6 1.1 1.0
C3' A:DT10 2.6 0.7 1.0
C5' A:DG11 2.7 1.2 1.0
H2'' A:DT10 2.7 0.8 1.0
H3' A:DT10 2.9 0.7 1.0
H5'' A:DG11 2.9 1.3 1.0
H5' A:DG11 2.9 1.1 1.0
C2' A:DT10 3.1 0.7 1.0
H8 A:DG11 3.4 0.9 1.0
H2' A:DT10 3.4 0.7 1.0
H3' A:DG11 3.8 1.3 1.0
C4' A:DG11 4.0 1.2 1.0
C4' A:DT10 4.0 0.6 1.0
H4' A:DT10 4.1 0.7 1.0
C3' A:DG11 4.4 1.3 1.0
C8 A:DG11 4.4 0.9 1.0
O4' A:DG11 4.4 1.0 1.0
C1' A:DT10 4.5 0.6 1.0
H2' A:DG11 4.6 1.1 1.0
H5'' A:DT10 4.7 0.6 1.0
H1' A:DT10 4.7 0.7 1.0
H4' A:DG11 4.8 1.3 1.0
C5' A:DT10 4.9 0.5 1.0
O4' A:DT10 4.9 0.6 1.0
C2' A:DG11 5.0 1.2 1.0

Reference:

I.S.Zegar, M.P.Stone. Solution Structure of An Oligodeoxynucleotide Containing the Human N-Ras Codon 12 Sequence Refined From 1H uc(Nmr) Using Molecular Dynamics Restrained By Nuclear Overhauser Effects. Chem.Res.Toxicol. V. 9 114 1996.
ISSN: ISSN 0893-228X
PubMed: 8924579
DOI: 10.1021/TX9500787
Page generated: Fri Sep 25 12:48:44 2020

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