Phosphorus in PDB 1ag3: Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure (pdb code 1ag3). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure, PDB code: 1ag3:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 1ag3

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Phosphorus binding site 1 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P-1

b:1.1
occ:1.00
P A:DT-1 0.0 1.1 1.0
OP1 A:DT-1 1.5 1.4 1.0
OP2 A:DT-1 1.5 2.0 1.0
O5' A:DT-1 1.6 1.0 1.0
O3' A:DA-2 1.6 1.2 1.0
H2'' A:DA-2 2.6 1.2 1.0
C5' A:DT-1 2.6 1.0 1.0
C3' A:DA-2 2.7 1.3 1.0
H5'' A:DT-1 2.9 1.1 1.0
H5' A:DT-1 2.9 1.1 1.0
H3' A:DA-2 3.0 1.4 1.0
C2' A:DA-2 3.1 1.2 1.0
H2' A:DA-2 3.6 1.2 1.0
H3' A:DT-1 3.7 0.9 1.0
C4' A:DA-2 4.0 1.4 1.0
C4' A:DT-1 4.0 0.9 1.0
H4' A:DA-2 4.0 1.5 1.0
H6 A:DT-1 4.0 0.8 1.0
C1' A:DA-2 4.4 1.3 1.0
C3' A:DT-1 4.4 0.9 1.0
H1' A:DA-2 4.5 1.3 1.0
O4' A:DT-1 4.5 0.9 1.0
H5'' A:DA-2 4.7 1.8 1.0
H4' A:DT-1 4.8 1.1 1.0
H71 A:DT-1 4.8 1.4 1.0
O4' A:DA-2 4.8 1.4 1.0
H2' A:DT-1 4.9 0.7 1.0
C5' A:DA-2 4.9 1.6 1.0

Phosphorus binding site 2 out of 22 in 1ag3

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Phosphorus binding site 2 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P1

b:1.0
occ:1.00
P A:DC1 0.0 1.0 1.0
OP1 A:DC1 1.5 1.8 1.0
OP2 A:DC1 1.5 1.6 1.0
O5' A:DC1 1.6 1.0 1.0
O3' A:DT-1 1.6 1.1 1.0
H2'' A:DT-1 2.6 0.8 1.0
C5' A:DC1 2.6 1.1 1.0
C3' A:DT-1 2.7 0.9 1.0
H5'' A:DC1 2.8 1.2 1.0
H5' A:DC1 2.9 1.1 1.0
H3' A:DT-1 3.0 0.9 1.0
C2' A:DT-1 3.1 0.8 1.0
H6 A:DC1 3.5 0.9 1.0
H2' A:DT-1 3.6 0.7 1.0
H3' A:DC1 3.7 1.2 1.0
C4' A:DC1 4.0 1.1 1.0
C4' A:DT-1 4.0 0.9 1.0
H4' A:DT-1 4.0 1.1 1.0
C3' A:DC1 4.4 1.1 1.0
C1' A:DT-1 4.4 0.7 1.0
H1' A:DT-1 4.4 0.8 1.0
O4' A:DC1 4.5 0.9 1.0
C6 A:DC1 4.5 0.8 1.0
H2' A:DC1 4.7 1.0 1.0
H5'' A:DT-1 4.8 1.1 1.0
H4' A:DC1 4.8 1.2 1.0
O4' A:DT-1 4.8 0.9 1.0
C5' A:DT-1 4.9 1.0 1.0
C2' A:DC1 5.0 1.0 1.0

Phosphorus binding site 3 out of 22 in 1ag3

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Phosphorus binding site 3 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:1.2
occ:1.00
P A:DG2 0.0 1.2 1.0
OP2 A:DG2 1.5 1.5 1.0
OP1 A:DG2 1.5 2.1 1.0
O3' A:DC1 1.6 1.3 1.0
O5' A:DG2 1.6 1.1 1.0
H2'' A:DC1 2.6 1.0 1.0
C5' A:DG2 2.6 1.1 1.0
C3' A:DC1 2.7 1.1 1.0
H5'' A:DG2 2.8 1.3 1.0
H3' A:DC1 2.9 1.2 1.0
H5' A:DG2 3.0 1.1 1.0
C2' A:DC1 3.1 1.0 1.0
H3' A:DG2 3.5 1.2 1.0
H8 A:DG2 3.6 1.0 1.0
H2' A:DC1 3.7 1.0 1.0
C4' A:DG2 3.9 1.1 1.0
C4' A:DC1 4.0 1.1 1.0
H4' A:DC1 4.0 1.2 1.0
C3' A:DG2 4.3 1.2 1.0
C1' A:DC1 4.4 0.8 1.0
H1' A:DC1 4.4 0.9 1.0
O4' A:DG2 4.5 1.0 1.0
C8 A:DG2 4.5 0.9 1.0
H4' A:DG2 4.8 1.2 1.0
O4' A:DC1 4.8 0.9 1.0
H5'' A:DC1 4.8 1.2 1.0
H2' A:DG2 4.9 1.1 1.0
C5' A:DC1 4.9 1.1 1.0

Phosphorus binding site 4 out of 22 in 1ag3

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Phosphorus binding site 4 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:1.4
occ:1.00
P A:DC3 0.0 1.4 1.0
OP1 A:DC3 1.5 2.6 1.0
OP2 A:DC3 1.5 1.0 1.0
O5' A:DC3 1.6 1.2 1.0
O3' A:DG2 1.6 1.3 1.0
H2'' A:DG2 2.6 1.1 1.0
C5' A:DC3 2.7 1.1 1.0
C3' A:DG2 2.7 1.2 1.0
H5'' A:DC3 2.9 1.2 1.0
H5' A:DC3 2.9 1.1 1.0
H3' A:DG2 3.0 1.2 1.0
C2' A:DG2 3.1 1.1 1.0
H6 A:DC3 3.4 1.1 1.0
H2' A:DG2 3.5 1.1 1.0
H3' A:DC3 3.7 1.1 1.0
C4' A:DG2 4.0 1.1 1.0
C4' A:DC3 4.0 1.0 1.0
H4' A:DG2 4.0 1.2 1.0
C6 A:DC3 4.3 1.0 1.0
C3' A:DC3 4.4 1.0 1.0
C1' A:DG2 4.4 1.0 1.0
O4' A:DC3 4.5 0.9 1.0
H5 A:DC3 4.6 1.1 1.0
H1' A:DG2 4.7 1.0 1.0
H5'' A:DG2 4.8 1.3 1.0
H4' A:DC3 4.8 0.9 1.0
O4' A:DG2 4.8 1.0 1.0
C5 A:DC3 4.9 1.0 1.0
H2' A:DC3 4.9 1.1 1.0
C5' A:DG2 4.9 1.1 1.0

Phosphorus binding site 5 out of 22 in 1ag3

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Phosphorus binding site 5 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:1.2
occ:1.00
P A:P4 0.0 1.2 1.0
OP1 A:P4 1.5 1.2 1.0
OP2 A:P4 1.5 2.4 1.0
O5' A:P4 1.6 1.3 1.0
O3' A:DC3 1.6 1.1 1.0
C5' A:P4 2.6 0.8 1.0
C3' A:DC3 2.7 1.0 1.0
H5' A:P4 2.8 1.2 1.0
H3' A:DC3 2.9 1.1 1.0
H2'' A:DC3 2.9 1.0 1.0
H5'' A:P4 3.0 1.0 1.0
H8 A:P4 3.0 0.9 1.0
C2' A:DC3 3.2 1.0 1.0
H2' A:DC3 3.6 1.1 1.0
C8 A:P4 3.9 0.9 1.0
H3' A:P4 3.9 0.9 1.0
C4' A:P4 4.0 0.8 1.0
C4' A:DC3 4.0 1.0 1.0
H4' A:DC3 4.0 0.9 1.0
O4' A:P4 4.3 0.8 1.0
N7 A:P4 4.5 0.9 1.0
C3' A:P4 4.5 0.8 1.0
C1' A:DC3 4.6 0.9 1.0
H5'' A:DC3 4.7 1.2 1.0
N9 A:P4 4.7 0.8 1.0
H4' A:P4 4.8 0.8 1.0
C5' A:DC3 4.9 1.1 1.0
H1' A:DC3 4.9 0.9 1.0
O4' A:DC3 4.9 0.9 1.0
C1' A:P4 5.0 0.8 1.0

Phosphorus binding site 6 out of 22 in 1ag3

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Phosphorus binding site 6 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 1.8 1.0
OP2 A:DC5 1.5 1.4 1.0
O5' A:DC5 1.6 0.9 1.0
O3' A:P4 1.6 0.8 1.0
C5' A:DC5 2.6 0.8 1.0
C3' A:P4 2.6 0.8 1.0
H5' A:DC5 2.8 0.9 1.0
H3' A:P4 2.8 0.9 1.0
H2'' A:P4 2.9 0.9 1.0
H5'' A:DC5 2.9 0.9 1.0
C2' A:P4 3.2 0.8 1.0
H2' A:P4 3.5 0.9 1.0
H6 A:DC5 3.7 0.9 1.0
H3' A:DC5 3.9 0.8 1.0
C4' A:P4 4.0 0.8 1.0
C4' A:DC5 4.0 0.8 1.0
H4' A:P4 4.0 0.8 1.0
C6 A:DC5 4.2 0.9 1.0
O4' A:DC5 4.3 0.8 1.0
C3' A:DC5 4.5 0.8 1.0
H5'' A:P4 4.5 1.0 1.0
H5 A:DC5 4.6 1.1 1.0
C1' A:P4 4.6 0.8 1.0
C5 A:DC5 4.7 1.0 1.0
H4' A:DC5 4.8 0.8 1.0
C5' A:P4 4.8 0.8 1.0
O4' A:P4 4.9 0.8 1.0
N1 A:DC5 4.9 0.9 1.0

Phosphorus binding site 7 out of 22 in 1ag3

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Phosphorus binding site 7 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.8
occ:1.00
P A:DG6 0.0 0.8 1.0
OP2 A:DG6 1.5 1.0 1.0
OP1 A:DG6 1.5 2.0 1.0
O5' A:DG6 1.6 0.8 1.0
O3' A:DC5 1.6 0.8 1.0
C5' A:DG6 2.6 0.8 1.0
C3' A:DC5 2.7 0.8 1.0
H5' A:DG6 2.8 0.9 1.0
H2'' A:DC5 2.9 0.9 1.0
H3' A:DC5 2.9 0.8 1.0
H5'' A:DG6 3.0 0.8 1.0
C2' A:DC5 3.2 0.9 1.0
H2' A:DC5 3.4 0.9 1.0
C4' A:DG6 4.0 0.8 1.0
C4' A:DC5 4.0 0.8 1.0
H4' A:DC5 4.0 0.8 1.0
H3' A:DG6 4.0 0.7 1.0
H8 A:DG6 4.1 0.7 1.0
O4' A:DG6 4.3 0.8 1.0
C3' A:DG6 4.6 0.8 1.0
H5'' A:DC5 4.6 0.9 1.0
C1' A:DC5 4.6 0.8 1.0
H4' A:DG6 4.8 0.9 1.0
C8 A:DG6 4.8 0.7 1.0
H2' A:DG6 4.8 0.7 1.0
C5' A:DC5 4.8 0.8 1.0
O4' A:DC5 4.9 0.8 1.0
H6 A:DC5 5.0 0.9 1.0
H1' A:DC5 5.0 0.9 1.0

Phosphorus binding site 8 out of 22 in 1ag3

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Phosphorus binding site 8 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:1.0
occ:1.00
P A:DG7 0.0 1.0 1.0
OP1 A:DG7 1.5 1.6 1.0
OP2 A:DG7 1.5 1.8 1.0
O5' A:DG7 1.6 0.9 1.0
O3' A:DG6 1.6 0.9 1.0
H2'' A:DG6 2.5 0.8 1.0
C5' A:DG7 2.6 1.0 1.0
C3' A:DG6 2.7 0.8 1.0
H5'' A:DG7 2.8 1.0 1.0
H5' A:DG7 2.9 1.0 1.0
H3' A:DG6 3.0 0.7 1.0
C2' A:DG6 3.1 0.8 1.0
H2' A:DG6 3.7 0.7 1.0
H3' A:DG7 3.8 0.9 1.0
C4' A:DG6 4.0 0.8 1.0
H8 A:DG7 4.0 0.7 1.0
C4' A:DG7 4.0 0.9 1.0
H4' A:DG6 4.0 0.9 1.0
C1' A:DG6 4.3 0.8 1.0
H1' A:DG6 4.3 0.9 1.0
C3' A:DG7 4.4 0.9 1.0
O4' A:DG7 4.5 0.9 1.0
H2' A:DG7 4.7 0.7 1.0
O4' A:DG6 4.7 0.8 1.0
H4' A:DG7 4.8 1.0 1.0
H5'' A:DG6 4.9 0.8 1.0
C8 A:DG7 4.9 0.7 1.0

Phosphorus binding site 9 out of 22 in 1ag3

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Phosphorus binding site 9 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:1.0
occ:1.00
P A:DC8 0.0 1.0 1.0
OP1 A:DC8 1.5 2.0 1.0
OP2 A:DC8 1.5 1.2 1.0
O5' A:DC8 1.6 0.9 1.0
O3' A:DG7 1.6 1.0 1.0
H2'' A:DG7 2.6 0.8 1.0
C5' A:DC8 2.6 0.9 1.0
C3' A:DG7 2.7 0.9 1.0
H5'' A:DC8 2.9 1.0 1.0
H5' A:DC8 2.9 1.0 1.0
H3' A:DG7 3.0 0.9 1.0
C2' A:DG7 3.1 0.8 1.0
H2' A:DG7 3.7 0.7 1.0
H6 A:DC8 3.8 0.7 1.0
H3' A:DC8 3.9 0.8 1.0
C4' A:DG7 4.0 0.9 1.0
C4' A:DC8 4.0 0.8 1.0
H4' A:DG7 4.0 1.0 1.0
C1' A:DG7 4.3 0.8 1.0
H1' A:DG7 4.3 0.8 1.0
O4' A:DC8 4.4 0.8 1.0
C3' A:DC8 4.4 0.8 1.0
H2' A:DC8 4.7 0.7 1.0
O4' A:DG7 4.8 0.9 1.0
H4' A:DC8 4.8 0.9 1.0
C6 A:DC8 4.8 0.6 1.0
H5'' A:DG7 4.9 1.0 1.0
C5' A:DG7 5.0 1.0 1.0

Phosphorus binding site 10 out of 22 in 1ag3

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Phosphorus binding site 10 out of 22 in the Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), 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 Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion, uc(Nmr), Minimized Average Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.8
occ:1.00
P A:DA9 0.0 0.8 1.0
OP1 A:DA9 1.5 1.9 1.0
OP2 A:DA9 1.5 0.9 1.0
O5' A:DA9 1.6 0.7 1.0
O3' A:DC8 1.6 0.8 1.0
C5' A:DA9 2.6 0.7 1.0
C3' A:DC8 2.7 0.8 1.0
H2'' A:DC8 2.7 0.6 1.0
H5'' A:DA9 2.9 0.7 1.0
H5' A:DA9 2.9 0.8 1.0
H3' A:DC8 2.9 0.8 1.0
C2' A:DC8 3.2 0.7 1.0
H8 A:DA9 3.6 0.5 1.0
H3' A:DA9 3.7 0.5 1.0
H2' A:DC8 3.8 0.7 1.0
C4' A:DA9 4.0 0.6 1.0
C4' A:DC8 4.0 0.8 1.0
H4' A:DC8 4.0 0.9 1.0
C1' A:DC8 4.4 0.7 1.0
C3' A:DA9 4.4 0.5 1.0
H1' A:DC8 4.4 0.6 1.0
O4' A:DA9 4.5 0.6 1.0
H2' A:DA9 4.5 0.4 1.0
C8 A:DA9 4.6 0.5 1.0
H5'' A:DC8 4.8 1.0 1.0
H4' A:DA9 4.8 0.7 1.0
O4' A:DC8 4.8 0.8 1.0
C2' A:DA9 4.9 0.4 1.0
C5' A:DC8 4.9 0.9 1.0

Reference:

J.P.Weisenseel, J.G.Moe, G.R.Reddy, L.J.Marnett, M.P.Stone. Structure of A Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite A Two-Base Deletion in the (Cpg)3 Frame Shift Hotspot of Salmonella Typhimurium HISD3052 Determined By 1H uc(Nmr) and Restrained Molecular Dynamics. Biochemistry V. 34 50 1995.
ISSN: ISSN 0006-2960
PubMed: 7819223
DOI: 10.1021/BI00001A007
Page generated: Fri Sep 25 12:49:37 2020

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