Phosphorus in PDB 169d: The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction (pdb code 169d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction, PDB code: 169d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 169d

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Phosphorus binding site 1 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.0
occ:1.00
P A:DG2 0.0 0.0 1.0
OP1 A:DG2 1.5 0.0 1.0
OP2 A:DG2 1.5 0.0 1.0
O3' A:DG1 1.6 0.0 1.0
O5' A:DG2 1.6 0.0 1.0
C5' A:DG2 2.7 0.0 1.0
C3' A:DG1 2.7 0.0 1.0
H2'' A:DG1 2.8 0.0 1.0
H5' A:DG2 2.9 0.0 1.0
H5'' A:DG2 2.9 0.0 1.0
H3' A:DG1 3.0 0.0 1.0
C2' A:DG1 3.2 0.0 1.0
H2' A:DG1 3.8 0.0 1.0
C4' A:DG1 4.0 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
H3' A:DG2 4.0 0.0 1.0
H4' A:DG1 4.1 0.0 1.0
H2' A:DG2 4.2 0.0 1.0
H1' A:DG1 4.3 0.0 1.0
C1' A:DG1 4.4 0.0 1.0
O4' A:DG2 4.5 0.0 1.0
C3' A:DG2 4.5 0.0 1.0
H5' A:DG1 4.6 0.0 1.0
H4' A:DG2 4.8 0.0 1.0
O4' A:DG1 4.9 0.0 1.0
H8 A:DG2 4.9 0.0 1.0
C5' A:DG1 4.9 0.0 1.0
C2' A:DG2 4.9 0.0 1.0

Phosphorus binding site 2 out of 18 in 169d

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Phosphorus binding site 2 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.0
occ:1.00
P A:DG3 0.0 0.0 1.0
OP1 A:DG3 1.5 0.0 1.0
OP2 A:DG3 1.5 0.0 1.0
O5' A:DG3 1.6 0.0 1.0
O3' A:DG2 1.6 0.0 1.0
C5' A:DG3 2.7 0.0 1.0
C3' A:DG2 2.7 0.0 1.0
H5'' A:DG3 2.9 0.0 1.0
H2'' A:DG2 2.9 0.0 1.0
H5' A:DG3 2.9 0.0 1.0
H3' A:DG2 3.0 0.0 1.0
C2' A:DG2 3.3 0.0 1.0
H1' A:DG2 3.7 0.0 1.0
H3' A:DG3 3.9 0.0 1.0
H4' A:DG2 4.0 0.0 1.0
C4' A:DG2 4.0 0.0 1.0
C4' A:DG3 4.0 0.0 1.0
C1' A:DG2 4.1 0.0 1.0
H2' A:DG2 4.1 0.0 1.0
H8 A:DG3 4.2 0.0 1.0
H2' A:DG3 4.3 0.0 1.0
O4' A:DG3 4.4 0.0 1.0
C3' A:DG3 4.5 0.0 1.0
O4' A:DG2 4.7 0.0 1.0
H4' A:DG3 4.8 0.0 1.0
C2' A:DG3 4.9 0.0 1.0
H5'' A:DG2 4.9 0.0 1.0

Phosphorus binding site 3 out of 18 in 169d

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Phosphorus binding site 3 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.0
occ:1.00
P A:DT4 0.0 0.0 1.0
OP1 A:DT4 1.5 0.0 1.0
OP2 A:DT4 1.5 0.0 1.0
O3' A:DG3 1.6 0.0 1.0
O5' A:DT4 1.6 0.0 1.0
C5' A:DT4 2.7 0.0 1.0
C3' A:DG3 2.7 0.0 1.0
H2'' A:DG3 2.8 0.0 1.0
H5' A:DT4 2.9 0.0 1.0
H5'' A:DT4 2.9 0.0 1.0
H3' A:DG3 3.0 0.0 1.0
C2' A:DG3 3.2 0.0 1.0
H1' A:DG3 3.9 0.0 1.0
C4' A:DG3 4.0 0.0 1.0
C4' A:DT4 4.0 0.0 1.0
H2' A:DG3 4.0 0.0 1.0
H4' A:DG3 4.0 0.0 1.0
H3' A:DT4 4.1 0.0 1.0
C1' A:DG3 4.2 0.0 1.0
O4' A:DT4 4.4 0.0 1.0
C3' A:DT4 4.6 0.0 1.0
O4' A:DG3 4.7 0.0 1.0
H4' A:DT4 4.8 0.0 1.0
H6 A:DT4 4.8 0.0 1.0
H5'' A:DG3 4.9 0.0 1.0
H2' A:DT4 5.0 0.0 1.0

Phosphorus binding site 4 out of 18 in 169d

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Phosphorus binding site 4 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.0
occ:1.00
P A:DA5 0.0 0.0 1.0
OP2 A:DA5 1.5 0.0 1.0
OP1 A:DA5 1.5 0.0 1.0
O5' A:DA5 1.6 0.0 1.0
O3' A:DT4 1.6 0.0 1.0
C5' A:DA5 2.7 0.0 1.0
C3' A:DT4 2.7 0.0 1.0
H2'' A:DT4 2.8 0.0 1.0
H5' A:DA5 2.9 0.0 1.0
H5'' A:DA5 2.9 0.0 1.0
H3' A:DT4 3.0 0.0 1.0
C2' A:DT4 3.2 0.0 1.0
H2' A:DT4 3.9 0.0 1.0
C4' A:DT4 4.0 0.0 1.0
C4' A:DA5 4.0 0.0 1.0
H4' A:DT4 4.0 0.0 1.0
H3' A:DA5 4.1 0.0 1.0
H1' A:DT4 4.2 0.0 1.0
C1' A:DT4 4.3 0.0 1.0
H2' A:DA5 4.4 0.0 1.0
O4' A:DA5 4.5 0.0 1.0
C3' A:DA5 4.5 0.0 1.0
H5'' A:DT4 4.6 0.0 1.0
H4' A:DA5 4.8 0.0 1.0
O4' A:DT4 4.8 0.0 1.0
C5' A:DT4 4.9 0.0 1.0
H8 A:DA5 4.9 0.0 1.0

Phosphorus binding site 5 out of 18 in 169d

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Phosphorus binding site 5 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.0
occ:1.00
P A:DT6 0.0 0.0 1.0
OP2 A:DT6 1.5 0.0 1.0
OP1 A:DT6 1.5 0.0 1.0
O5' A:DT6 1.6 0.0 1.0
O3' A:DA5 1.6 0.0 1.0
C5' A:DT6 2.7 0.0 1.0
C3' A:DA5 2.7 0.0 1.0
H2'' A:DA5 2.9 0.0 1.0
H5' A:DT6 2.9 0.0 1.0
H3' A:DA5 2.9 0.0 1.0
H5'' A:DT6 2.9 0.0 1.0
C2' A:DA5 3.3 0.0 1.0
H1' A:DA5 3.8 0.0 1.0
C4' A:DA5 4.0 0.0 1.0
C4' A:DT6 4.0 0.0 1.0
H4' A:DA5 4.0 0.0 1.0
H3' A:DT6 4.1 0.0 1.0
H2' A:DA5 4.1 0.0 1.0
C1' A:DA5 4.2 0.0 1.0
O4' A:DT6 4.3 0.0 1.0
H6 A:DT6 4.4 0.0 1.0
C3' A:DT6 4.6 0.0 1.0
H2' A:DT6 4.7 0.0 1.0
O4' A:DA5 4.7 0.0 1.0
H4' A:DT6 4.8 0.0 1.0
H5'' A:DA5 4.8 0.0 1.0

Phosphorus binding site 6 out of 18 in 169d

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Phosphorus binding site 6 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.0
occ:1.00
P A:DA7 0.0 0.0 1.0
OP1 A:DA7 1.5 0.0 1.0
OP2 A:DA7 1.5 0.0 1.0
O5' A:DA7 1.6 0.0 1.0
O3' A:DT6 1.6 0.0 1.0
C5' A:DA7 2.7 0.0 1.0
C3' A:DT6 2.7 0.0 1.0
H2'' A:DT6 2.8 0.0 1.0
H5'' A:DA7 2.9 0.0 1.0
H5' A:DA7 2.9 0.0 1.0
H3' A:DT6 3.0 0.0 1.0
C2' A:DT6 3.3 0.0 1.0
H2' A:DT6 4.0 0.0 1.0
C4' A:DT6 4.0 0.0 1.0
C4' A:DA7 4.0 0.0 1.0
H3' A:DA7 4.0 0.0 1.0
H4' A:DT6 4.0 0.0 1.0
H1' A:DT6 4.0 0.0 1.0
C1' A:DT6 4.3 0.0 1.0
O4' A:DA7 4.4 0.0 1.0
C3' A:DA7 4.5 0.0 1.0
H2' A:DA7 4.5 0.0 1.0
H5'' A:DT6 4.7 0.0 1.0
H4' A:DA7 4.8 0.0 1.0
O4' A:DT6 4.8 0.0 1.0
H8 A:DA7 4.9 0.0 1.0
C5' A:DT6 5.0 0.0 1.0

Phosphorus binding site 7 out of 18 in 169d

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Phosphorus binding site 7 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.0
occ:1.00
P A:DC8 0.0 0.0 1.0
OP2 A:DC8 1.5 0.0 1.0
OP1 A:DC8 1.5 0.0 1.0
O5' A:DC8 1.6 0.0 1.0
O3' A:DA7 1.6 0.0 1.0
C5' A:DC8 2.6 0.0 1.0
C3' A:DA7 2.7 0.0 1.0
H2'' A:DA7 2.8 0.0 1.0
H5' A:DC8 2.9 0.0 1.0
H3' A:DA7 2.9 0.0 1.0
H5'' A:DC8 3.0 0.0 1.0
C2' A:DA7 3.3 0.0 1.0
C4' A:DC8 4.0 0.0 1.0
C4' A:DA7 4.0 0.0 1.0
H4' A:DA7 4.0 0.0 1.0
H1' A:DA7 4.0 0.0 1.0
H2' A:DA7 4.1 0.0 1.0
H3' A:DC8 4.1 0.0 1.0
C1' A:DA7 4.3 0.0 1.0
O4' A:DC8 4.3 0.0 1.0
C3' A:DC8 4.6 0.0 1.0
H5'' A:DA7 4.7 0.0 1.0
H4' A:DC8 4.8 0.0 1.0
O4' A:DA7 4.8 0.0 1.0
H6 A:DC8 4.9 0.0 1.0
C5' A:DA7 5.0 0.0 1.0

Phosphorus binding site 8 out of 18 in 169d

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Phosphorus binding site 8 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.0
occ:1.00
P A:DG9 0.0 0.0 1.0
OP1 A:DG9 1.5 0.0 1.0
OP2 A:DG9 1.5 0.0 1.0
O5' A:DG9 1.6 0.0 1.0
O3' A:DC8 1.6 0.0 1.0
C5' A:DG9 2.6 0.0 1.0
C3' A:DC8 2.7 0.0 1.0
H5' A:DG9 2.8 0.0 1.0
H2'' A:DC8 2.9 0.0 1.0
H3' A:DC8 2.9 0.0 1.0
H5'' A:DG9 3.0 0.0 1.0
C2' A:DC8 3.3 0.0 1.0
H2' A:DC8 3.9 0.0 1.0
H3' A:DG9 3.9 0.0 1.0
C4' A:DC8 4.0 0.0 1.0
C4' A:DG9 4.0 0.0 1.0
H4' A:DC8 4.0 0.0 1.0
H1' A:DC8 4.3 0.0 1.0
O4' A:DG9 4.4 0.0 1.0
C1' A:DC8 4.4 0.0 1.0
C3' A:DG9 4.5 0.0 1.0
H5'' A:DC8 4.5 0.0 1.0
H4' A:DG9 4.8 0.0 1.0
C5' A:DC8 4.9 0.0 1.0
O4' A:DC8 4.9 0.0 1.0

Phosphorus binding site 9 out of 18 in 169d

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Phosphorus binding site 9 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.0
occ:1.00
P A:DC10 0.0 0.0 1.0
OP2 A:DC10 1.5 0.0 1.0
OP1 A:DC10 1.5 0.0 1.0
O5' A:DC10 1.6 0.0 1.0
O3' A:DG9 1.6 0.0 1.0
C5' A:DC10 2.7 0.0 1.0
C3' A:DG9 2.7 0.0 1.0
H5' A:DC10 2.9 0.0 1.0
H2'' A:DG9 2.9 0.0 1.0
H3' A:DG9 3.0 0.0 1.0
H5'' A:DC10 3.0 0.0 1.0
C2' A:DG9 3.2 0.0 1.0
H2' A:DG9 3.5 0.0 1.0
H3' A:DC10 4.0 0.0 1.0
C4' A:DC10 4.0 0.0 1.0
C4' A:DG9 4.0 0.0 1.0
H4' A:DG9 4.2 0.0 1.0
C1' A:DG9 4.5 0.0 1.0
O4' A:DC10 4.6 0.0 1.0
C3' A:DC10 4.6 0.0 1.0
H5'' A:DG9 4.6 0.0 1.0
H1' A:DG9 4.6 0.0 1.0
H4' A:DC10 4.8 0.0 1.0
C5' A:DG9 4.9 0.0 1.0
O4' A:DG9 4.9 0.0 1.0

Phosphorus binding site 10 out of 18 in 169d

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Phosphorus binding site 10 out of 18 in the The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Solution Structure of the R(Gcg)D(Tataccc) :D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:0.0
occ:1.00
P B:C12 0.0 0.0 1.0
OP1 B:C12 1.5 0.0 1.0
OP2 B:C12 1.5 0.0 1.0
O5' B:C12 1.6 0.0 1.0
O3' B:G11 1.6 0.0 1.0
C3' B:G11 2.6 0.0 1.0
C5' B:C12 2.6 0.0 1.0
H3' B:G11 2.8 0.0 1.0
H5' B:C12 2.9 0.0 1.0
H5'' B:C12 2.9 0.0 1.0
HO2' B:G11 3.4 0.0 1.0
H2' B:G11 3.4 0.0 1.0
C2' B:G11 3.5 0.0 1.0
H6 B:C12 3.6 0.0 1.0
O2' B:G11 4.0 0.0 1.0
C4' B:G11 4.0 0.0 1.0
C4' B:C12 4.0 0.0 1.0
H5'' B:G11 4.1 0.0 1.0
H3' B:C12 4.2 0.0 1.0
H4' B:G11 4.2 0.0 1.0
O4' B:C12 4.4 0.0 1.0
C5' B:G11 4.5 0.0 1.0
C3' B:C12 4.6 0.0 1.0
C6 B:C12 4.7 0.0 1.0
O5' B:G11 4.7 0.0 1.0
H4' B:C12 4.8 0.0 1.0
C1' B:G11 4.8 0.0 1.0
O4' B:G11 5.0 0.0 1.0

Reference:

M.Salazar, O.Y.U.Fedoroff, L.Zhu, B.R.Reid. The Solution Structure of the R(Gcg)D(Tataccc):D(Gggtatacgc) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected By A Junction. J.Mol.Biol. V. 241 440 1994.
ISSN: ISSN 0022-2836
PubMed: 8064857
DOI: 10.1006/JMBI.1994.1519
Page generated: Fri Sep 25 11:39:07 2020

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