Phosphorus in PDB 170d: Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement

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 Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement (pdb code 170d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement, PDB code: 170d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 170d

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Phosphorus binding site 1 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:0.4
occ:1.00
P A:DG2 0.0 0.4 1.0
OP1 A:DG2 1.5 0.4 1.0
OP2 A:DG2 1.5 0.4 1.0
O5' A:DG2 1.6 0.4 1.0
O3' A:DC1 1.6 0.4 1.0
C5' A:DG2 2.6 0.4 1.0
C3' A:DC1 2.6 0.4 1.0
H2'' A:DC1 2.8 0.3 1.0
H5' A:DG2 2.8 0.5 1.0
H5'' A:DG2 2.8 0.5 1.0
H3' A:DC1 2.9 0.4 1.0
C2' A:DC1 3.2 0.3 1.0
H2' A:DC1 3.7 0.3 1.0
H8 A:DG2 3.8 0.3 1.0
C4' A:DC1 3.9 0.4 1.0
C4' A:DG2 3.9 0.4 1.0
H4' A:DC1 4.0 0.4 1.0
H2' A:DG2 4.1 0.3 1.0
H3' A:DG2 4.1 0.4 1.0
O4' A:DG2 4.3 0.3 1.0
C1' A:DC1 4.4 0.4 1.0
C3' A:DG2 4.5 0.3 1.0
H5' A:DC1 4.5 0.5 1.0
H1' A:DC1 4.6 0.4 1.0
C2' A:DG2 4.7 0.3 1.0
H4' A:DG2 4.7 0.4 1.0
C5' A:DC1 4.7 0.5 1.0
C8 A:DG2 4.8 0.3 1.0
O4' A:DC1 4.8 0.4 1.0
C1' A:DG2 5.0 0.3 1.0

Phosphorus binding site 2 out of 22 in 170d

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Phosphorus binding site 2 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:0.3
occ:1.00
P A:DC3 0.0 0.3 1.0
OP1 A:DC3 1.5 0.4 1.0
OP2 A:DC3 1.5 0.4 1.0
O3' A:DG2 1.6 0.3 1.0
O5' A:DC3 1.6 0.3 1.0
C5' A:DC3 2.6 0.3 1.0
C3' A:DG2 2.6 0.3 1.0
H5' A:DC3 2.8 0.3 1.0
H3' A:DG2 2.8 0.4 1.0
H2'' A:DG2 2.9 0.3 1.0
H5'' A:DC3 2.9 0.3 1.0
C2' A:DG2 3.3 0.3 1.0
H3' A:DC3 3.8 0.3 1.0
C4' A:DG2 3.9 0.4 1.0
H4' A:DG2 3.9 0.4 1.0
C4' A:DC3 3.9 0.3 1.0
H1' A:DG2 4.0 0.3 1.0
H2' A:DG2 4.0 0.3 1.0
C1' A:DG2 4.2 0.3 1.0
H6 A:DC3 4.3 0.2 1.0
C3' A:DC3 4.4 0.3 1.0
O4' A:DC3 4.4 0.2 1.0
O4' A:DG2 4.7 0.3 1.0
H5'' A:DG2 4.7 0.5 1.0
H2' A:DC3 4.7 0.3 1.0
H4' A:DC3 4.8 0.2 1.0
C5' A:DG2 4.9 0.4 1.0

Phosphorus binding site 3 out of 22 in 170d

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Phosphorus binding site 3 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:0.3
occ:1.00
P A:DG4 0.0 0.3 1.0
OP2 A:DG4 1.5 0.3 1.0
OP1 A:DG4 1.5 0.3 1.0
O5' A:DG4 1.6 0.2 1.0
O3' A:DC3 1.6 0.3 1.0
C3' A:DC3 2.6 0.3 1.0
C5' A:DG4 2.6 0.2 1.0
H5'' A:DG4 2.7 0.2 1.0
H2'' A:DC3 2.8 0.2 1.0
H3' A:DC3 2.8 0.3 1.0
H5' A:DG4 3.0 0.2 1.0
C2' A:DC3 3.2 0.2 1.0
H3' A:DG4 3.4 0.2 1.0
H2' A:DC3 3.8 0.3 1.0
C4' A:DC3 3.9 0.3 1.0
C4' A:DG4 3.9 0.2 1.0
H4' A:DC3 4.0 0.2 1.0
C3' A:DG4 4.1 0.2 1.0
H2' A:DG4 4.2 0.2 1.0
H1' A:DC3 4.3 0.2 1.0
C1' A:DC3 4.3 0.2 1.0
H4' A:DG4 4.7 0.2 1.0
O4' A:DG4 4.7 0.2 1.0
C2' A:DG4 4.7 0.2 1.0
H5'' A:DC3 4.7 0.3 1.0
O4' A:DC3 4.8 0.2 1.0
C5' A:DC3 4.8 0.3 1.0
H8 A:DG4 5.0 0.2 1.0

Phosphorus binding site 4 out of 22 in 170d

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Phosphorus binding site 4 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:0.3
occ:1.00
P A:DA5 0.0 0.3 1.0
OP1 A:DA5 1.5 0.3 1.0
OP2 A:DA5 1.5 0.3 1.0
O5' A:DA5 1.6 0.2 1.0
O3' A:DG4 1.6 0.2 1.0
H2'' A:DG4 2.5 0.2 1.0
C5' A:DA5 2.6 0.2 1.0
C3' A:DG4 2.6 0.2 1.0
H5'' A:DA5 2.8 0.2 1.0
H5' A:DA5 3.0 0.2 1.0
C2' A:DG4 3.0 0.2 1.0
H3' A:DG4 3.0 0.2 1.0
H3' A:DA5 3.5 0.2 1.0
H1' A:DG4 3.5 0.2 1.0
C1' A:DG4 3.8 0.2 1.0
H2' A:DG4 3.9 0.2 1.0
C4' A:DG4 3.9 0.2 1.0
C4' A:DA5 3.9 0.2 1.0
H4' A:DG4 4.0 0.2 1.0
C3' A:DA5 4.2 0.2 1.0
H2' A:DA5 4.5 0.2 1.0
O4' A:DG4 4.5 0.2 1.0
O4' A:DA5 4.5 0.2 1.0
H4' A:DA5 4.7 0.2 1.0
H8 A:DA5 4.9 0.2 1.0
C2' A:DA5 4.9 0.2 1.0

Phosphorus binding site 5 out of 22 in 170d

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Phosphorus binding site 5 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:0.2
occ:1.00
P A:DA6 0.0 0.2 1.0
OP1 A:DA6 1.5 0.2 1.0
OP2 A:DA6 1.5 0.2 1.0
O5' A:DA6 1.6 0.2 1.0
O3' A:DA5 1.6 0.2 1.0
H2'' A:DA5 2.6 0.2 1.0
C5' A:DA6 2.6 0.2 1.0
C3' A:DA5 2.6 0.2 1.0
H5' A:DA6 2.7 0.3 1.0
H3' A:DA5 2.9 0.2 1.0
H5'' A:DA6 3.0 0.3 1.0
C2' A:DA5 3.1 0.2 1.0
H8 A:DA6 3.8 0.2 1.0
H2' A:DA5 3.8 0.2 1.0
H1' A:DA5 3.9 0.2 1.0
C4' A:DA5 3.9 0.2 1.0
C4' A:DA6 3.9 0.2 1.0
H4' A:DA5 4.0 0.2 1.0
H3' A:DA6 4.0 0.2 1.0
C1' A:DA5 4.1 0.2 1.0
O4' A:DA6 4.2 0.2 1.0
H2' A:DA6 4.3 0.2 1.0
C3' A:DA6 4.4 0.2 1.0
O4' A:DA5 4.7 0.2 1.0
C8 A:DA6 4.7 0.2 1.0
H4' A:DA6 4.8 0.2 1.0
C2' A:DA6 4.8 0.2 1.0
C5' A:DA5 5.0 0.2 1.0
H5'' A:DA5 5.0 0.2 1.0

Phosphorus binding site 6 out of 22 in 170d

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Phosphorus binding site 6 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:0.2
occ:1.00
P A:DT7 0.0 0.2 1.0
OP1 A:DT7 1.5 0.2 1.0
OP2 A:DT7 1.5 0.2 1.0
O5' A:DT7 1.6 0.2 1.0
O3' A:DA6 1.6 0.2 1.0
C5' A:DT7 2.6 0.2 1.0
C3' A:DA6 2.6 0.2 1.0
H2'' A:DA6 2.7 0.2 1.0
H5'' A:DT7 2.8 0.2 1.0
H5' A:DT7 2.8 0.2 1.0
H3' A:DA6 2.9 0.2 1.0
C2' A:DA6 3.2 0.2 1.0
H3' A:DT7 3.6 0.2 1.0
H2' A:DA6 3.9 0.2 1.0
C4' A:DA6 3.9 0.2 1.0
C4' A:DT7 3.9 0.2 1.0
H4' A:DA6 4.0 0.2 1.0
H1' A:DA6 4.1 0.2 1.0
C1' A:DA6 4.2 0.2 1.0
C3' A:DT7 4.2 0.2 1.0
H2' A:DT7 4.3 0.2 1.0
H6 A:DT7 4.4 0.2 1.0
O4' A:DT7 4.6 0.2 1.0
H4' A:DT7 4.7 0.2 1.0
O4' A:DA6 4.7 0.2 1.0
C2' A:DT7 4.8 0.1 1.0
H5'' A:DA6 4.8 0.3 1.0
C5' A:DA6 4.9 0.2 1.0

Phosphorus binding site 7 out of 22 in 170d

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Phosphorus binding site 7 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:0.1
occ:1.00
P A:DT8 0.0 0.1 1.0
OP2 A:DT8 1.5 0.2 1.0
OP1 A:DT8 1.5 0.2 1.0
O5' A:DT8 1.6 0.1 1.0
O3' A:DT7 1.6 0.2 1.0
C5' A:DT8 2.6 0.1 1.0
C3' A:DT7 2.6 0.2 1.0
H2'' A:DT7 2.7 0.1 1.0
H5'' A:DT8 2.8 0.1 1.0
H3' A:DT7 2.9 0.2 1.0
H5' A:DT8 2.9 0.1 1.0
C2' A:DT7 3.1 0.1 1.0
H3' A:DT8 3.8 0.1 1.0
H2' A:DT7 3.9 0.2 1.0
H1' A:DT7 3.9 0.2 1.0
C4' A:DT7 3.9 0.2 1.0
C4' A:DT8 3.9 0.1 1.0
H4' A:DT7 4.0 0.2 1.0
C1' A:DT7 4.1 0.2 1.0
H6 A:DT8 4.3 0.1 1.0
O4' A:DT8 4.3 0.1 1.0
C3' A:DT8 4.4 0.1 1.0
H2' A:DT8 4.5 0.1 1.0
O4' A:DT7 4.7 0.2 1.0
H4' A:DT8 4.8 0.1 1.0
C2' A:DT8 4.9 0.1 1.0
C5' A:DT7 5.0 0.2 1.0

Phosphorus binding site 8 out of 22 in 170d

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Phosphorus binding site 8 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:0.1
occ:1.00
P A:CAR9 0.0 0.1 1.0
OP2 A:CAR9 1.5 0.1 1.0
OP1 A:CAR9 1.5 0.2 1.0
O3' A:DT8 1.6 0.1 1.0
O5' A:CAR9 1.6 0.2 1.0
H2'' A:DT8 2.5 0.1 1.0
C5' A:CAR9 2.6 0.2 1.0
C3' A:DT8 2.7 0.1 1.0
H5'' A:CAR9 2.8 0.2 1.0
H5' A:CAR9 2.9 0.2 1.0
C2' A:DT8 3.0 0.1 1.0
H3' A:DT8 3.0 0.1 1.0
H1' A:DT8 3.8 0.1 1.0
H3' A:CAR9 3.8 0.2 1.0
H2' A:DT8 3.8 0.1 1.0
C4' A:DT8 3.9 0.1 1.0
H4' A:DT8 4.0 0.1 1.0
C4' A:CAR9 4.0 0.2 1.0
C1' A:DT8 4.0 0.1 1.0
H6 A:CAR9 4.2 0.1 1.0
O4' A:CAR9 4.4 0.2 1.0
C3' A:CAR9 4.4 0.2 1.0
O4' A:DT8 4.6 0.1 1.0
H4' A:CAR9 4.8 0.2 1.0
H5'' A:DT8 4.9 0.1 1.0

Phosphorus binding site 9 out of 22 in 170d

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Phosphorus binding site 9 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:0.2
occ:1.00
P A:DG10 0.0 0.2 1.0
OP1 A:DG10 1.5 0.3 1.0
OP2 A:DG10 1.5 0.2 1.0
O3' A:CAR9 1.6 0.2 1.0
O5' A:DG10 1.6 0.2 1.0
C3' A:CAR9 2.6 0.2 1.0
C5' A:DG10 2.6 0.2 1.0
HO2' A:CAR9 2.7 0.2 1.0
H5'' A:DG10 2.8 0.2 1.0
H3' A:CAR9 2.8 0.2 1.0
H5' A:DG10 2.9 0.2 1.0
H2' A:CAR9 3.0 0.2 1.0
C2' A:CAR9 3.1 0.2 1.0
O2' A:CAR9 3.4 0.2 1.0
H8 A:DG10 3.6 0.1 1.0
C4' A:CAR9 3.9 0.2 1.0
C4' A:DG10 3.9 0.2 1.0
H4' A:CAR9 4.1 0.2 1.0
H2' A:DG10 4.2 0.1 1.0
O4' A:DG10 4.2 0.1 1.0
H3' A:DG10 4.2 0.2 1.0
H5'' A:CAR9 4.3 0.2 1.0
C3' A:DG10 4.5 0.2 1.0
C8 A:DG10 4.6 0.1 1.0
C1' A:CAR9 4.6 0.1 1.0
C5' A:CAR9 4.6 0.2 1.0
H4' A:DG10 4.7 0.2 1.0
C2' A:DG10 4.8 0.1 1.0
O4' A:CAR9 4.9 0.2 1.0
C1' A:DG10 5.0 0.1 1.0

Phosphorus binding site 10 out of 22 in 170d

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Phosphorus binding site 10 out of 22 in the Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Solution Structure of A Dna Dodecamer Containing the Anti- Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics and Full Relaxation Matrix Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:0.2
occ:1.00
P A:DC11 0.0 0.2 1.0
OP2 A:DC11 1.5 0.2 1.0
OP1 A:DC11 1.5 0.2 1.0
O3' A:DG10 1.6 0.2 1.0
O5' A:DC11 1.6 0.1 1.0
H2'' A:DG10 2.6 0.1 1.0
C3' A:DG10 2.6 0.2 1.0
C5' A:DC11 2.6 0.1 1.0
H5'' A:DC11 2.7 0.1 1.0
H3' A:DG10 2.9 0.2 1.0
H5' A:DC11 3.0 0.1 1.0
C2' A:DG10 3.1 0.1 1.0
H3' A:DC11 3.6 0.1 1.0
H1' A:DG10 3.8 0.1 1.0
H2' A:DG10 3.9 0.1 1.0
C4' A:DG10 3.9 0.2 1.0
C4' A:DC11 3.9 0.1 1.0
H4' A:DG10 4.0 0.2 1.0
C1' A:DG10 4.0 0.1 1.0
C3' A:DC11 4.3 0.1 1.0
H6 A:DC11 4.4 0.1 1.0
O4' A:DC11 4.4 0.1 1.0
H2' A:DC11 4.5 0.1 1.0
O4' A:DG10 4.6 0.1 1.0
H4' A:DC11 4.8 0.1 1.0
H5'' A:DG10 4.8 0.2 1.0
C2' A:DC11 4.9 0.1 1.0

Reference:

B.I.Schweitzer, T.Mikita, G.W.Kellogg, K.H.Gardner, G.P.Beardsley. Solution Structure of A Dna Dodecamer Containing the Anti-Neoplastic Agent Arabinosylcytosine: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Matrix Refinement. Biochemistry V. 33 11460 1994.
ISSN: ISSN 0006-2960
PubMed: 7918360
DOI: 10.1021/BI00204A008
Page generated: Fri Sep 25 11:39:53 2020

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