Phosphorus in PDB 1ac9: Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures

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

Binding sites:

The binding sites of Phosphorus atom in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures (pdb code 1ac9). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures, PDB code: 1ac9:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P2 b:0.9 occ:1.00 P A:DT2 0.0 0.9 1.0 OP1 A:DT2 1.5 1.1 1.0 OP2 A:DT2 1.5 1.0 1.0 O3' A:DC1 1.6 0.9 1.0 O5' A:DT2 1.6 0.8 1.0 C5' A:DT2 2.6 0.8 1.0 C3' A:DC1 2.7 0.9 1.0 H2'' A:DC1 2.7 0.8 1.0 H5' A:DT2 2.9 0.9 1.0 H5'' A:DT2 2.9 1.0 1.0 H3' A:DC1 3.0 1.0 1.0 C2' A:DC1 3.1 0.8 1.0 H2' A:DC1 3.5 0.8 1.0 H6 A:DT2 3.9 0.7 1.0 C4' A:DC1 4.0 1.0 1.0 C4' A:DT2 4.0 0.8 1.0 H3' A:DT2 4.0 0.8 1.0 H4' A:DC1 4.0 1.1 1.0 H2' A:DT2 4.3 0.7 1.0 O4' A:DT2 4.4 0.7 1.0 C1' A:DC1 4.4 0.8 1.0 C3' A:DT2 4.5 0.8 1.0 H5'' A:DC1 4.5 1.2 1.0 H1' A:DC1 4.6 0.8 1.0 H4' A:DT2 4.8 0.8 1.0 C5' A:DC1 4.8 1.2 1.0 C2' A:DT2 4.9 0.7 1.0 O4' A:DC1 4.9 0.9 1.0 C6 A:DT2 5.0 0.6 1.0

Phosphorus binding site 2 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P3 b:0.9 occ:1.00 P A:DG3 0.0 0.9 1.0 OP1 A:DG3 1.5 1.0 1.0 OP2 A:DG3 1.5 0.9 1.0 O3' A:DT2 1.6 0.8 1.0 O5' A:DG3 1.6 0.7 1.0 C5' A:DG3 2.6 0.7 1.0 C3' A:DT2 2.7 0.8 1.0 H2'' A:DT2 2.7 0.7 1.0 H5'' A:DG3 2.8 0.8 1.0 H3' A:DT2 2.9 0.8 1.0 H5' A:DG3 3.0 0.7 1.0 C2' A:DT2 3.2 0.7 1.0 H3' A:DG3 3.8 0.7 1.0 H1' A:DT2 3.9 0.6 1.0 C4' A:DT2 4.0 0.8 1.0 C4' A:DG3 4.0 0.6 1.0 H2' A:DT2 4.0 0.7 1.0 H4' A:DT2 4.0 0.8 1.0 C1' A:DT2 4.2 0.6 1.0 H2' A:DG3 4.3 0.7 1.0 C3' A:DG3 4.4 0.6 1.0 H8 A:DG3 4.5 0.6 1.0 O4' A:DG3 4.5 0.5 1.0 O4' A:DT2 4.7 0.7 1.0 H4' A:DG3 4.8 0.6 1.0 H5'' A:DT2 4.8 1.0 1.0 C2' A:DG3 4.9 0.6 1.0

Phosphorus binding site 3 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P4 b:0.8 occ:1.00 P A:LGP4 0.0 0.8 1.0 OP1 A:LGP4 1.5 0.9 1.0 OP2 A:LGP4 1.5 0.9 1.0 O3' A:DG3 1.6 0.7 1.0 O5' A:LGP4 1.6 0.8 1.0 H2'' A:DG3 2.6 0.7 1.0 C3' A:DG3 2.7 0.6 1.0 C5' A:LGP4 2.7 0.7 1.0 H5'' A:LGP4 2.7 0.7 1.0 H3' A:DG3 2.9 0.7 1.0 C2' A:DG3 3.1 0.6 1.0 H5' A:LGP4 3.2 0.8 1.0 H1'1 A:LGP4 3.7 0.5 1.0 H2' A:DG3 3.9 0.7 1.0 H1' A:DG3 3.9 0.5 1.0 C4' A:LGP4 3.9 0.5 1.0 C4' A:DG3 4.0 0.6 1.0 H4' A:DG3 4.1 0.6 1.0 C1' A:DG3 4.1 0.5 1.0 O4' A:LGP4 4.1 0.5 1.0 C1' A:LGP4 4.4 0.4 1.0 O3' A:LGP4 4.5 0.6 1.0 C3' A:LGP4 4.6 0.6 1.0 H3'1 A:LGP4 4.7 0.7 1.0 O4' A:DG3 4.7 0.5 1.0 H8 A:LGP4 4.7 0.5 1.0 H4' A:LGP4 4.7 0.5 1.0 H5'' A:DG3 5.0 0.8 1.0

Phosphorus binding site 4 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P5 b:0.7 occ:1.00 P A:DA5 0.0 0.7 1.0 OP1 A:DA5 1.5 0.9 1.0 OP2 A:DA5 1.5 0.8 1.0 O3' A:LGP4 1.6 0.6 1.0 O5' A:DA5 1.6 0.6 1.0 C3' A:LGP4 2.6 0.6 1.0 H3'2 A:LGP4 2.7 0.6 1.0 C5' A:DA5 2.7 0.6 1.0 H5' A:DA5 2.8 0.6 1.0 H5'' A:LGP4 3.0 0.7 1.0 H5'' A:DA5 3.1 0.6 1.0 H3'1 A:LGP4 3.5 0.7 1.0 C4' A:LGP4 3.5 0.5 1.0 H4' A:LGP4 3.6 0.5 1.0 H3' A:DA5 3.6 0.5 1.0 C5' A:LGP4 3.7 0.7 1.0 C4' A:DA5 4.0 0.5 1.0 H5' A:LGP4 4.0 0.8 1.0 C3' A:DA5 4.2 0.5 1.0 O4' A:DA5 4.7 0.5 1.0 H4' A:DA5 4.7 0.5 1.0 O3' A:DA5 4.8 0.5 1.0 O4' A:LGP4 4.8 0.5 1.0 H8 A:DA5 5.0 0.4 1.0 O5' A:LGP4 5.0 0.8 1.0

Phosphorus binding site 5 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P6 b:0.6 occ:1.00 P A:DT6 0.0 0.6 1.0 OP1 A:DT6 1.5 0.7 1.0 OP2 A:DT6 1.5 0.7 1.0 O5' A:DT6 1.6 0.5 1.0 O3' A:DA5 1.6 0.5 1.0 C5' A:DT6 2.7 0.5 1.0 C3' A:DA5 2.7 0.5 1.0 H2'' A:DA5 2.8 0.5 1.0 H5'' A:DT6 2.8 0.5 1.0 H5' A:DT6 3.0 0.5 1.0 H3' A:DA5 3.1 0.5 1.0 C2' A:DA5 3.1 0.4 1.0 H2' A:DA5 3.2 0.5 1.0 H6 A:DT6 3.3 0.4 1.0 C4' A:DA5 4.0 0.5 1.0 C4' A:DT6 4.0 0.4 1.0 H3' A:DT6 4.0 0.5 1.0 H4' A:DA5 4.0 0.5 1.0 H2' A:DT6 4.1 0.5 1.0 H72 A:DT6 4.1 0.6 1.0 C6 A:DT6 4.3 0.4 1.0 O4' A:DT6 4.4 0.4 1.0 H71 A:DT6 4.4 0.6 1.0 C3' A:DT6 4.5 0.5 1.0 C1' A:DA5 4.5 0.4 1.0 O5' A:DA5 4.5 0.6 1.0 C7 A:DT6 4.7 0.5 1.0 C2' A:DT6 4.7 0.5 1.0 C5' A:DA5 4.8 0.6 1.0 H4' A:DT6 4.8 0.5 1.0 H1' A:DA5 4.9 0.4 1.0 O4' A:DA5 4.9 0.5 1.0 H5'' A:DA5 5.0 0.6 1.0

Phosphorus binding site 6 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P7 b:0.6 occ:1.00 P A:DC7 0.0 0.6 1.0 OP2 A:DC7 1.5 0.7 1.0 OP1 A:DC7 1.5 0.8 1.0 O5' A:DC7 1.6 0.5 1.0 O3' A:DT6 1.6 0.5 1.0 C5' A:DC7 2.6 0.6 1.0 C3' A:DT6 2.7 0.5 1.0 H2'' A:DT6 2.7 0.5 1.0 H5' A:DC7 2.9 0.6 1.0 H5'' A:DC7 2.9 0.7 1.0 H3' A:DT6 2.9 0.5 1.0 C2' A:DT6 3.2 0.5 1.0 H6 A:DC7 3.8 0.4 1.0 H2' A:DT6 4.0 0.5 1.0 C4' A:DC7 4.0 0.5 1.0 C4' A:DT6 4.0 0.4 1.0 H1' A:DT6 4.0 0.5 1.0 H4' A:DT6 4.0 0.5 1.0 H3' A:DC7 4.1 0.5 1.0 C1' A:DT6 4.2 0.4 1.0 H2' A:DC7 4.2 0.4 1.0 O4' A:DC7 4.4 0.5 1.0 C3' A:DC7 4.5 0.5 1.0 C6 A:DC7 4.7 0.3 1.0 O4' A:DT6 4.7 0.4 1.0 H4' A:DC7 4.8 0.6 1.0 C2' A:DC7 4.8 0.4 1.0 H5'' A:DT6 4.9 0.5 1.0

Phosphorus binding site 7 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P8 b:0.5 occ:1.00 P A:DC8 0.0 0.5 1.0 OP1 A:DC8 1.5 0.7 1.0 OP2 A:DC8 1.5 0.6 1.0 O5' A:DC8 1.6 0.5 1.0 O3' A:DC7 1.6 0.5 1.0 C5' A:DC8 2.6 0.5 1.0 C3' A:DC7 2.7 0.5 1.0 H2'' A:DC7 2.7 0.4 1.0 H5'' A:DC8 2.8 0.6 1.0 H5' A:DC8 2.9 0.6 1.0 H3' A:DC7 2.9 0.5 1.0 C2' A:DC7 3.2 0.4 1.0 H6 A:DC8 3.5 0.3 1.0 H2' A:DC7 4.0 0.4 1.0 C4' A:DC7 4.0 0.5 1.0 C4' A:DC8 4.0 0.5 1.0 H3' A:DC8 4.0 0.5 1.0 H1' A:DC7 4.0 0.4 1.0 H4' A:DC7 4.0 0.6 1.0 H2' A:DC8 4.0 0.4 1.0 C1' A:DC7 4.2 0.4 1.0 O4' A:DC8 4.4 0.4 1.0 C3' A:DC8 4.4 0.4 1.0 C6 A:DC8 4.5 0.3 1.0 C2' A:DC8 4.7 0.4 1.0 O4' A:DC7 4.7 0.5 1.0 H4' A:DC8 4.8 0.5 1.0 H5'' A:DC7 4.8 0.7 1.0

Phosphorus binding site 8 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P9 b:0.6 occ:1.00 P A:DA9 0.0 0.6 1.0 OP2 A:DA9 1.5 0.6 1.0 OP1 A:DA9 1.5 0.7 1.0 O3' A:DC8 1.6 0.5 1.0 O5' A:DA9 1.6 0.5 1.0 H2'' A:DC8 2.6 0.4 1.0 C5' A:DA9 2.7 0.5 1.0 C3' A:DC8 2.7 0.4 1.0 H5'' A:DA9 2.7 0.6 1.0 H3' A:DC8 3.0 0.5 1.0 C2' A:DC8 3.1 0.4 1.0 H5' A:DA9 3.1 0.5 1.0 H3' A:DA9 3.4 0.6 1.0 H1' A:DC8 3.8 0.4 1.0 C4' A:DA9 3.9 0.5 1.0 H2' A:DC8 3.9 0.4 1.0 C4' A:DC8 4.0 0.5 1.0 C1' A:DC8 4.0 0.3 1.0 H4' A:DC8 4.1 0.5 1.0 H2' A:DA9 4.1 0.5 1.0 C3' A:DA9 4.1 0.5 1.0 H8 A:DA9 4.5 0.4 1.0 O4' A:DC8 4.6 0.4 1.0 O4' A:DA9 4.6 0.4 1.0 C2' A:DA9 4.7 0.5 1.0 H4' A:DA9 4.7 0.5 1.0

Phosphorus binding site 9 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:P10 b:0.6 occ:1.00 P A:DG10 0.0 0.6 1.0 OP1 A:DG10 1.5 0.8 1.0 OP2 A:DG10 1.5 0.8 1.0 O5' A:DG10 1.6 0.7 1.0 O3' A:DA9 1.6 0.6 1.0 C5' A:DG10 2.6 0.8 1.0 C3' A:DA9 2.7 0.5 1.0 H2'' A:DA9 2.8 0.5 1.0 H5' A:DG10 2.8 0.8 1.0 H3' A:DA9 2.9 0.6 1.0 H5'' A:DG10 2.9 0.8 1.0 C2' A:DA9 3.2 0.5 1.0 H3' A:DG10 3.8 1.0 1.0 C4' A:DG10 4.0 0.9 1.0 C4' A:DA9 4.0 0.5 1.0 H2' A:DA9 4.0 0.5 1.0 H4' A:DA9 4.0 0.5 1.0 H1' A:DA9 4.1 0.4 1.0 C1' A:DA9 4.2 0.4 1.0 O4' A:DG10 4.3 0.8 1.0 C3' A:DG10 4.4 1.1 1.0 H8 A:DG10 4.5 0.8 1.0 O4' A:DA9 4.7 0.4 1.0 H4' A:DG10 4.8 1.1 1.0 H5'' A:DA9 4.9 0.6 1.0 C5' A:DA9 5.0 0.5 1.0

Phosphorus binding site 10 out of 18 in the Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures


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 Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Refinement, 6 Structures within 5.0Å range: probe atom residue distance (Å) B Occ B:P12 b:0.7 occ:1.00 P B:DT12 0.0 0.7 1.0 OP1 B:DT12 1.5 0.9 1.0 OP2 B:DT12 1.5 0.8 1.0 O3' B:DC11 1.6 0.8 1.0 O5' B:DT12 1.6 0.7 1.0 C5' B:DT12 2.6 0.7 1.0 C3' B:DC11 2.7 0.7 1.0 H2'' B:DC11 2.7 0.7 1.0 H5' B:DT12 2.9 0.7 1.0 H5'' B:DT12 2.9 0.7 1.0 H3' B:DC11 3.0 0.8 1.0 C2' B:DC11 3.1 0.6 1.0 H2' B:DC11 3.5 0.7 1.0 H6 B:DT12 3.9 0.6 1.0 C4' B:DC11 4.0 0.8 1.0 C4' B:DT12 4.0 0.6 1.0 H3' B:DT12 4.0 0.7 1.0 H4' B:DC11 4.0 0.9 1.0 H2' B:DT12 4.3 0.6 1.0 O4' B:DT12 4.4 0.6 1.0 C1' B:DC11 4.4 0.7 1.0 C3' B:DT12 4.5 0.6 1.0 H5'' B:DC11 4.5 1.0 1.0 H1' B:DC11 4.6 0.7 1.0 H4' B:DT12 4.8 0.7 1.0 C5' B:DC11 4.8 1.0 1.0 C2' B:DT12 4.9 0.6 1.0 O4' B:DC11 4.9 0.8 1.0 C6 B:DT12 5.0 0.5 1.0

M.Foti, S.Marshalko, E.Schurter, S.Kumar, G.P.Beardsley, B.I.Schweitzer. Solution Structure of A Dna Decamer Containing the Antiviral Drug Ganciclovir: Combined Use of uc(Nmr), Restrained Molecular Dynamics, and Full Relaxation Matrix Refinement. Biochemistry V. 36 5336 1997.
ISSN: ISSN 0006-2960
PubMed: 9154915
DOI: 10.1021/BI962604E