Phosphorus in PDB 1a9h: Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure

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

Binding sites:

The binding sites of Phosphorus atom in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure (pdb code 1a9h). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure, PDB code: 1a9h:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure 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 OP2 A:DG2 1.3 0.0 1.0 OP1 A:DG2 1.3 0.0 1.0 O5' A:DG2 1.5 0.0 1.0 O3' A:DC1 1.6 0.0 1.0 C5' A:DG2 2.5 0.0 1.0 H5' A:DG2 2.6 0.0 1.0 C3' A:DC1 2.7 0.0 1.0 H5'' A:DG2 2.8 0.0 1.0 H2'' A:DC1 2.8 0.0 1.0 H3' A:DC1 2.9 0.0 1.0 C2' A:DC1 3.2 0.0 1.0 H8 A:DG2 3.5 0.0 1.0 H2' A:DG2 3.6 0.0 1.0 H1' A:DC1 3.7 0.0 1.0 C4' A:DG2 3.7 0.0 1.0 H4' A:DC1 3.8 0.0 1.0 C4' A:DC1 3.9 0.0 1.0 C1' A:DC1 4.0 0.0 1.0 H2' A:DC1 4.1 0.0 1.0 H3' A:DG2 4.1 0.0 1.0 O4' A:DG2 4.1 0.0 1.0 C3' A:DG2 4.3 0.0 1.0 C2' A:DG2 4.4 0.0 1.0 H4' A:DG2 4.4 0.0 1.0 C8 A:DG2 4.5 0.0 1.0 O4' A:DC1 4.6 0.0 1.0 C1' A:DG2 4.8 0.0 1.0 H5'' A:DC1 4.8 0.0 1.0 C5' A:DC1 5.0 0.0 1.0

Phosphorus binding site 2 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:P3 b:0.0 occ:1.00 P A:DC3 0.0 0.0 1.0 OP2 A:DC3 1.3 0.0 1.0 OP1 A:DC3 1.4 0.0 1.0 O5' A:DC3 1.5 0.0 1.0 O3' A:DG2 1.6 0.0 1.0 C5' A:DC3 2.5 0.0 1.0 H5'' A:DC3 2.6 0.0 1.0 C3' A:DG2 2.6 0.0 1.0 H2'' A:DG2 2.8 0.0 1.0 H5' A:DC3 2.9 0.0 1.0 H3' A:DG2 3.0 0.0 1.0 C2' A:DG2 3.2 0.0 1.0 H1' A:DG2 3.3 0.0 1.0 H3' A:DC3 3.6 0.0 1.0 H2' A:DC3 3.6 0.0 1.0 C4' A:DC3 3.7 0.0 1.0 H6 A:DC3 3.8 0.0 1.0 C1' A:DG2 3.8 0.0 1.0 H4' A:DG2 3.8 0.0 1.0 C4' A:DG2 3.9 0.0 1.0 C3' A:DC3 4.1 0.0 1.0 H2' A:DG2 4.1 0.0 1.0 O4' A:DC3 4.3 0.0 1.0 O4' A:DG2 4.4 0.0 1.0 H4' A:DC3 4.4 0.0 1.0 C2' A:DC3 4.4 0.0 1.0 C6 A:DC3 4.7 0.0 1.0 C1' A:DC3 5.0 0.0 1.0

Phosphorus binding site 3 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:P4 b:0.0 occ:1.00 P A:DG4 0.0 0.0 1.0 OP1 A:DG4 1.4 0.0 1.0 OP2 A:DG4 1.4 0.0 1.0 O3' A:DC3 1.5 0.0 1.0 O5' A:DG4 1.6 0.0 1.0 C5' A:DG4 2.6 0.0 1.0 C3' A:DC3 2.6 0.0 1.0 H5'' A:DG4 2.8 0.0 1.0 H2'' A:DC3 2.9 0.0 1.0 H5' A:DG4 2.9 0.0 1.0 H3' A:DC3 3.0 0.0 1.0 C2' A:DC3 3.3 0.0 1.0 H1' A:DC3 3.7 0.0 1.0 H4' A:DC3 3.7 0.0 1.0 H2' A:DG4 3.7 0.0 1.0 C4' A:DC3 3.8 0.0 1.0 C4' A:DG4 4.0 0.0 1.0 H3' A:DG4 4.0 0.0 1.0 C1' A:DC3 4.1 0.0 1.0 H2' A:DC3 4.2 0.0 1.0 H8 A:DG4 4.4 0.0 1.0 C3' A:DG4 4.4 0.0 1.0 O4' A:DG4 4.5 0.0 1.0 O4' A:DC3 4.5 0.0 1.0 C2' A:DG4 4.6 0.0 1.0 H4' A:DG4 4.8 0.0 1.0 H5'' A:DC3 4.8 0.0 1.0 C5' A:DC3 4.9 0.0 1.0

Phosphorus binding site 4 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure 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 1.4 0.0 1.0 OP1 A:DA5 1.4 0.0 1.0 O5' A:DA5 1.6 0.0 1.0 O3' A:DG4 1.6 0.0 1.0 C5' A:DA5 2.6 0.0 1.0 C3' A:DG4 2.7 0.0 1.0 H5' A:DA5 2.7 0.0 1.0 H3' A:DG4 2.8 0.0 1.0 H5'' A:DA5 3.0 0.0 1.0 H2'' A:DG4 3.1 0.0 1.0 H8 A:DA5 3.3 0.0 1.0 C2' A:DG4 3.4 0.0 1.0 H2' A:DA5 3.7 0.0 1.0 H1' A:DG4 3.8 0.0 1.0 C4' A:DA5 3.9 0.0 1.0 C4' A:DG4 4.0 0.0 1.0 H4' A:DG4 4.0 0.0 1.0 O4' A:DA5 4.1 0.0 1.0 C1' A:DG4 4.1 0.0 1.0 C8 A:DA5 4.2 0.0 1.0 H2' A:DG4 4.2 0.0 1.0 C2' A:DA5 4.5 0.0 1.0 H3' A:DA5 4.6 0.0 1.0 C3' A:DA5 4.6 0.0 1.0 H4' A:DA5 4.7 0.0 1.0 O4' A:DG4 4.7 0.0 1.0 C1' A:DA5 4.8 0.0 1.0 N9 A:DA5 4.8 0.0 1.0 H5'' A:DG4 5.0 0.0 1.0

Phosphorus binding site 5 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:P6 b:0.0 occ:1.00 P A:AAB6 0.0 0.0 1.0 O1P A:AAB6 1.4 0.0 1.0 O2P A:AAB6 1.5 0.0 1.0 O5' A:AAB6 1.6 0.0 1.0 O3' A:DA5 1.6 0.0 1.0 C5' A:AAB6 2.6 0.0 1.0 H5'2 A:AAB6 2.7 0.0 1.0 C3' A:DA5 2.7 0.0 1.0 H2'' A:DA5 2.9 0.0 1.0 H5'1 A:AAB6 3.0 0.0 1.0 H1' A:DA5 3.1 0.0 1.0 H3' A:DA5 3.1 0.0 1.0 C2' A:DA5 3.2 0.0 1.0 C1' A:DA5 3.6 0.0 1.0 H2'2 A:AAB6 3.6 0.0 1.0 H3' A:AAB6 3.7 0.0 1.0 C4' A:AAB6 3.9 0.0 1.0 C4' A:DA5 3.9 0.0 1.0 H4' A:DA5 3.9 0.0 1.0 C3' A:AAB6 4.1 0.0 1.0 H2' A:DA5 4.2 0.0 1.0 O4' A:DA5 4.2 0.0 1.0 H62 A:DA7 4.3 0.0 1.0 C2' A:AAB6 4.3 0.0 1.0 N6 A:DA7 4.5 0.0 1.0 O4' A:AAB6 4.6 0.0 1.0 H4' A:AAB6 4.6 0.0 1.0 H61 A:DA7 4.7 0.0 1.0 N9 A:DA5 4.9 0.0 1.0 H2'1 A:AAB6 4.9 0.0 1.0

Phosphorus binding site 6 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure 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 O3' A:AAB6 1.6 0.0 1.0 O5' A:DA7 1.6 0.0 1.0 C5' A:DA7 2.7 0.0 1.0 C3' A:AAB6 2.7 0.0 1.0 H5' A:DA7 2.7 0.0 1.0 H8 A:DA7 2.8 0.0 1.0 H3' A:AAB6 2.8 0.0 1.0 H5'' A:DA7 3.2 0.0 1.0 H4' A:AAB6 3.4 0.0 1.0 H2' A:DA7 3.4 0.0 1.0 C8 A:DA7 3.5 0.0 1.0 C4' A:AAB6 3.7 0.0 1.0 H1' A:AAB6 3.7 0.0 1.0 C2' A:AAB6 3.7 0.0 1.0 H2'1 A:AAB6 3.8 0.0 1.0 C4' A:DA7 3.8 0.0 1.0 O4' A:DA7 4.0 0.0 1.0 N9 A:DA7 4.1 0.0 1.0 C1' A:AAB6 4.2 0.0 1.0 N7 A:DA7 4.2 0.0 1.0 C2' A:DA7 4.2 0.0 1.0 C1' A:DA7 4.4 0.0 1.0 O4' A:AAB6 4.4 0.0 1.0 C3' A:DA7 4.5 0.0 1.0 H3' A:DA7 4.5 0.0 1.0 H5'2 A:AAB6 4.6 0.0 1.0 H4' A:DA7 4.7 0.0 1.0 H2'2 A:AAB6 4.7 0.0 1.0 C5' A:AAB6 4.8 0.0 1.0

Phosphorus binding site 7 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure 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 OP1 A:DC8 1.4 0.0 1.0 OP2 A:DC8 1.5 0.0 1.0 O3' A:DA7 1.6 0.0 1.0 O5' A:DC8 1.6 0.0 1.0 C5' A:DC8 2.6 0.0 1.0 C3' A:DA7 2.6 0.0 1.0 H5' A:DC8 2.8 0.0 1.0 H5'' A:DC8 2.8 0.0 1.0 H3' A:DA7 2.9 0.0 1.0 H2'' A:DA7 2.9 0.0 1.0 C2' A:DA7 3.3 0.0 1.0 H1' A:DA7 3.8 0.0 1.0 C4' A:DA7 3.9 0.0 1.0 H3' A:DC8 3.9 0.0 1.0 H4' A:DA7 3.9 0.0 1.0 C4' A:DC8 4.0 0.0 1.0 C1' A:DA7 4.0 0.0 1.0 H2' A:DA7 4.1 0.0 1.0 H2' A:DC8 4.4 0.0 1.0 O4' A:DA7 4.4 0.0 1.0 C3' A:DC8 4.5 0.0 1.0 O4' A:DC8 4.5 0.0 1.0 H4' A:DC8 4.7 0.0 1.0

Phosphorus binding site 8 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure 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 OP2 A:DG9 1.4 0.0 1.0 OP1 A:DG9 1.4 0.0 1.0 O3' A:DC8 1.5 0.0 1.0 O5' A:DG9 1.6 0.0 1.0 C5' A:DG9 2.6 0.0 1.0 C3' A:DC8 2.6 0.0 1.0 H5'' A:DG9 2.7 0.0 1.0 H2'' A:DC8 2.7 0.0 1.0 H5' A:DG9 2.9 0.0 1.0 H3' A:DC8 3.0 0.0 1.0 C2' A:DC8 3.1 0.0 1.0 H1' A:DC8 3.5 0.0 1.0 H3' A:DG9 3.7 0.0 1.0 H2' A:DG9 3.7 0.0 1.0 H4' A:DC8 3.8 0.0 1.0 C4' A:DC8 3.8 0.0 1.0 C4' A:DG9 3.9 0.0 1.0 C1' A:DC8 3.9 0.0 1.0 H2' A:DC8 3.9 0.0 1.0 C3' A:DG9 4.2 0.0 1.0 O4' A:DC8 4.5 0.0 1.0 O4' A:DG9 4.5 0.0 1.0 C2' A:DG9 4.5 0.0 1.0 H4' A:DG9 4.6 0.0 1.0 H5'' A:DC8 4.9 0.0 1.0 H8 A:DG9 4.9 0.0 1.0 C5' A:DC8 4.9 0.0 1.0

Phosphorus binding site 9 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure 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 1.4 0.0 1.0 OP1 A:DC10 1.4 0.0 1.0 O5' A:DC10 1.5 0.0 1.0 O3' A:DG9 1.6 0.0 1.0 C5' A:DC10 2.5 0.0 1.0 H5' A:DC10 2.5 0.0 1.0 C3' A:DG9 2.6 0.0 1.0 H5'' A:DC10 2.7 0.0 1.0 H2'' A:DG9 2.8 0.0 1.0 H3' A:DG9 2.9 0.0 1.0 H6 A:DC10 3.0 0.0 1.0 C2' A:DG9 3.2 0.0 1.0 H1' A:DG9 3.3 0.0 1.0 H2' A:DC10 3.5 0.0 1.0 C1' A:DG9 3.8 0.0 1.0 C4' A:DC10 3.9 0.0 1.0 C4' A:DG9 3.9 0.0 1.0 H4' A:DG9 3.9 0.0 1.0 C6 A:DC10 4.0 0.0 1.0 H2' A:DG9 4.1 0.0 1.0 H3' A:DC10 4.2 0.0 1.0 O4' A:DC10 4.2 0.0 1.0 C2' A:DC10 4.3 0.0 1.0 C3' A:DC10 4.4 0.0 1.0 O4' A:DG9 4.4 0.0 1.0 H5 A:DC10 4.6 0.0 1.0 H4' A:DC10 4.6 0.0 1.0 C1' A:DC10 4.7 0.0 1.0 C5 A:DC10 4.7 0.0 1.0 N1 A:DC10 4.8 0.0 1.0 N9 A:DG9 4.9 0.0 1.0 H5'' A:DG9 4.9 0.0 1.0 C5' A:DG9 5.0 0.0 1.0

Phosphorus binding site 10 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Apurinic Dna with Bound Water at the Damaged Site and O2 of Cytosine, Beta Form, uc(Nmr), 1 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:P11 b:0.0 occ:1.00 P A:DC11 0.0 0.0 1.0 OP2 A:DC11 1.4 0.0 1.0 OP1 A:DC11 1.5 0.0 1.0 O3' A:DC10 1.5 0.0 1.0 O5' A:DC11 1.5 0.0 1.0 C5' A:DC11 2.6 0.0 1.0 C3' A:DC10 2.6 0.0 1.0 H2'' A:DC10 2.7 0.0 1.0 H5'' A:DC11 2.8 0.0 1.0 H3' A:DC10 2.9 0.0 1.0 H5' A:DC11 2.9 0.0 1.0 H2' A:DC11 3.1 0.0 1.0 C2' A:DC10 3.2 0.0 1.0 H6 A:DC11 3.3 0.0 1.0 H1' A:DC10 3.5 0.0 1.0 C4' A:DC11 3.9 0.0 1.0 C4' A:DC10 3.9 0.0 1.0 C1' A:DC10 3.9 0.0 1.0 H4' A:DC10 4.0 0.0 1.0 H2' A:DC10 4.0 0.0 1.0 C2' A:DC11 4.1 0.0 1.0 C6 A:DC11 4.2 0.0 1.0 H3' A:DC11 4.2 0.0 1.0 O4' A:DC11 4.3 0.0 1.0 C3' A:DC11 4.3 0.0 1.0 O4' A:DC10 4.4 0.0 1.0 C1' A:DC11 4.6 0.0 1.0 H4' A:DC11 4.7 0.0 1.0 H2'' A:DC11 4.8 0.0 1.0 N1 A:DC11 4.8 0.0 1.0 H5 A:DC11 5.0 0.0 1.0

R.D.Beger, P.H.Bolton. Structures of Apurinic and Apyrimidinic Sites in Duplex Dnas. J.Biol.Chem. V. 273 15565 1998.
ISSN: ISSN 0021-9258
PubMed: 9624147
DOI: 10.1074/JBC.273.25.15565