Phosphorus in PDB 1a9j: Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, Beta Form, uc(Nmr), 1 Structure (pdb code 1a9j). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the Apyrimidinic Dna with Bound Water at the Damaged Site, Beta Form, uc(Nmr), 1 Structure, PDB code: 1a9j:
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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 OP1 A:DG2 1.2 0.0 1.0 OP2 A:DG2 1.3 0.0 1.0 O3' A:DC1 1.5 0.0 1.0 O5' A:DG2 1.5 0.0 1.0 C3' A:DC1 2.5 0.0 1.0 C5' A:DG2 2.5 0.0 1.0 H3' A:DC1 2.7 0.0 1.0 H5'' A:DG2 2.7 0.0 1.0 H5' A:DG2 2.8 0.0 1.0 H2'' A:DC1 2.9 0.0 1.0 C2' A:DC1 3.2 0.0 1.0 H1' A:DC1 3.6 0.0 1.0 H4' A:DC1 3.7 0.0 1.0 C4' A:DC1 3.7 0.0 1.0 C4' A:DG2 3.8 0.0 1.0 C1' A:DC1 4.0 0.0 1.0 H2' A:DC1 4.0 0.0 1.0 H4' A:DG2 4.2 0.0 1.0 HO5' A:DC1 4.2 0.0 1.0 O4' A:DG2 4.3 0.0 1.0 O4' A:DC1 4.3 0.0 1.0 C5' A:DC1 4.7 0.0 1.0 O5' A:DC1 4.8 0.0 1.0 H3' A:DG2 4.9 0.0 1.0 C3' A:DG2 5.0 0.0 1.0 H2' A:DG2 5.0 0.0 1.0

Phosphorus binding site 2 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 1.4 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 2.6 0.0 1.0 C3' A:DG2 2.7 0.0 1.0 H5'' A:DC3 2.7 0.0 1.0 H2'' A:DG2 2.9 0.0 1.0 H5' A:DC3 3.0 0.0 1.0 H3' A:DG2 3.0 0.0 1.0 C2' A:DG2 3.2 0.0 1.0 H6 A:DC3 3.3 0.0 1.0 H2' A:DC3 3.4 0.0 1.0 H1' A:DG2 3.4 0.0 1.0 C1' A:DG2 3.8 0.0 1.0 C4' A:DC3 3.8 0.0 1.0 H3' A:DC3 3.9 0.0 1.0 C4' A:DG2 3.9 0.0 1.0 H4' A:DG2 3.9 0.0 1.0 H2' A:DG2 4.1 0.0 1.0 C3' A:DC3 4.2 0.0 1.0 C2' A:DC3 4.3 0.0 1.0 C6 A:DC3 4.3 0.0 1.0 O4' A:DG2 4.5 0.0 1.0 O4' A:DC3 4.5 0.0 1.0 H4' A:DC3 4.6 0.0 1.0 C1' A:DC3 4.9 0.0 1.0 H5 A:DC3 5.0 0.0 1.0

Phosphorus binding site 3 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 OP2 A:DG4 1.4 0.0 1.0 OP1 A:DG4 1.4 0.0 1.0 O3' A:DC3 1.6 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 2.7 0.0 1.0 H5'' A:DG4 2.8 0.0 1.0 H3' A:DC3 2.9 0.0 1.0 H5' A:DG4 3.0 0.0 1.0 H2'' A:DC3 3.1 0.0 1.0 C2' A:DC3 3.4 0.0 1.0 H1' A:DC3 3.7 0.0 1.0 H4' A:DC3 3.8 0.0 1.0 C4' A:DC3 3.9 0.0 1.0 C4' A:DG4 3.9 0.0 1.0 C1' A:DC3 4.1 0.0 1.0 O4' A:DG4 4.2 0.0 1.0 H2' A:DC3 4.3 0.0 1.0 H4' A:DG4 4.3 0.0 1.0 O4' A:DC3 4.4 0.0 1.0 H5'' A:DC3 5.0 0.0 1.0

Phosphorus binding site 4 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 OP1 A:DA5 1.4 0.0 1.0 OP2 A:DA5 1.4 0.0 1.0 O5' A:DA5 1.5 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 2.6 0.0 1.0 H5' A:DA5 2.7 0.0 1.0 H8 A:DA5 2.7 0.0 1.0 H3' A:DG4 2.7 0.0 1.0 H5'' A:DA5 3.0 0.0 1.0 H2'' A:DG4 3.2 0.0 1.0 C2' A:DG4 3.4 0.0 1.0 C8 A:DA5 3.7 0.0 1.0 H2' A:DA5 3.7 0.0 1.0 C4' A:DA5 3.9 0.0 1.0 H4' A:DG4 3.9 0.0 1.0 C4' A:DG4 3.9 0.0 1.0 H1' A:DG4 4.0 0.0 1.0 O4' A:DA5 4.1 0.0 1.0 H2' A:DG4 4.2 0.0 1.0 C1' A:DG4 4.3 0.0 1.0 H3' A:DA5 4.5 0.0 1.0 C2' A:DA5 4.5 0.0 1.0 N7 A:DA5 4.6 0.0 1.0 N9 A:DA5 4.6 0.0 1.0 C3' A:DA5 4.6 0.0 1.0 H4' A:DA5 4.6 0.0 1.0 C1' A:DA5 4.7 0.0 1.0 O4' A:DG4 4.7 0.0 1.0 H5' A:DG4 4.8 0.0 1.0 C5' A:DG4 4.9 0.0 1.0

Phosphorus binding site 5 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 O2P A:AAB6 1.5 0.0 1.0 O1P A:AAB6 1.5 0.0 1.0 O3' A:DA5 1.6 0.0 1.0 O5' A:AAB6 1.6 0.0 1.0 C3' A:DA5 2.7 0.0 1.0 C5' A:AAB6 2.7 0.0 1.0 H5'2 A:AAB6 2.8 0.0 1.0 H2'' A:DA5 3.0 0.0 1.0 H3' A:DA5 3.0 0.0 1.0 H5'1 A:AAB6 3.1 0.0 1.0 H2'2 A:AAB6 3.2 0.0 1.0 C2' A:DA5 3.3 0.0 1.0 H1' A:DA5 3.6 0.0 1.0 H4' A:DA5 3.9 0.0 1.0 C4' A:DA5 3.9 0.0 1.0 C4' A:AAB6 3.9 0.0 1.0 C1' A:DA5 4.0 0.0 1.0 H3' A:AAB6 4.0 0.0 1.0 H2' A:DA5 4.2 0.0 1.0 C2' A:AAB6 4.2 0.0 1.0 C3' A:AAB6 4.3 0.0 1.0 O4' A:DA5 4.4 0.0 1.0 O4' A:AAB6 4.4 0.0 1.0 H4' A:AAB6 4.8 0.0 1.0 C1' A:AAB6 4.9 0.0 1.0 H2'1 A:AAB6 4.9 0.0 1.0 O1' A:AAB6 5.0 0.0 1.0

Phosphorus binding site 6 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 1.4 0.0 1.0 OP2 A:DA7 1.4 0.0 1.0 O5' A:DA7 1.6 0.0 1.0 O3' A:AAB6 1.6 0.0 1.0 C5' A:DA7 2.6 0.0 1.0 C3' A:AAB6 2.7 0.0 1.0 H5'' A:DA7 2.9 0.0 1.0 H5' A:DA7 2.9 0.0 1.0 H2'1 A:AAB6 2.9 0.0 1.0 H3' A:AAB6 3.0 0.0 1.0 C2' A:AAB6 3.2 0.0 1.0 H1' A:AAB6 3.5 0.0 1.0 C1' A:AAB6 3.9 0.0 1.0 H2' A:DA7 3.9 0.0 1.0 C4' A:DA7 4.0 0.0 1.0 C4' A:AAB6 4.0 0.0 1.0 H4' A:AAB6 4.1 0.0 1.0 H2'2 A:AAB6 4.2 0.0 1.0 H3' A:DA7 4.2 0.0 1.0 O4' A:DA7 4.5 0.0 1.0 O4' A:AAB6 4.5 0.0 1.0 C3' A:DA7 4.6 0.0 1.0 H8 A:DA7 4.7 0.0 1.0 C2' A:DA7 4.7 0.0 1.0 H4' A:DA7 4.7 0.0 1.0

Phosphorus binding site 7 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 1.4 0.0 1.0 O5' A:DC8 1.5 0.0 1.0 O3' A:DA7 1.6 0.0 1.0 C5' A:DC8 2.5 0.0 1.0 H5' A:DC8 2.7 0.0 1.0 C3' A:DA7 2.7 0.0 1.0 H5'' A:DC8 2.8 0.0 1.0 H2'' A:DA7 2.8 0.0 1.0 H3' A:DA7 3.0 0.0 1.0 C2' A:DA7 3.2 0.0 1.0 H1' A:DA7 3.5 0.0 1.0 C4' A:DC8 3.8 0.0 1.0 C1' A:DA7 3.9 0.0 1.0 H2' A:DC8 3.9 0.0 1.0 H6 A:DC8 3.9 0.0 1.0 C4' A:DA7 3.9 0.0 1.0 H4' A:DA7 4.0 0.0 1.0 H2' A:DA7 4.1 0.0 1.0 O4' A:DC8 4.1 0.0 1.0 H3' A:DC8 4.2 0.0 1.0 C3' A:DC8 4.5 0.0 1.0 O4' A:DA7 4.5 0.0 1.0 H4' A:DC8 4.5 0.0 1.0 C2' A:DC8 4.6 0.0 1.0 C6 A:DC8 4.8 0.0 1.0 C1' A:DC8 5.0 0.0 1.0

Phosphorus binding site 8 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 OP1 A:DG9 1.4 0.0 1.0 OP2 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 2.7 0.0 1.0 H5'' A:DG9 2.8 0.0 1.0 H5' A:DG9 2.9 0.0 1.0 H2'' A:DC8 2.9 0.0 1.0 H3' A:DC8 3.0 0.0 1.0 C2' A:DC8 3.3 0.0 1.0 H1' A:DC8 3.6 0.0 1.0 H2' A:DG9 3.7 0.0 1.0 H4' A:DC8 3.9 0.0 1.0 C4' A:DC8 3.9 0.0 1.0 C4' A:DG9 3.9 0.0 1.0 C1' A:DC8 4.0 0.0 1.0 H3' A:DG9 4.1 0.0 1.0 H2' A:DC8 4.1 0.0 1.0 H8 A:DG9 4.1 0.0 1.0 O4' A:DG9 4.4 0.0 1.0 C3' A:DG9 4.5 0.0 1.0 C2' A:DG9 4.6 0.0 1.0 O4' A:DC8 4.6 0.0 1.0 H4' A:DG9 4.7 0.0 1.0 H5'' A:DC8 5.0 0.0 1.0

Phosphorus binding site 9 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 OP1 A:DC10 1.4 0.0 1.0 OP2 A:DC10 1.4 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 2.6 0.0 1.0 C3' A:DG9 2.7 0.0 1.0 H2'' A:DG9 2.8 0.0 1.0 H5'' A:DC10 2.8 0.0 1.0 H6 A:DC10 2.9 0.0 1.0 H5' A:DC10 3.0 0.0 1.0 H3' A:DG9 3.0 0.0 1.0 C2' A:DG9 3.2 0.0 1.0 H1' A:DG9 3.4 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 4.0 0.0 1.0 C6 A:DC10 4.0 0.0 1.0 H4' A:DG9 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 4.4 0.0 1.0 C2' A:DC10 4.4 0.0 1.0 C3' A:DC10 4.5 0.0 1.0 H5 A:DC10 4.5 0.0 1.0 O4' A:DG9 4.5 0.0 1.0 C5 A:DC10 4.7 0.0 1.0 H4' A:DC10 4.7 0.0 1.0 C1' A:DC10 4.8 0.0 1.0 N1 A:DC10 4.9 0.0 1.0

Phosphorus binding site 10 out of 20 in the Apyrimidinic Dna with Bound Water at the Damaged Site, 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 Apyrimidinic Dna with Bound Water at the Damaged Site, 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 1.4 0.0 1.0 O5' A:DC11 1.5 0.0 1.0 O3' A:DC10 1.6 0.0 1.0 C5' A:DC11 2.6 0.0 1.0 H5' A:DC11 2.7 0.0 1.0 C3' A:DC10 2.7 0.0 1.0 H2'' A:DC10 3.0 0.0 1.0 H3' A:DC10 3.0 0.0 1.0 H5'' A:DC11 3.1 0.0 1.0 C2' A:DC10 3.3 0.0 1.0 H1' A:DC10 3.7 0.0 1.0 C4' A:DC11 3.8 0.0 1.0 H4' A:DC11 3.9 0.0 1.0 C4' A:DC10 4.0 0.0 1.0 H4' A:DC10 4.0 0.0 1.0 C1' A:DC10 4.0 0.0 1.0 H2' A:DC10 4.2 0.0 1.0 H6 A:DC11 4.4 0.0 1.0 O4' A:DC11 4.4 0.0 1.0 O4' A:DC10 4.5 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