Phosphorus in PDB 1a9g: Apurinic Dna with Bound Water at the Damaged Site and N3 of Cytosine, Beta Form, uc(Nmr), 1 Structure

Phosphorus Binding Sites:

Pages:

>>> 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 N3 of Cytosine, Beta Form, uc(Nmr), 1 Structure (pdb code 1a9g). 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 N3 of Cytosine, Beta Form, uc(Nmr), 1 Structure, PDB code: 1a9g:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 1 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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
OP1 A:DG2 1.3 0.0 1.0
OP2 A:DG2 1.4 0.0 1.0
O3' A:DC1 1.4 0.0 1.0
O5' A:DG2 1.4 0.0 1.0
C3' A:DC1 2.4 0.0 1.0
C5' A:DG2 2.5 0.0 1.0
H3' A:DC1 2.5 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 3.0 0.0 1.0
C2' A:DC1 3.2 0.0 1.0
H1' A:DC1 3.4 0.0 1.0
H4' A:DC1 3.5 0.0 1.0
C4' A:DC1 3.5 0.0 1.0
H2' A:DG2 3.6 0.0 1.0
H8 A:DG2 3.7 0.0 1.0
C4' A:DG2 3.8 0.0 1.0
C1' A:DC1 3.8 0.0 1.0
H3' A:DG2 3.9 0.0 1.0
H2' A:DC1 4.0 0.0 1.0
O4' A:DG2 4.2 0.0 1.0
O4' A:DC1 4.2 0.0 1.0
C3' A:DG2 4.3 0.0 1.0
H5'' A:DC1 4.3 0.0 1.0
C2' A:DG2 4.4 0.0 1.0
C5' A:DC1 4.5 0.0 1.0
H4' A:DG2 4.6 0.0 1.0
C8 A:DG2 4.6 0.0 1.0
C1' A:DG2 4.9 0.0 1.0
O5' A:DC1 5.0 0.0 1.0

Phosphorus binding site 2 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 2 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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 1.3 0.0 1.0
O5' A:DC3 1.4 0.0 1.0
O3' A:DG2 1.6 0.0 1.0
C5' A:DC3 2.4 0.0 1.0
H5'' 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 2.8 0.0 1.0
H3' A:DG2 3.0 0.0 1.0
C2' A:DG2 3.2 0.0 1.0
H3' A:DC3 3.4 0.0 1.0
H1' A:DG2 3.5 0.0 1.0
H6 A:DC3 3.6 0.0 1.0
C4' A:DC3 3.6 0.0 1.0
H2' A:DC3 3.8 0.0 1.0
C4' A:DG2 3.9 0.0 1.0
C1' A:DG2 3.9 0.0 1.0
H4' A:DG2 3.9 0.0 1.0
C3' A:DC3 4.0 0.0 1.0
H2' A:DG2 4.1 0.0 1.0
O4' A:DC3 4.1 0.0 1.0
H4' A:DC3 4.3 0.0 1.0
O4' A:DG2 4.5 0.0 1.0
C2' A:DC3 4.5 0.0 1.0
C6 A:DC3 4.6 0.0 1.0
C1' A:DC3 4.9 0.0 1.0

Phosphorus binding site 3 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 3 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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 1.6 0.0 1.0
O5' A:DG4 1.6 0.0 1.0
H2'' A:DC3 2.6 0.0 1.0
C3' A:DC3 2.6 0.0 1.0
C5' A:DG4 2.6 0.0 1.0
H5'' A:DG4 2.8 0.0 1.0
H5' A:DG4 3.0 0.0 1.0
H3' A:DC3 3.0 0.0 1.0
C2' A:DC3 3.1 0.0 1.0
H2' A:DG4 3.8 0.0 1.0
C4' A:DC3 3.8 0.0 1.0
H2' A:DC3 3.8 0.0 1.0
H4' A:DC3 3.8 0.0 1.0
H1' A:DC3 3.9 0.0 1.0
H3' A:DG4 3.9 0.0 1.0
C4' A:DG4 3.9 0.0 1.0
H8 A:DG4 4.0 0.0 1.0
C1' A:DC3 4.1 0.0 1.0
C3' A:DG4 4.4 0.0 1.0
O4' A:DG4 4.6 0.0 1.0
O4' A:DC3 4.6 0.0 1.0
C2' A:DG4 4.6 0.0 1.0
H5'' A:DC3 4.6 0.0 1.0
H4' A:DG4 4.7 0.0 1.0
C5' A:DC3 4.8 0.0 1.0
C8 A:DG4 5.0 0.0 1.0

Phosphorus binding site 4 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 4 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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
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 1.5 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
H3' A:DG4 2.8 0.0 1.0
H5'' A:DA5 2.9 0.0 1.0
H8 A:DA5 2.9 0.0 1.0
H2'' A:DG4 3.1 0.0 1.0
C2' A:DG4 3.4 0.0 1.0
H4' A:DG4 3.8 0.0 1.0
H1' A:DG4 3.9 0.0 1.0
H2' A:DA5 3.9 0.0 1.0
C4' A:DG4 3.9 0.0 1.0
C8 A:DA5 3.9 0.0 1.0
C4' A:DA5 3.9 0.0 1.0
C1' A:DG4 4.1 0.0 1.0
H2' A:DG4 4.2 0.0 1.0
O4' A:DA5 4.3 0.0 1.0
H3' A:DA5 4.4 0.0 1.0
C3' A:DA5 4.6 0.0 1.0
O4' A:DG4 4.6 0.0 1.0
C2' A:DA5 4.6 0.0 1.0
H4' A:DA5 4.6 0.0 1.0
N7 A:DA5 4.7 0.0 1.0
N9 A:DA5 4.7 0.0 1.0
C1' A:DA5 4.9 0.0 1.0
H5'' A:DG4 4.9 0.0 1.0
C5' A:DG4 5.0 0.0 1.0

Phosphorus binding site 5 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 5 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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
O2P A:AAB6 1.4 0.0 1.0
O1P A:AAB6 1.4 0.0 1.0
O5' A:AAB6 1.5 0.0 1.0
O3' A:DA5 1.5 0.0 1.0
C3' A:DA5 2.6 0.0 1.0
C5' A:AAB6 2.6 0.0 1.0
H5'2 A:AAB6 2.8 0.0 1.0
H2'' A:DA5 2.9 0.0 1.0
H3' A:DA5 3.0 0.0 1.0
H5'1 A:AAB6 3.0 0.0 1.0
C2' A:DA5 3.2 0.0 1.0
H2'2 A:AAB6 3.3 0.0 1.0
H1' A:DA5 3.6 0.0 1.0
C4' A:DA5 3.8 0.0 1.0
H4' A:DA5 3.8 0.0 1.0
H3' A:AAB6 3.8 0.0 1.0
C1' A:DA5 3.9 0.0 1.0
C4' A:AAB6 3.9 0.0 1.0
H2' A:DA5 4.1 0.0 1.0
C2' A:AAB6 4.2 0.0 1.0
C3' A:AAB6 4.2 0.0 1.0
O4' A:DA5 4.3 0.0 1.0
O4' A:AAB6 4.4 0.0 1.0
H4' A:AAB6 4.7 0.0 1.0
H2'1 A:AAB6 4.8 0.0 1.0
C1' A:AAB6 5.0 0.0 1.0

Phosphorus binding site 6 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 6 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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 1.4 0.0 1.0
OP2 A:DA7 1.4 0.0 1.0
O5' A:DA7 1.5 0.0 1.0
O3' A:AAB6 1.6 0.0 1.0
C5' A:DA7 2.5 0.0 1.0
H5' A:DA7 2.7 0.0 1.0
C3' A:AAB6 2.7 0.0 1.0
H3' A:AAB6 2.8 0.0 1.0
H5'' A:DA7 3.0 0.0 1.0
H8 A:DA7 3.1 0.0 1.0
H2' A:DA7 3.4 0.0 1.0
H2'1 A:AAB6 3.6 0.0 1.0
C2' A:AAB6 3.6 0.0 1.0
H4' A:AAB6 3.8 0.0 1.0
C8 A:DA7 3.8 0.0 1.0
C4' A:DA7 3.8 0.0 1.0
C4' A:AAB6 3.9 0.0 1.0
H1' A:AAB6 3.9 0.0 1.0
O4' A:DA7 4.1 0.0 1.0
C1' A:AAB6 4.2 0.0 1.0
C2' A:DA7 4.3 0.0 1.0
N9 A:DA7 4.3 0.0 1.0
H3' A:DA7 4.5 0.0 1.0
C3' A:DA7 4.5 0.0 1.0
N7 A:DA7 4.5 0.0 1.0
C1' A:DA7 4.5 0.0 1.0
H4' A:DA7 4.6 0.0 1.0
H2'2 A:AAB6 4.6 0.0 1.0
O4' A:AAB6 4.6 0.0 1.0
H5'2 A:AAB6 4.7 0.0 1.0
C5' A:AAB6 4.9 0.0 1.0

Phosphorus binding site 7 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 7 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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
OP2 A:DC8 1.4 0.0 1.0
OP1 A:DC8 1.4 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 2.9 0.0 1.0
H2'' A:DA7 2.9 0.0 1.0
H5' A:DC8 2.9 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 3.4 0.0 1.0
C1' A:DA7 3.8 0.0 1.0
C4' A:DA7 3.8 0.0 1.0
H3' A:DC8 3.8 0.0 1.0
C4' A:DC8 3.9 0.0 1.0
H4' A:DA7 3.9 0.0 1.0
H2' A:DC8 4.0 0.0 1.0
H2' A:DA7 4.1 0.0 1.0
O4' A:DA7 4.2 0.0 1.0
O4' A:DC8 4.3 0.0 1.0
C3' A:DC8 4.3 0.0 1.0
H4' A:DC8 4.6 0.0 1.0
C2' A:DC8 4.7 0.0 1.0

Phosphorus binding site 8 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 8 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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
OP1 A:DG9 1.4 0.0 1.0
OP2 A:DG9 1.4 0.0 1.0
O3' A:DC8 1.6 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
H2'' 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
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
H4' A:DC8 3.8 0.0 1.0
C4' A:DC8 3.8 0.0 1.0
H3' A:DG9 3.8 0.0 1.0
C1' A:DC8 3.9 0.0 1.0
C4' A:DG9 3.9 0.0 1.0
H2' A:DC8 3.9 0.0 1.0
H2' A:DG9 4.0 0.0 1.0
C3' A:DG9 4.3 0.0 1.0
O4' A:DG9 4.4 0.0 1.0
O4' A:DC8 4.5 0.0 1.0
H4' A:DG9 4.7 0.0 1.0
C2' A:DG9 4.7 0.0 1.0
H8 A:DG9 4.9 0.0 1.0
H5'' A:DC8 4.9 0.0 1.0
C5' A:DC8 5.0 0.0 1.0

Phosphorus binding site 9 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 9 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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
C3' A:DG9 2.7 0.0 1.0
H5'' A:DC10 2.7 0.0 1.0
H2'' A:DG9 2.8 0.0 1.0
H5' A:DC10 2.8 0.0 1.0
H3' A:DG9 3.0 0.0 1.0
H6 A:DC10 3.1 0.0 1.0
C2' A:DG9 3.2 0.0 1.0
H2' A:DC10 3.4 0.0 1.0
H1' A:DG9 3.4 0.0 1.0
C4' A:DC10 3.8 0.0 1.0
C1' A:DG9 3.9 0.0 1.0
H4' A:DG9 3.9 0.0 1.0
C4' A:DG9 3.9 0.0 1.0
H3' A:DC10 4.0 0.0 1.0
H2' A:DG9 4.1 0.0 1.0
C6 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 4.3 0.0 1.0
H4' A:DC10 4.5 0.0 1.0
O4' A:DG9 4.6 0.0 1.0
C1' A:DC10 4.8 0.0 1.0
H5 A:DC10 4.8 0.0 1.0
N1 A:DC10 5.0 0.0 1.0

Phosphorus binding site 10 out of 20 in 1a9g

Go back to Phosphorus Binding Sites List in 1a9g
Phosphorus binding site 10 out of 20 in the Apurinic Dna with Bound Water at the Damaged Site and N3 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 N3 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 1.4 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
H5'' A:DC11 2.7 0.0 1.0
H2'' A:DC10 2.8 0.0 1.0
H3' A:DC10 2.9 0.0 1.0
H5' A:DC11 3.1 0.0 1.0
C2' A:DC10 3.1 0.0 1.0
H2' A:DC11 3.2 0.0 1.0
H1' A:DC10 3.3 0.0 1.0
C1' A:DC10 3.8 0.0 1.0
H3' A:DC11 3.8 0.0 1.0
H6 A:DC11 3.8 0.0 1.0
C4' A:DC10 3.9 0.0 1.0
C4' A:DC11 3.9 0.0 1.0
H4' A:DC10 3.9 0.0 1.0
H2' A:DC10 4.0 0.0 1.0
C3' A:DC11 4.2 0.0 1.0
C2' A:DC11 4.2 0.0 1.0
O4' A:DC10 4.3 0.0 1.0
O4' A:DC11 4.5 0.0 1.0
H4' A:DC11 4.6 0.0 1.0
C6 A:DC11 4.8 0.0 1.0
H2'' A:DC11 4.9 0.0 1.0
C1' A:DC11 4.9 0.0 1.0

Reference:

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
Page generated: Fri Sep 25 12:32:22 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy