Phosphorus in PDB 112d: Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Protein crystallography data
The structure of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations, PDB code: 112d
was solved by
T.Brown,
W.N.Hunter,
G.Kneale,
O.Kennard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
25.690,
41.960,
65.190,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
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 Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
(pdb code 112d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the
Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations, PDB code: 112d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Phosphorus binding site 1 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 1 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:10.0
occ:1.00
|
P
|
A:DG2
|
0.0
|
10.0
|
1.0
|
OP1
|
A:DG2
|
1.5
|
10.0
|
1.0
|
OP2
|
A:DG2
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DG2
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DC1
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DC1
|
2.7
|
10.0
|
1.0
|
C5'
|
A:DG2
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DC1
|
3.2
|
10.0
|
1.0
|
C4'
|
A:DG2
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DC1
|
4.0
|
10.0
|
1.0
|
O
|
A:HOH65
|
4.1
|
10.0
|
1.0
|
C1'
|
A:DC1
|
4.2
|
10.0
|
1.0
|
C3'
|
A:DG2
|
4.3
|
10.0
|
1.0
|
O4'
|
A:DG2
|
4.3
|
10.0
|
1.0
|
C2'
|
A:DG2
|
4.3
|
10.0
|
1.0
|
O4'
|
A:DC1
|
4.7
|
10.0
|
1.0
|
C1'
|
A:DG2
|
4.8
|
10.0
|
1.0
|
C8
|
A:DG2
|
4.9
|
10.0
|
1.0
|
O5'
|
A:DC1
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 2 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 2 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:10.0
occ:1.00
|
P
|
A:DC3
|
0.0
|
10.0
|
1.0
|
OP1
|
A:DC3
|
1.5
|
10.0
|
1.0
|
OP2
|
A:DC3
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DG2
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DC3
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DG2
|
2.6
|
10.0
|
1.0
|
C5'
|
A:DC3
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DG2
|
3.3
|
10.0
|
1.0
|
C4'
|
A:DC3
|
3.7
|
10.0
|
1.0
|
O4'
|
A:DC3
|
3.7
|
10.0
|
1.0
|
C4'
|
A:DG2
|
3.9
|
10.0
|
1.0
|
C1'
|
A:DG2
|
4.3
|
10.0
|
1.0
|
C3'
|
A:DC3
|
4.5
|
10.0
|
1.0
|
C6
|
A:DC3
|
4.6
|
10.0
|
1.0
|
O
|
A:HOH105
|
4.6
|
10.0
|
1.0
|
O4'
|
A:DG2
|
4.7
|
10.0
|
1.0
|
O
|
A:HOH65
|
4.8
|
10.0
|
1.0
|
C1'
|
A:DC3
|
4.9
|
10.0
|
1.0
|
C5'
|
A:DG2
|
4.9
|
10.0
|
1.0
|
|
Phosphorus binding site 3 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 3 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:10.0
occ:1.00
|
P
|
A:DG4
|
0.0
|
10.0
|
1.0
|
OP1
|
A:DG4
|
1.5
|
10.0
|
1.0
|
OP2
|
A:DG4
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DG4
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DC3
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DC3
|
2.6
|
10.0
|
1.0
|
C5'
|
A:DG4
|
2.6
|
10.0
|
1.0
|
C2'
|
A:DC3
|
3.3
|
10.0
|
1.0
|
C4'
|
A:DG4
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DC3
|
3.9
|
10.0
|
1.0
|
C8
|
A:DG4
|
4.2
|
10.0
|
1.0
|
O4'
|
A:DG4
|
4.3
|
10.0
|
1.0
|
C3'
|
A:DG4
|
4.3
|
10.0
|
1.0
|
C2'
|
A:DG4
|
4.4
|
10.0
|
1.0
|
C5'
|
A:DC3
|
4.4
|
10.0
|
1.0
|
C1'
|
A:DG4
|
4.6
|
10.0
|
1.0
|
C1'
|
A:DC3
|
4.6
|
10.0
|
1.0
|
N9
|
A:DG4
|
4.7
|
10.0
|
1.0
|
O5'
|
A:DC3
|
4.8
|
10.0
|
1.0
|
O4'
|
A:DC3
|
4.9
|
10.0
|
1.0
|
|
Phosphorus binding site 4 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 4 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:10.0
occ:1.00
|
P
|
A:DA5
|
0.0
|
10.0
|
1.0
|
OP1
|
A:DA5
|
1.5
|
10.0
|
1.0
|
OP2
|
A:DA5
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DA5
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DG4
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DA5
|
2.7
|
10.0
|
1.0
|
C3'
|
A:DG4
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DG4
|
3.2
|
10.0
|
1.0
|
C4'
|
A:DA5
|
3.8
|
10.0
|
1.0
|
C4'
|
A:DG4
|
3.9
|
10.0
|
1.0
|
C1'
|
A:DG4
|
4.2
|
10.0
|
1.0
|
C3'
|
A:DA5
|
4.2
|
10.0
|
1.0
|
C2'
|
A:DA5
|
4.4
|
10.0
|
1.0
|
O4'
|
A:DG4
|
4.5
|
10.0
|
1.0
|
C8
|
A:DA5
|
4.6
|
10.0
|
1.0
|
O4'
|
A:DA5
|
4.8
|
10.0
|
1.0
|
|
Phosphorus binding site 5 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 5 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:10.0
occ:1.00
|
P
|
A:DA6
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DA6
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DA6
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DA5
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DA6
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DA6
|
2.6
|
10.0
|
1.0
|
C3'
|
A:DA5
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DA5
|
3.3
|
10.0
|
1.0
|
O
|
A:HOH68
|
3.4
|
10.0
|
1.0
|
O
|
A:HOH86
|
3.6
|
10.0
|
1.0
|
C4'
|
A:DA6
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DA5
|
3.9
|
10.0
|
1.0
|
C1'
|
A:DA5
|
4.0
|
10.0
|
1.0
|
O4'
|
A:DA5
|
4.3
|
10.0
|
1.0
|
O
|
A:HOH81
|
4.5
|
10.0
|
1.0
|
C3'
|
A:DA6
|
4.5
|
10.0
|
1.0
|
O4'
|
A:DA6
|
4.6
|
10.0
|
1.0
|
|
Phosphorus binding site 6 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 6 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:10.0
occ:1.00
|
P
|
A:DT7
|
0.0
|
10.0
|
1.0
|
OP1
|
A:DT7
|
1.5
|
10.0
|
1.0
|
OP2
|
A:DT7
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DA6
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DT7
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DA6
|
2.7
|
10.0
|
1.0
|
C5'
|
A:DT7
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DA6
|
3.3
|
10.0
|
1.0
|
C4'
|
A:DT7
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DA6
|
3.9
|
10.0
|
1.0
|
O
|
A:HOH33
|
4.1
|
10.0
|
1.0
|
C1'
|
A:DA6
|
4.2
|
10.0
|
1.0
|
C3'
|
A:DT7
|
4.4
|
10.0
|
1.0
|
O4'
|
A:DT7
|
4.4
|
10.0
|
1.0
|
O4'
|
A:DA6
|
4.6
|
10.0
|
1.0
|
O
|
A:HOH86
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 7 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 7 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:10.0
occ:1.00
|
P
|
A:DT8
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DT8
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DT8
|
1.5
|
10.0
|
1.0
|
O5'
|
A:DT8
|
1.6
|
10.0
|
1.0
|
O3'
|
A:DT7
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DT7
|
2.7
|
10.0
|
1.0
|
C5'
|
A:DT8
|
2.7
|
10.0
|
1.0
|
C2'
|
A:DT7
|
3.3
|
10.0
|
1.0
|
O
|
A:HOH74
|
3.8
|
10.0
|
1.0
|
O
|
A:HOH85
|
3.8
|
10.0
|
1.0
|
C4'
|
A:DT8
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DT7
|
3.9
|
10.0
|
1.0
|
O4'
|
A:DT8
|
4.3
|
10.0
|
1.0
|
C3'
|
A:DT8
|
4.5
|
10.0
|
1.0
|
C1'
|
A:DT7
|
4.5
|
10.0
|
1.0
|
O
|
B:HOH55
|
4.8
|
10.0
|
1.0
|
C5'
|
A:DT7
|
4.8
|
10.0
|
1.0
|
O4'
|
A:DT7
|
4.9
|
10.0
|
1.0
|
C6
|
A:DT8
|
4.9
|
10.0
|
1.0
|
|
Phosphorus binding site 8 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 8 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P9
b:10.0
occ:1.00
|
P
|
A:DA9
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DA9
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DA9
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DT8
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DA9
|
1.6
|
10.0
|
1.0
|
C5'
|
A:DA9
|
2.7
|
10.0
|
1.0
|
C3'
|
A:DT8
|
2.7
|
10.0
|
1.0
|
O
|
A:HOH72
|
3.4
|
10.0
|
1.0
|
C2'
|
A:DT8
|
3.4
|
10.0
|
1.0
|
C4'
|
A:DA9
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DT8
|
3.9
|
10.0
|
1.0
|
C3'
|
A:DA9
|
4.3
|
10.0
|
1.0
|
O4'
|
A:DA9
|
4.4
|
10.0
|
1.0
|
C1'
|
A:DT8
|
4.5
|
10.0
|
1.0
|
O4'
|
A:DT8
|
4.8
|
10.0
|
1.0
|
N3
|
A:DA9
|
4.9
|
10.0
|
1.0
|
C5'
|
A:DT8
|
4.9
|
10.0
|
1.0
|
O
|
A:HOH74
|
5.0
|
10.0
|
1.0
|
|
Phosphorus binding site 9 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 9 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P10
b:10.0
occ:1.00
|
P
|
A:DG10
|
0.0
|
10.0
|
1.0
|
OP2
|
A:DG10
|
1.5
|
10.0
|
1.0
|
OP1
|
A:DG10
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DA9
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DG10
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DA9
|
2.6
|
10.0
|
1.0
|
C5'
|
A:DG10
|
2.6
|
10.0
|
1.0
|
C2'
|
A:DA9
|
3.2
|
10.0
|
1.0
|
O
|
A:HOH71
|
3.4
|
10.0
|
1.0
|
O
|
A:HOH103
|
3.5
|
10.0
|
1.0
|
O
|
A:HOH51
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DA9
|
3.9
|
10.0
|
1.0
|
C4'
|
A:DG10
|
3.9
|
10.0
|
1.0
|
C1'
|
A:DA9
|
4.3
|
10.0
|
1.0
|
O
|
A:HOH67
|
4.3
|
10.0
|
1.0
|
O4'
|
A:DG10
|
4.5
|
10.0
|
1.0
|
C3'
|
A:DG10
|
4.5
|
10.0
|
1.0
|
C2'
|
A:DG10
|
4.5
|
10.0
|
1.0
|
O4'
|
A:DA9
|
4.8
|
10.0
|
1.0
|
C5'
|
A:DA9
|
4.9
|
10.0
|
1.0
|
C1'
|
A:DG10
|
4.9
|
10.0
|
1.0
|
|
Phosphorus binding site 10 out
of 22 in 112d
Go back to
Phosphorus Binding Sites List in 112d
Phosphorus binding site 10 out
of 22 in the Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P11
b:10.0
occ:1.00
|
P
|
A:DC11
|
0.0
|
10.0
|
1.0
|
OP1
|
A:DC11
|
1.5
|
10.0
|
1.0
|
OP2
|
A:DC11
|
1.5
|
10.0
|
1.0
|
O3'
|
A:DG10
|
1.6
|
10.0
|
1.0
|
O5'
|
A:DC11
|
1.6
|
10.0
|
1.0
|
C3'
|
A:DG10
|
2.6
|
10.0
|
1.0
|
C5'
|
A:DC11
|
2.6
|
10.0
|
1.0
|
O
|
A:HOH56
|
3.6
|
10.0
|
1.0
|
C4'
|
A:DG10
|
3.7
|
10.0
|
1.0
|
C4'
|
A:DC11
|
3.7
|
10.0
|
1.0
|
C2'
|
A:DG10
|
3.8
|
10.0
|
1.0
|
O4'
|
A:DC11
|
3.8
|
10.0
|
1.0
|
C6
|
A:DC11
|
3.9
|
10.0
|
1.0
|
C2'
|
A:DC11
|
4.5
|
10.0
|
1.0
|
C3'
|
A:DC11
|
4.5
|
10.0
|
1.0
|
C1'
|
A:DC11
|
4.5
|
10.0
|
1.0
|
C1'
|
A:DG10
|
4.6
|
10.0
|
1.0
|
O
|
A:HOH107
|
4.6
|
10.0
|
1.0
|
O4'
|
A:DG10
|
4.6
|
10.0
|
1.0
|
C5'
|
A:DG10
|
4.7
|
10.0
|
1.0
|
N1
|
A:DC11
|
4.7
|
10.0
|
1.0
|
C5
|
A:DC11
|
4.7
|
10.0
|
1.0
|
|
Reference:
T.Brown,
W.N.Hunter,
G.Kneale,
O.Kennard.
Molecular Structure of the G.A Base Pair in Dna and Its Implications For the Mechanism of Transversion Mutations. Proc.Natl.Acad.Sci.Usa V. 83 2402 1986.
ISSN: ISSN 0027-8424
PubMed: 3458205
DOI: 10.1073/PNAS.83.8.2402
Page generated: Fri Sep 25 11:08:20 2020
|