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

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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


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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

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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


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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

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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


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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

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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


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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

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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


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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

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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


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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

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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


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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

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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


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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

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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


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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

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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


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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

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