Phosphorus in PDB 194d: X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex

Protein crystallography data

The structure of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex, PDB code: 194d was solved by K.Balendiran, S.T.Rao, C.Y.Sekharudu, G.Zon, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.700, 40.500, 67.000, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 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 X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex (pdb code 194d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex, PDB code: 194d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 194d

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Phosphorus binding site 1 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:54.3
occ:1.00
P A:DG2 0.0 54.3 1.0
OP2 A:DG2 1.5 51.7 1.0
OP1 A:DG2 1.5 49.3 1.0
O5' A:DG2 1.6 49.7 1.0
O3' A:DC1 1.6 46.2 1.0
C5' A:DG2 2.6 46.6 1.0
C3' A:DC1 2.7 43.9 1.0
C2' A:DC1 3.5 39.4 1.0
C4' A:DG2 3.8 42.0 1.0
O A:HOH44 3.9 49.3 1.0
O A:HOH58 3.9 48.3 1.0
C3' A:DG2 4.0 40.7 1.0
C4' A:DC1 4.0 41.9 1.0
C2' A:DG2 4.3 35.3 1.0
C1' A:DC1 4.4 34.3 1.0
O A:HOH81 4.4 57.6 1.0
O4' A:DG2 4.7 40.6 1.0
O5' A:DC1 4.8 37.0 1.0
O4' A:DC1 4.9 34.8 1.0
C8 A:DG2 5.0 29.7 1.0

Phosphorus binding site 2 out of 22 in 194d

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Phosphorus binding site 2 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:38.8
occ:1.00
P A:DC3 0.0 38.8 1.0
OP2 A:DC3 1.5 32.0 1.0
OP1 A:DC3 1.5 33.0 1.0
O3' A:DG2 1.6 43.0 1.0
O5' A:DC3 1.6 36.8 1.0
C5' A:DC3 2.6 40.1 1.0
C3' A:DG2 2.6 40.7 1.0
C2' A:DG2 3.1 35.3 1.0
O A:HOH42 3.4 41.3 1.0
O A:HOH32 3.9 22.6 1.0
C4' A:DC3 3.9 34.2 1.0
C4' A:DG2 4.0 42.0 1.0
C1' A:DG2 4.0 32.0 1.0
O A:HOH58 4.2 48.3 1.0
O4' A:DC3 4.3 36.4 1.0
C3' A:DC3 4.4 35.2 1.0
O A:HOH85 4.4 54.2 1.0
O4' A:DG2 4.6 40.6 1.0
C6 A:DC3 4.7 17.6 1.0
C2' A:DC3 4.8 32.5 1.0

Phosphorus binding site 3 out of 22 in 194d

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Phosphorus binding site 3 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:47.1
occ:1.00
P A:DG4 0.0 47.1 1.0
OP1 A:DG4 1.5 50.5 1.0
OP2 A:DG4 1.5 39.2 1.0
O5' A:DG4 1.6 48.0 1.0
O3' A:DC3 1.6 38.5 1.0
C3' A:DC3 2.6 35.2 1.0
C5' A:DG4 2.7 43.3 1.0
C2' A:DC3 3.2 32.5 1.0
C4' A:DC3 3.9 34.2 1.0
C4' A:DG4 4.0 46.9 1.0
O A:HOH72 4.2 50.4 1.0
O A:HOH82 4.2 79.6 1.0
C1' A:DC3 4.4 24.7 1.0
O4' A:DG4 4.5 50.0 1.0
C3' A:DG4 4.5 47.2 1.0
C8 A:DG4 4.6 26.8 1.0
O A:HOH32 4.6 22.6 1.0
C2' A:DG4 4.7 45.5 1.0
O4' A:DC3 4.8 36.4 1.0
C5' A:DC3 4.8 40.1 1.0
O A:HOH27 4.9 31.8 1.0

Phosphorus binding site 4 out of 22 in 194d

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Phosphorus binding site 4 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:50.9
occ:1.00
P A:DT5 0.0 50.9 1.0
OP1 A:DT5 1.5 53.3 1.0
OP2 A:DT5 1.5 54.1 1.0
O5' A:DT5 1.6 47.0 1.0
O3' A:DG4 1.6 49.7 1.0
C5' A:DT5 2.5 48.1 1.0
C3' A:DG4 2.7 47.2 1.0
O A:HOH34 3.2 31.4 1.0
C2' A:DG4 3.4 45.5 1.0
C4' A:DT5 3.8 51.0 1.0
C4' A:DG4 3.9 46.9 1.0
O4' A:DT5 4.0 50.1 1.0
O A:HOH84 4.0 64.8 1.0
O A:HOH72 4.2 50.4 1.0
C1' A:DG4 4.4 43.7 1.0
C3' A:DT5 4.6 49.6 1.0
O A:HOH55 4.7 62.2 1.0
O4' A:DG4 4.7 50.0 1.0
C5' A:DG4 4.9 43.3 1.0

Phosphorus binding site 5 out of 22 in 194d

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Phosphorus binding site 5 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:52.1
occ:1.00
P A:DT6 0.0 52.1 1.0
OP2 A:DT6 1.5 46.9 1.0
OP1 A:DT6 1.5 52.2 1.0
O3' A:DT5 1.6 52.5 1.0
O5' A:DT6 1.6 49.9 1.0
C5' A:DT6 2.6 39.4 1.0
C3' A:DT5 2.6 49.6 1.0
C2' A:DT5 3.5 48.0 1.0
O A:HOH59 3.8 56.3 1.0
C4' A:DT5 3.9 51.0 1.0
O A:HOH70 3.9 68.5 1.0
C4' A:DT6 4.0 37.1 1.0
O4' A:DT6 4.3 33.3 1.0
C1' A:DT5 4.5 40.3 1.0
O A:HOH33 4.5 37.2 1.0
C3' A:DT6 4.7 36.7 1.0
C5' A:DT5 4.8 48.1 1.0
O4' A:DT5 4.8 50.1 1.0

Phosphorus binding site 6 out of 22 in 194d

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Phosphorus binding site 6 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:45.9
occ:1.00
P A:DA7 0.0 45.9 1.0
OP2 A:DA7 1.5 42.3 1.0
OP1 A:DA7 1.5 39.5 1.0
O3' A:DT6 1.6 34.8 1.0
O5' A:DA7 1.6 36.6 1.0
C3' A:DT6 2.6 36.7 1.0
C5' A:DA7 2.6 28.9 1.0
C2' A:DT6 3.3 37.1 1.0
C4' A:DT6 3.9 37.1 1.0
C4' A:DA7 3.9 21.8 1.0
O4' A:DA7 4.3 17.2 1.0
C1' A:DT6 4.4 26.5 1.0
C3' A:DA7 4.4 26.3 1.0
C2' A:DA7 4.7 25.0 1.0
O4' A:DT6 4.8 33.3 1.0
C5' A:DT6 4.8 39.4 1.0
C8 A:DA7 4.9 27.1 1.0

Phosphorus binding site 7 out of 22 in 194d

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Phosphorus binding site 7 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:32.6
occ:1.00
P A:DA8 0.0 32.6 1.0
OP1 A:DA8 1.5 40.3 1.0
OP2 A:DA8 1.5 32.4 1.0
O5' A:DA8 1.6 37.8 1.0
O3' A:DA7 1.6 25.4 1.0
C5' A:DA8 2.5 30.7 1.0
C3' A:DA7 2.6 26.3 1.0
C2' A:DA7 3.4 25.0 1.0
O A:HOH31 3.9 28.8 1.0
C4' A:DA8 3.9 19.8 1.0
C4' A:DA7 3.9 21.8 1.0
O A:HOH75 4.2 48.0 1.0
C1' A:DA7 4.5 19.7 1.0
C3' A:DA8 4.5 23.1 1.0
O4' A:DA8 4.6 19.9 1.0
C5' A:DA7 4.8 28.9 1.0
O4' A:DA7 4.8 17.2 1.0

Phosphorus binding site 8 out of 22 in 194d

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Phosphorus binding site 8 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:34.0
occ:1.00
P A:DC9 0.0 34.0 1.0
OP1 A:DC9 1.5 39.0 1.0
OP2 A:DC9 1.5 42.8 1.0
O5' A:DC9 1.6 37.0 1.0
O3' A:DA8 1.6 26.2 1.0
C5' A:DC9 2.6 35.0 1.0
C3' A:DA8 2.7 23.1 1.0
C2' A:DA8 3.3 26.7 1.0
C4' A:DC9 3.9 43.2 1.0
O A:HOH89 3.9 95.4 1.0
C4' A:DA8 3.9 19.8 1.0
O A:HOH91 4.2 33.4 1.0
O4' A:DC9 4.4 44.0 1.0
C3' A:DC9 4.4 45.0 1.0
C1' A:DA8 4.4 20.8 1.0
C2' A:DC9 4.7 40.1 1.0
O4' A:DA8 4.7 19.9 1.0
O A:HOH35 4.7 26.3 1.0
C5' A:DA8 4.9 30.7 1.0

Phosphorus binding site 9 out of 22 in 194d

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Phosphorus binding site 9 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:54.6
occ:1.00
P A:DG10 0.0 54.6 1.0
OP2 A:DG10 1.5 44.3 1.0
OP1 A:DG10 1.5 48.7 1.0
O3' A:DC9 1.6 53.8 1.0
O5' A:DG10 1.6 52.6 1.0
C3' A:DC9 2.6 45.0 1.0
C5' A:DG10 2.7 49.5 1.0
C4' A:DC9 3.6 43.2 1.0
C2' A:DC9 3.7 40.1 1.0
C4' A:DG10 4.0 50.7 1.0
C2' A:DG10 4.4 45.9 1.0
C5' A:DC9 4.4 35.0 1.0
C3' A:DG10 4.4 50.6 1.0
C1' A:DC9 4.5 34.5 1.0
O4' A:DG10 4.6 50.6 1.0
O4' A:DC9 4.7 44.0 1.0
C1' A:DG10 4.9 44.7 1.0
O5' A:DC9 5.0 37.0 1.0

Phosphorus binding site 10 out of 22 in 194d

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Phosphorus binding site 10 out of 22 in the X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:62.8
occ:1.00
P A:DC11 0.0 62.8 1.0
OP1 A:DC11 1.5 63.9 1.0
OP2 A:DC11 1.5 58.8 1.0
O3' A:DG10 1.6 58.3 1.0
O5' A:DC11 1.6 60.0 1.0
C3' A:DG10 2.7 50.6 1.0
C5' A:DC11 2.7 56.4 1.0
C4' A:DG10 3.6 50.7 1.0
C2' A:DG10 3.8 45.9 1.0
C4' A:DC11 4.0 55.6 1.0
O A:HOH80 4.2 64.5 1.0
O4' A:DC11 4.2 53.8 1.0
C6 A:DC11 4.2 44.9 1.0
O4' A:DG10 4.3 50.6 1.0
C1' A:DG10 4.3 44.7 1.0
O A:HOH71 4.5 47.1 1.0
C2' A:DC11 4.6 48.9 1.0
C3' A:DC11 4.6 54.8 1.0
C5' A:DG10 4.8 49.5 1.0
C5 A:DC11 4.9 44.8 1.0
C1' A:DC11 4.9 45.9 1.0

Reference:

K.Balendiran, S.T.Rao, C.Y.Sekharudu, G.Zon, M.Sundaralingam. X-Ray Structures of the B-Dna Dodecamer D(Cgcgttaacgcg) with An Inverted Central Tetranucleotide and Its Netropsin Complex. Acta Crystallogr.,Sect.D V. 51 190 1995.
ISSN: ISSN 0907-4449
PubMed: 15299320
DOI: 10.1107/S0907444994010759
Page generated: Fri Sep 25 11:50:54 2020

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