Phosphorus in PDB 160d: High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets

Protein crystallography data

The structure of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets, PDB code: 160d was solved by B.Ramakrishnan, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.880, 44.600, 46.970, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets (pdb code 160d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets, PDB code: 160d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 160d

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Phosphorus binding site 1 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:39.3
occ:1.00
P A:DC2 0.0 39.3 1.0
OP2 A:DC2 1.5 33.0 1.0
OP1 A:DC2 1.5 41.4 1.0
O3' A:DC1 1.5 41.3 1.0
O5' A:DC2 1.7 38.8 1.0
C3' A:DC1 2.5 21.8 1.0
C5' A:DC2 2.6 19.4 1.0
C2' A:DC1 3.4 18.6 1.0
C4' A:DC1 3.7 38.2 1.0
O A:HOH41 3.8 55.1 1.0
O A:HOH122 3.8 51.4 1.0
C4' A:DC2 3.9 28.9 1.0
C5' A:DC1 4.0 30.6 1.0
O A:HOH71 4.2 59.8 1.0
O4' A:DC2 4.3 24.0 1.0
C6 A:DC2 4.4 19.9 1.0
C3' A:DC2 4.6 27.3 1.0
C1' A:DC1 4.7 24.8 1.0
O4' A:DC1 4.7 33.3 1.0
O5' A:DC1 4.7 29.6 1.0

Phosphorus binding site 2 out of 18 in 160d

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Phosphorus binding site 2 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:34.1
occ:1.00
P A:DC3 0.0 34.1 1.0
OP2 A:DC3 1.4 25.9 1.0
OP1 A:DC3 1.5 53.8 1.0
O3' A:DC2 1.6 31.2 1.0
O5' A:DC3 1.6 34.3 1.0
C5' A:DC3 2.7 13.8 1.0
C3' A:DC2 2.7 27.3 1.0
C2' A:DC2 3.5 18.7 1.0
O A:HOH103 3.7 60.4 1.0
O A:HOH26 3.8 56.5 1.0
C4' A:DC2 4.0 28.9 1.0
C4' A:DC3 4.0 29.1 1.0
O4' A:DC3 4.2 26.7 1.0
C5' A:DC2 4.5 19.4 1.0
O A:HOH50 4.7 66.2 1.0
C3' A:DC3 4.7 32.7 1.0
C6 A:DC3 4.8 17.2 1.0
C1' A:DC2 4.9 23.9 1.0
O A:HOH41 4.9 55.1 1.0

Phosphorus binding site 3 out of 18 in 160d

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Phosphorus binding site 3 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:35.8
occ:1.00
P A:DG4 0.0 35.8 1.0
OP2 A:DG4 1.4 48.9 1.0
OP1 A:DG4 1.5 58.9 1.0
O3' A:DC3 1.6 33.2 1.0
O5' A:DG4 1.7 28.8 1.0
C5' A:DG4 2.6 21.9 1.0
C3' A:DC3 2.6 32.7 1.0
C2' A:DC3 3.3 23.5 1.0
O A:HOH23 3.7 53.9 1.0
C4' A:DC3 3.9 29.1 1.0
C4' A:DG4 3.9 12.1 1.0
O A:HOH50 4.0 66.2 1.0
C3' A:DG4 4.3 13.2 1.0
O A:HOH84 4.4 84.0 1.0
C8 A:DG4 4.4 14.4 1.0
O4' A:DG4 4.5 14.2 1.0
OP2 A:DG5 4.5 22.2 1.0
C5' A:DC3 4.6 13.8 1.0
C1' A:DC3 4.6 16.2 1.0
O3' A:DG4 4.8 20.9 1.0
O4' A:DC3 4.9 26.7 1.0

Phosphorus binding site 4 out of 18 in 160d

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Phosphorus binding site 4 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:26.8
occ:1.00
P A:DG5 0.0 26.8 1.0
OP2 A:DG5 1.4 22.2 1.0
OP1 A:DG5 1.5 33.2 1.0
O3' A:DG4 1.6 20.9 1.0
O5' A:DG5 1.6 19.8 1.0
C5' A:DG5 2.6 15.2 1.0
C3' A:DG4 2.7 13.2 1.0
C2' A:DG4 3.6 22.4 1.0
O A:HOH35 3.6 89.2 1.0
O A:HOH69 3.8 93.3 1.0
C4' A:DG5 3.8 23.4 1.0
C4' A:DG4 3.9 12.1 1.0
O A:HOH37 3.9 51.9 1.0
O4' A:DG5 4.3 16.8 1.0
O A:HOH84 4.3 84.0 1.0
O A:HOH23 4.3 53.9 1.0
C5' A:DG4 4.3 21.9 1.0
O5' A:DG4 4.7 28.8 1.0
OP1 A:DG4 4.8 58.9 1.0
C1' A:DG4 4.9 15.2 1.0

Phosphorus binding site 5 out of 18 in 160d

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Phosphorus binding site 5 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:29.2
occ:1.00
P A:DC6 0.0 29.2 1.0
OP2 A:DC6 1.4 19.0 1.0
OP1 A:DC6 1.5 45.3 1.0
O3' A:DG5 1.6 29.2 1.0
O5' A:DC6 1.6 25.3 1.0
C5' A:DC6 2.6 21.8 1.0
C3' A:DG5 2.7 11.7 1.0
C2' A:DG5 3.6 19.5 1.0
O A:HOH89 3.6 65.7 1.0
O A:HOH63 3.8 44.4 1.0
C4' A:DC6 3.8 29.4 1.0
C4' A:DG5 3.9 23.4 1.0
O A:HOH45 4.1 64.6 1.0
O A:HOH49 4.1 67.5 1.0
O4' A:DC6 4.1 25.6 1.0
O A:HOH32 4.2 94.9 1.0
C6 A:DC6 4.2 10.2 1.0
C3' A:DC6 4.2 20.9 1.0
C5' A:DG5 4.3 15.2 1.0
OP2 A:DC7 4.7 33.4 1.0
O3' A:DC6 4.8 32.8 1.0
C1' A:DG5 4.9 16.8 1.0
C5 A:DC6 4.9 23.4 1.0
O A:HOH97 5.0 65.9 1.0
O4' A:DG5 5.0 16.8 1.0

Phosphorus binding site 6 out of 18 in 160d

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Phosphorus binding site 6 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:30.9
occ:1.00
P A:DC7 0.0 30.9 1.0
OP2 A:DC7 1.4 33.4 1.0
OP1 A:DC7 1.5 42.3 1.0
O3' A:DC6 1.6 32.8 1.0
O5' A:DC7 1.7 28.3 1.0
C5' A:DC7 2.6 23.8 1.0
C3' A:DC6 2.7 20.9 1.0
C2' A:DC6 3.6 17.2 1.0
C4' A:DC7 3.9 25.0 1.0
C4' A:DC6 3.9 29.4 1.0
O A:HOH49 4.1 67.5 1.0
O4' A:DC7 4.1 21.6 1.0
O A:HOH108 4.2 0.2 1.0
O A:HOH51 4.2 53.4 1.0
O5' A:DC6 4.3 25.3 1.0
C5' A:DC6 4.4 21.8 1.0
O A:HOH32 4.4 94.9 1.0
C3' A:DC7 4.5 27.6 1.0
O A:HOH112 4.6 90.3 1.0
O A:HOH110 4.7 88.5 1.0
C6 A:DC7 4.7 20.6 1.0
O A:HOH92 4.8 69.2 1.0
C1' A:DC6 4.9 29.8 1.0
O4' A:DC6 5.0 25.6 1.0

Phosphorus binding site 7 out of 18 in 160d

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Phosphorus binding site 7 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:31.3
occ:1.00
P A:DG8 0.0 31.3 1.0
OP1 A:DG8 1.4 50.0 1.0
OP2 A:DG8 1.5 29.0 1.0
O3' A:DC7 1.6 37.5 1.0
O5' A:DG8 1.7 27.0 1.0
C5' A:DG8 2.4 13.1 1.0
C3' A:DC7 2.7 27.6 1.0
C2' A:DC7 3.4 16.4 1.0
C4' A:DG8 3.8 15.3 1.0
O A:HOH98 3.8 78.6 1.0
C4' A:DC7 4.0 25.0 1.0
O A:HOH48 4.2 52.0 1.0
O A:HOH74 4.2 49.9 1.0
O4' A:DG8 4.2 10.8 1.0
C3' A:DG8 4.5 12.4 1.0
C5' A:DC7 4.6 23.8 1.0
O A:HOH86 4.6 61.0 1.0
O A:HOH51 4.7 53.4 1.0
O5' A:DC7 4.8 28.3 1.0
C1' A:DC7 4.8 11.1 1.0
C8 A:DG8 4.8 17.9 1.0
O4' A:DC7 4.9 21.6 1.0

Phosphorus binding site 8 out of 18 in 160d

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Phosphorus binding site 8 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:23.4
occ:1.00
P A:DG9 0.0 23.4 1.0
OP2 A:DG9 1.4 17.8 1.0
OP1 A:DG9 1.4 26.1 1.0
O3' A:DG8 1.6 18.2 1.0
O5' A:DG9 1.7 15.3 1.0
C5' A:DG9 2.6 17.0 1.0
C3' A:DG8 2.6 12.4 1.0
C2' A:DG8 3.4 6.0 1.0
C4' A:DG8 3.9 15.3 1.0
C4' A:DG9 3.9 14.9 1.0
O A:HOH74 3.9 49.9 1.0
O A:HOH48 4.0 52.0 1.0
O4' A:DG9 4.2 12.4 1.0
O A:HOH55 4.3 48.1 1.0
C3' A:DG9 4.5 21.2 1.0
C5' A:DG8 4.5 13.1 1.0
O A:HOH53 4.6 46.2 1.0
C8 A:DG9 4.6 19.1 1.0
O5' A:DG8 4.8 27.0 1.0
C1' A:DG8 4.8 16.1 1.0
O A:HOH42 4.9 59.0 1.0
O4' A:DG8 4.9 10.8 1.0

Phosphorus binding site 9 out of 18 in 160d

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Phosphorus binding site 9 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:20.2
occ:1.00
P A:DG10 0.0 20.2 1.0
OP2 A:DG10 1.4 31.9 1.0
OP1 A:DG10 1.5 21.1 1.0
O3' A:DG9 1.7 14.3 1.0
O5' A:DG10 1.7 14.4 1.0
C3' A:DG9 2.6 21.2 1.0
C5' A:DG10 2.9 18.4 1.0
O A:HOH44 3.5 50.5 1.0
C2' A:DG9 3.5 12.5 1.0
O A:HOH42 3.7 59.0 1.0
O A:HOH22 3.8 32.5 1.0
C4' A:DG9 3.8 14.9 1.0
O A:HOH28 3.9 45.2 1.0
C4' A:DG10 4.0 9.2 1.0
O A:HOH53 4.1 46.2 1.0
C3' A:DG10 4.4 13.6 1.0
O A:HOH55 4.4 48.1 1.0
O4' A:DG10 4.4 22.2 1.0
C5' A:DG9 4.5 17.0 1.0
O5' A:DG9 4.7 15.3 1.0
C8 A:DG10 4.7 15.2 1.0
C1' A:DG9 4.8 23.2 1.0
O3' A:DG10 4.9 15.3 1.0
O4' A:DG9 4.9 12.4 1.0

Phosphorus binding site 10 out of 18 in 160d

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Phosphorus binding site 10 out of 18 in the High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg): Novel Intermolecular Base-Paired G*(G.C) Triplets within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:37.4
occ:1.00
P B:DC12 0.0 37.4 1.0
OP2 B:DC12 1.4 28.2 1.0
OP1 B:DC12 1.5 36.0 1.0
O5' B:DC12 1.6 22.0 1.0
O3' B:DC11 1.6 23.1 1.0
C3' B:DC11 2.7 32.5 1.0
C5' B:DC12 2.8 21.7 1.0
C2' B:DC11 3.4 18.2 1.0
O B:HOH64 3.7 71.9 1.0
C4' B:DC12 3.9 20.3 1.0
C4' B:DC11 3.9 38.5 1.0
O B:HOH123 4.0 79.3 1.0
O B:HOH25 4.1 47.7 1.0
O B:HOH46 4.1 61.1 1.0
O5' B:DC11 4.2 54.4 1.0
O4' B:DC12 4.2 28.2 1.0
C3' B:DC12 4.3 20.8 1.0
C6 B:DC12 4.3 13.9 1.0
O B:HOH106 4.3 82.8 1.0
C5' B:DC11 4.5 43.2 1.0
O B:HOH107 4.6 80.4 1.0
C1' B:DC11 4.8 33.2 1.0
OP2 B:DC13 4.8 22.4 1.0
C5 B:DC12 5.0 13.6 1.0
O4' B:DC11 5.0 56.0 1.0

Reference:

B.Ramakrishnan, M.Sundaralingam. High Resolution Crystal Structure of the A-Dna Decamer D(Cccggccggg). Novel Intermolecular Base-Paired G*(G.C) Triplets. J.Mol.Biol. V. 231 431 1993.
ISSN: ISSN 0022-2836
PubMed: 8510155
DOI: 10.1006/JMBI.1993.1292
Page generated: Fri Sep 25 11:35:14 2020

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