Phosphorus in PDB 123d: Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor

Protein crystallography data

The structure of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor, PDB code: 123d was solved by M.Hahn, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.70
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 53.770, 53.770, 34.350, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / n/a

Phosphorus Binding Sites:

Pages:

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

Binding sites:

The binding sites of Phosphorus atom in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor (pdb code 123d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor, PDB code: 123d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 123d

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Phosphorus binding site 1 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:53.0
occ:1.00
P A:DC2 0.0 53.0 1.0
OP1 A:DC2 1.5 53.5 1.0
OP2 A:DC2 1.5 52.0 1.0
O3' A:DC1 1.6 51.6 1.0
O5' A:DC2 1.6 49.4 1.0
C5' A:DC2 2.7 42.5 1.0
C3' A:DC1 2.8 47.2 1.0
C4' A:DC1 3.4 49.6 1.0
C4' A:DC2 3.7 33.8 1.0
O A:HOH47 3.9 25.9 1.0
O4' A:DC1 3.9 43.6 1.0
C3' A:DC2 3.9 30.4 1.0
C2' A:DC1 4.0 40.5 1.0
C2' A:DC2 4.1 27.4 1.0
C1' A:DC1 4.2 34.5 1.0
O4' A:DC2 4.7 31.2 1.0
C5' A:DC1 4.7 56.5 1.0
C1' A:DC2 5.0 23.6 1.0

Phosphorus binding site 2 out of 18 in 123d

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Phosphorus binding site 2 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:31.1
occ:1.00
P A:DA3 0.0 31.1 1.0
OP1 A:DA3 1.5 31.9 1.0
OP2 A:DA3 1.5 32.4 1.0
O5' A:DA3 1.6 32.4 1.0
O3' A:DC2 1.6 32.6 1.0
C5' A:DA3 2.7 29.2 1.0
C3' A:DC2 2.8 30.4 1.0
O A:HOH87 3.4 44.0 1.0
C4' A:DC2 3.7 33.8 1.0
C2' A:DC2 3.8 27.4 1.0
C4' A:DA3 3.9 26.4 1.0
C8 A:DA3 4.0 17.0 1.0
O A:HOH94 4.0 63.7 1.0
O A:HOH58 4.1 35.6 1.0
O4' A:DA3 4.3 23.8 1.0
O4' A:DC2 4.3 31.2 1.0
C1' A:DC2 4.4 23.6 1.0
C3' A:DA3 4.5 23.2 1.0
C2' A:DA3 4.5 20.1 1.0
N9 A:DA3 4.7 14.2 1.0
N7 A:DA3 4.7 17.7 1.0
C1' A:DA3 4.8 19.4 1.0

Phosphorus binding site 3 out of 18 in 123d

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Phosphorus binding site 3 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:21.8
occ:1.00
P A:DG4 0.0 21.8 1.0
OP2 A:DG4 1.5 24.9 1.0
OP1 A:DG4 1.5 21.7 1.0
O5' A:DG4 1.6 21.2 1.0
O3' A:DA3 1.6 23.3 1.0
C5' A:DG4 2.6 20.1 1.0
C3' A:DA3 2.7 23.2 1.0
C2' A:DA3 3.6 20.1 1.0
C4' A:DA3 3.9 26.4 1.0
C4' A:DG4 4.0 17.8 1.0
O A:HOH46 4.0 35.3 1.0
O4' A:DG4 4.4 12.8 1.0
C1' A:DA3 4.4 19.4 1.0
C3' A:DG4 4.4 17.5 1.0
O A:HOH89 4.5 39.0 1.0
O4' A:DA3 4.6 23.8 1.0
O A:HOH75 4.6 48.2 1.0
C2' A:DG4 4.7 13.6 1.0

Phosphorus binding site 4 out of 18 in 123d

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Phosphorus binding site 4 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:12.2
occ:1.00
P A:DG5 0.0 12.2 1.0
OP1 A:DG5 1.5 12.6 1.0
OP2 A:DG5 1.5 13.3 1.0
O5' A:DG5 1.6 13.4 1.0
O3' A:DG4 1.6 21.3 1.0
C5' A:DG5 2.6 13.8 1.0
C3' A:DG4 2.7 17.5 1.0
O A:HOH23 3.7 14.1 1.0
C4' A:DG5 3.8 12.6 1.0
C2' A:DG4 3.8 13.6 1.0
C4' A:DG4 3.8 17.8 1.0
O A:HOH66 3.8 44.6 1.0
O A:HOH35 3.8 33.8 1.0
O A:HOH27 3.9 21.7 1.0
O4' A:DG5 4.0 15.0 1.0
C3' A:DG5 4.4 13.9 1.0
C1' A:DG4 4.4 10.8 1.0
C2' A:DG5 4.7 9.7 1.0
O4' A:DG4 4.8 12.8 1.0
C5' A:DG4 4.8 20.1 1.0
C8 A:DG5 4.8 13.7 1.0
C1' A:DG5 5.0 10.4 1.0

Phosphorus binding site 5 out of 18 in 123d

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Phosphorus binding site 5 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:13.0
occ:1.00
P A:DC6 0.0 13.0 1.0
OP2 A:DC6 1.5 17.1 1.0
OP1 A:DC6 1.5 19.2 1.0
O3' A:DG5 1.5 11.6 1.0
O5' A:DC6 1.6 18.5 1.0
C3' A:DG5 2.6 13.9 1.0
C5' A:DC6 2.7 20.0 1.0
C2' A:DG5 3.3 9.7 1.0
O A:HOH30 3.8 27.5 1.0
C4' A:DC6 3.9 23.0 1.0
C4' A:DG5 3.9 12.6 1.0
O A:HOH80 4.0 49.3 1.0
O A:HOH48 4.0 44.2 1.0
C1' A:DG5 4.2 10.4 1.0
O4' A:DC6 4.2 21.9 1.0
C3' A:DC6 4.4 18.9 1.0
O4' A:DG5 4.7 15.0 1.0
C2' A:DC6 4.9 21.7 1.0
C5' A:DG5 5.0 13.8 1.0
O A:HOH90 5.0 64.9 1.0

Phosphorus binding site 6 out of 18 in 123d

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Phosphorus binding site 6 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:21.9
occ:1.00
P A:5CM7 0.0 21.9 1.0
OP1 A:5CM7 1.5 22.7 1.0
OP2 A:5CM7 1.5 20.1 1.0
O5' A:5CM7 1.6 23.3 1.0
O3' A:DC6 1.6 22.5 1.0
C5' A:5CM7 2.7 22.1 1.0
C3' A:DC6 2.7 18.9 1.0
C2' A:DC6 3.4 21.7 1.0
O A:HOH92 3.5 64.5 1.0
C4' A:5CM7 3.9 20.3 1.0
C4' A:DC6 4.0 23.0 1.0
O A:HOH95 4.1 61.7 1.0
O4' A:5CM7 4.3 16.5 1.0
C3' A:5CM7 4.3 22.6 1.0
C1' A:DC6 4.4 18.1 1.0
O A:HOH77 4.8 43.6 1.0
C5' A:DC6 4.9 20.0 1.0
O4' A:DC6 4.9 21.9 1.0
C2' A:5CM7 5.0 19.3 1.0

Phosphorus binding site 7 out of 18 in 123d

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Phosphorus binding site 7 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:30.1
occ:1.00
P A:DT8 0.0 30.1 1.0
OP1 A:DT8 1.4 32.9 1.0
OP2 A:DT8 1.5 27.1 1.0
O5' A:DT8 1.5 28.8 1.0
O3' A:5CM7 1.6 25.7 1.0
C5' A:DT8 2.5 27.6 1.0
C3' A:5CM7 2.7 22.6 1.0
C2' A:5CM7 3.4 19.3 1.0
C4' A:DT8 3.8 22.0 1.0
C4' A:5CM7 3.9 20.3 1.0
O A:HOH62 4.0 40.7 1.0
O A:HOH77 4.1 43.6 1.0
C3' A:DT8 4.2 24.1 1.0
O4' A:DT8 4.3 16.9 1.0
C1' A:5CM7 4.4 14.9 1.0
C2' A:DT8 4.5 18.6 1.0
C5' A:5CM7 4.8 22.1 1.0
O4' A:5CM7 4.8 16.5 1.0

Phosphorus binding site 8 out of 18 in 123d

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Phosphorus binding site 8 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:26.6
occ:1.00
P A:DG9 0.0 26.6 1.0
OP1 A:DG9 1.5 26.7 1.0
OP2 A:DG9 1.5 27.5 1.0
O5' A:DG9 1.6 23.0 1.0
O3' A:DT8 1.7 26.9 1.0
C5' A:DG9 2.6 25.6 1.0
C3' A:DT8 2.7 24.1 1.0
C2' A:DT8 3.8 18.6 1.0
O A:HOH42 3.8 32.9 1.0
C4' A:DT8 3.8 22.0 1.0
C4' A:DG9 3.9 27.1 1.0
C8 A:DG9 4.3 15.3 1.0
O4' A:DG9 4.4 24.9 1.0
C2' A:DG9 4.4 26.8 1.0
C3' A:DG9 4.5 31.6 1.0
C1' A:DT8 4.6 17.6 1.0
C5' A:DT8 4.7 27.6 1.0
C1' A:DG9 4.7 22.4 1.0
N9 A:DG9 4.7 16.9 1.0
O4' A:DT8 4.8 16.9 1.0
N7 A:DG9 5.0 14.6 1.0

Phosphorus binding site 9 out of 18 in 123d

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Phosphorus binding site 9 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:34.4
occ:1.00
P A:DG10 0.0 34.4 1.0
OP2 A:DG10 1.4 33.1 1.0
OP1 A:DG10 1.5 35.8 1.0
O3' A:DG9 1.6 35.6 1.0
O5' A:DG10 1.6 36.9 1.0
C5' A:DG10 2.6 38.0 1.0
C3' A:DG9 2.6 31.6 1.0
C2' A:DG9 3.4 26.8 1.0
C4' A:DG9 3.9 27.1 1.0
C4' A:DG10 4.0 34.6 1.0
C1' A:DG9 4.2 22.4 1.0
O4' A:DG9 4.5 24.9 1.0
C3' A:DG10 4.6 32.1 1.0

Phosphorus binding site 10 out of 18 in 123d

Go back to Phosphorus Binding Sites List in 123d
Phosphorus binding site 10 out of 18 in the Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(Ccaggcm==5==Ctgg) Derived From Nuclsq, Tnt, and X-Plor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:40.4
occ:1.00
P B:DC12 0.0 40.4 1.0
OP2 B:DC12 1.5 37.9 1.0
OP1 B:DC12 1.5 42.0 1.0
O3' B:DC11 1.6 37.3 1.0
O5' B:DC12 1.6 40.5 1.0
C3' B:DC11 2.5 36.2 1.0
C5' B:DC12 2.7 35.2 1.0
C2' B:DC11 3.4 32.0 1.0
C4' B:DC11 3.9 39.5 1.0
C4' B:DC12 4.0 31.0 1.0
O4' B:DC12 4.3 29.1 1.0
C1' B:DC11 4.4 31.5 1.0
C3' B:DC12 4.4 32.0 1.0
O5' B:DC11 4.6 47.0 1.0
C2' B:DC12 4.6 27.1 1.0
C5' B:DC11 4.8 42.6 1.0
O4' B:DC11 4.8 37.7 1.0

Reference:

M.Hahn, U.Heinemann. Dna Helix Structure and Refinement Algorithm: Comparison of Models For D(CCAGGCM5CTGG) Derived From Nuclsq, Tnt and X-Plor. Acta Crystallogr.,Sect.D V. 49 468 1993.
ISSN: ISSN 0907-4449
PubMed: 15299506
DOI: 10.1107/S0907444993004858
Page generated: Fri Sep 25 11:14:17 2020

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