Phosphorus in PDB 197d: Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure

Protein crystallography data

The structure of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure, PDB code: 197d was solved by B.Langlois D'estaintot, A.Dautant, C.Courseille, G.Precigoux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.19
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 38.605, 50.824, 21.740, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Phosphorus atom in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure (pdb code 197d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 14 binding sites of Phosphorus where determined in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure, PDB code: 197d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 14 in 197d

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Phosphorus binding site 1 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:8.4
occ:1.00
 P A:DT2 0.0 8.4 1.0
OP2 A:DT2 1.5 8.1 1.0
OP1 A:DT2 1.5 6.3 1.0
O5' A:DT2 1.6 7.9 1.0
O3' A:DG1 1.7 8.1 1.0
C3' A:DG1 2.7 6.4 1.0
C5' A:DT2 2.7 6.9 1.0
C2' A:DG1 3.6 4.4 1.0
C4' A:DG1 3.9 6.6 1.0
C4' A:DT2 3.9 6.7 1.0
O A:HOH31 4.0 4.1 1.0
O4' A:DT2 4.2 5.7 1.0
C6 A:DT2 4.3 3.8 1.0
C5' A:DG1 4.4 7.2 1.0
C7 A:DT2 4.6 5.4 1.0
C3' A:DT2 4.8 6.5 1.0
C1' A:DG1 4.9 5.4 1.0
O B:HOH66 4.9 38.7 1.0
O A:HOH17 4.9 23.5 1.0
O4' A:DG1 5.0 7.5 1.0
C5 A:DT2 5.0 3.4 1.0

Phosphorus binding site 2 out of 14 in 197d

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Phosphorus binding site 2 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:6.2
occ:1.00
 P A:DA3 0.0 6.2 1.0
OP1 A:DA3 1.5 4.6 1.0
OP2 A:DA3 1.5 5.3 1.0
O5' A:DA3 1.6 4.1 1.0
O3' A:DT2 1.6 6.3 1.0
C3' A:DT2 2.6 6.5 1.0
C5' A:DA3 2.7 4.3 1.0
C2' A:DT2 3.5 6.4 1.0
C4' A:DT2 3.9 6.7 1.0
C4' A:DA3 3.9 3.6 1.0
O A:HOH47 4.1 2.0 1.0
C3' A:DA3 4.2 3.1 1.0
C8 A:DA3 4.3 2.7 1.0
O A:HOH48 4.4 13.6 1.0
C5' A:DT2 4.4 6.9 1.0
O4' A:DA3 4.7 3.1 1.0
C1' A:DT2 4.8 5.6 1.0
O A:HOH37 4.8 15.5 1.0
O A:HOH63 4.8 22.7 1.0
O3' A:DA3 4.9 2.2 1.0
OP2 A:DC4 4.9 3.0 1.0
O4' A:DT2 4.9 5.7 1.0

Phosphorus binding site 3 out of 14 in 197d

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Phosphorus binding site 3 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:5.0
occ:1.00
 P A:DC4 0.0 5.0 1.0
OP1 A:DC4 1.5 4.8 1.0
OP2 A:DC4 1.5 3.0 1.0
O3' A:DA3 1.6 2.2 1.0
O5' A:DC4 1.6 4.2 1.0
C3' A:DA3 2.6 3.1 1.0
C5' A:DC4 2.7 6.7 1.0
C2' A:DA3 3.2 3.2 1.0
C4' A:DA3 3.9 3.6 1.0
C6 A:DC4 3.9 6.7 1.0
C4' A:DC4 3.9 6.8 1.0
O4' A:DC4 4.1 7.7 1.0
C5 A:DC4 4.4 4.7 1.0
C5' A:DA3 4.6 4.3 1.0
C3' A:DC4 4.6 7.9 1.0
C1' A:DA3 4.6 2.9 1.0
O A:HOH47 4.7 2.0 1.0
O5' A:DA3 4.7 4.1 1.0
O4' A:DA3 4.8 3.1 1.0
N1 A:DC4 4.9 5.8 1.0

Phosphorus binding site 4 out of 14 in 197d

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Phosphorus binding site 4 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:11.7
occ:1.00
 P A:DG5 0.0 11.7 1.0
OP1 A:DG5 1.5 12.2 1.0
OP2 A:DG5 1.5 12.2 1.0
O5' A:DG5 1.6 9.6 1.0
O3' A:DC4 1.6 9.6 1.0
C5' A:DG5 2.5 9.6 1.0
C3' A:DC4 2.6 7.9 1.0
C2' A:DC4 3.6 6.7 1.0
C4' A:DG5 3.9 7.5 1.0
C4' A:DC4 3.9 6.8 1.0
O A:HOH69 4.2 3.4 1.0
C3' A:DG5 4.3 7.8 1.0
C5' A:DC4 4.4 6.7 1.0
O4' A:DG5 4.4 8.1 1.0
O A:HOH52 4.6 21.4 1.0
O3' A:DG5 4.6 8.1 1.0
O A:HOH79 4.6 30.8 1.0
C1' A:DC4 4.8 7.0 1.0
O A:HOH54 4.8 10.5 1.0
C8 A:DG5 4.9 4.6 1.0
O5' A:DC4 4.9 4.2 1.0
O4' A:DC4 4.9 7.7 1.0

Phosphorus binding site 5 out of 14 in 197d

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Phosphorus binding site 5 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:8.2
occ:1.00
 P A:DT6 0.0 8.2 1.0
OP2 A:DT6 1.5 8.1 1.0
OP1 A:DT6 1.5 10.7 1.0
O3' A:DG5 1.6 8.1 1.0
O5' A:DT6 1.6 7.5 1.0
C3' A:DG5 2.6 7.8 1.0
C5' A:DT6 2.7 6.5 1.0
C2' A:DG5 3.4 6.1 1.0
C4' A:DG5 3.9 7.5 1.0
C4' A:DT6 3.9 5.5 1.0
O4' A:DT6 4.2 4.5 1.0
O A:HOH30 4.3 32.8 1.0
O5' A:DG5 4.3 9.6 1.0
C5' A:DG5 4.4 9.6 1.0
C6 A:DT6 4.5 2.0 1.0
C3' A:DT6 4.5 6.3 1.0
O A:HOH76 4.6 19.4 1.0
C7 A:DT6 4.6 2.0 1.0
C1' A:DG5 4.7 6.7 1.0
OP2 A:DA7 4.9 10.5 1.0
O4' A:DG5 4.9 8.1 1.0

Phosphorus binding site 6 out of 14 in 197d

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Phosphorus binding site 6 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:9.1
occ:1.00
 P A:DA7 0.0 9.1 1.0
OP1 A:DA7 1.5 9.6 1.0
OP2 A:DA7 1.5 10.5 1.0
O5' A:DA7 1.6 9.8 1.0
O3' A:DT6 1.6 7.7 1.0
C5' A:DA7 2.6 10.4 1.0
C3' A:DT6 2.6 6.3 1.0
C2' A:DT6 3.7 5.5 1.0
C4' A:DT6 3.8 5.5 1.0
C4' A:DA7 3.8 10.7 1.0
O A:HOH36 4.0 40.8 1.0
C5' A:DT6 4.2 6.5 1.0
O4' A:DA7 4.2 10.1 1.0
O A:HOH34 4.4 27.3 1.0
O A:HOH30 4.6 32.8 1.0
O5' A:DT6 4.8 7.5 1.0
O4' A:DT6 4.9 4.5 1.0
C1' A:DT6 5.0 4.8 1.0

Phosphorus binding site 7 out of 14 in 197d

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Phosphorus binding site 7 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:15.8
occ:1.00
 P A:DC8 0.0 15.8 1.0
OP2 A:DC8 1.5 15.2 1.0
OP1 A:DC8 1.5 16.7 1.0
O3' A:DA7 1.6 14.0 1.0
O5' A:DC8 1.7 16.2 1.0
C5' A:DC8 2.7 16.8 1.0
C3' A:DA7 2.7 11.2 1.0
O A:HOH81 3.6 12.8 1.0
C2' A:DA7 3.7 10.4 1.0
C4' A:DC8 3.8 16.7 1.0
C3' A:DC8 3.9 17.0 1.0
C4' A:DA7 3.9 10.7 1.0
C2' A:DC8 4.0 16.3 1.0
C5' A:DA7 4.4 10.4 1.0
O4' A:DC8 4.4 16.2 1.0
C6 A:DC8 4.6 15.2 1.0
O A:HOH73 4.8 27.8 1.0
C1' A:DC8 4.8 15.4 1.0
C1' A:DA7 4.9 9.3 1.0

Phosphorus binding site 8 out of 14 in 197d

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Phosphorus binding site 8 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:6.6
occ:1.00
 P B:DT10 0.0 6.6 1.0
OP1 B:DT10 1.5 5.7 1.0
OP2 B:DT10 1.5 5.5 1.0
O5' B:DT10 1.6 7.0 1.0
O3' B:DG9 1.6 6.0 1.0
C3' B:DG9 2.6 6.5 1.0
C5' B:DT10 2.6 7.7 1.0
C2' B:DG9 3.6 6.7 1.0
C4' B:DG9 3.8 5.7 1.0
C4' B:DT10 3.9 7.1 1.0
C5' B:DG9 4.2 5.0 1.0
O4' B:DT10 4.4 8.9 1.0
C3' B:DT10 4.5 7.7 1.0
O B:HOH20 4.5 33.5 1.0
C6 B:DT10 4.6 9.7 1.0
O B:HOH43 4.8 32.5 1.0
C7 B:DT10 4.9 7.2 1.0
C1' B:DG9 4.9 6.7 1.0
O4' B:DG9 4.9 7.2 1.0
OP2 B:DA11 4.9 7.6 1.0
O B:HOH21 5.0 23.5 1.0

Phosphorus binding site 9 out of 14 in 197d

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Phosphorus binding site 9 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:6.8
occ:1.00
 P B:DA11 0.0 6.8 1.0
OP1 B:DA11 1.4 8.2 1.0
OP2 B:DA11 1.5 7.6 1.0
O3' B:DT10 1.6 7.7 1.0
O5' B:DA11 1.6 7.4 1.0
C3' B:DT10 2.5 7.7 1.0
C5' B:DA11 2.6 6.4 1.0
C2' B:DT10 3.4 8.2 1.0
O B:HOH28 3.7 7.6 1.0
C4' B:DT10 3.8 7.1 1.0
C4' B:DA11 3.9 6.0 1.0
O4' B:DA11 4.1 5.1 1.0
C5' B:DT10 4.2 7.7 1.0
O B:HOH33 4.2 2.7 1.0
O5' B:DT10 4.3 7.0 1.0
C3' B:DA11 4.4 6.4 1.0
O B:HOH67 4.4 15.1 1.0
C8 B:DA11 4.5 7.9 1.0
OP2 B:DC12 4.6 6.4 1.0
C1' B:DT10 4.7 8.2 1.0
O4' B:DT10 4.8 8.9 1.0

Phosphorus binding site 10 out of 14 in 197d

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Phosphorus binding site 10 out of 14 in the Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:6.7
occ:1.00
 P B:DC12 0.0 6.7 1.0
OP1 B:DC12 1.5 5.8 1.0
OP2 B:DC12 1.5 6.4 1.0
O5' B:DC12 1.6 6.7 1.0
O3' B:DA11 1.6 6.0 1.0
C5' B:DC12 2.6 8.9 1.0
C3' B:DA11 2.6 6.4 1.0
C2' B:DA11 3.6 5.7 1.0
C4' B:DC12 3.9 8.6 1.0
C4' B:DA11 3.9 6.0 1.0
O4' B:DC12 4.0 10.0 1.0
O B:HOH75 4.1 41.2 1.0
C5' B:DA11 4.3 6.4 1.0
C6 B:DC12 4.3 8.8 1.0
O5' B:DA11 4.4 7.4 1.0
C3' B:DC12 4.7 9.5 1.0
C1' B:DA11 4.9 5.9 1.0
C5 B:DC12 4.9 10.2 1.0
OP2 B:DG13 4.9 11.3 1.0
O4' B:DA11 5.0 5.1 1.0

Reference:

B.Langlois D'estaintot, A.Dautant, C.Courseille, G.Precigoux. Orthorhombic Crystal Structure of the A-Dna Octamer D(Gtacgtac). Comparison with the Tetragonal Structure. Eur.J.Biochem. V. 213 673 1993.
ISSN: ISSN 0014-2956
PubMed: 8477741
DOI: 10.1111/J.1432-1033.1993.TB17807.X
Page generated: Fri Sep 25 11:52:56 2020

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