Phosphorus in PDB 118d: Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes

Protein crystallography data

The structure of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes, PDB code: 118d was solved by C.Bingman, X.Li, G.Zon, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.64
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.220, 42.220, 25.070, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes (pdb code 118d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 7 binding sites of Phosphorus where determined in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes, PDB code: 118d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7;

Phosphorus binding site 1 out of 7 in 118d

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Phosphorus binding site 1 out of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:25.7
occ:1.00
P A:DT2 0.0 25.7 1.0
OP2 A:DT2 1.5 25.8 1.0
OP1 A:DT2 1.5 35.1 1.0
O5' A:DT2 1.6 22.3 1.0
O3' A:DG1 1.6 26.5 1.0
C3' A:DG1 2.7 23.6 1.0
C5' A:DT2 2.7 24.8 1.0
C2' A:DG1 3.6 23.2 1.0
O A:HOH20 3.9 49.0 1.0
O A:HOH21 3.9 45.6 1.0
C4' A:DG1 3.9 24.1 1.0
C4' A:DT2 4.0 29.3 1.0
O4' A:DT2 4.4 30.1 1.0
C6 A:DT2 4.4 20.6 1.0
C5' A:DG1 4.4 25.0 1.0
C3' A:DT2 4.5 29.9 1.0
C7 A:DT2 4.6 18.5 1.0
O5' A:DG1 4.7 27.7 1.0
C1' A:DG1 4.9 23.6 1.0

Phosphorus binding site 2 out of 7 in 118d

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Phosphorus binding site 2 out of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:37.6
occ:1.00
P A:DG3 0.0 37.6 1.0
OP2 A:DG3 1.5 37.1 1.0
OP1 A:DG3 1.5 39.8 1.0
O5' A:DG3 1.6 32.6 1.0
O3' A:DT2 1.6 37.0 1.0
C5' A:DG3 2.6 34.1 1.0
C3' A:DT2 2.7 29.9 1.0
C2' A:DT2 3.4 28.9 1.0
C4' A:DG3 3.9 35.0 1.0
C4' A:DT2 4.0 29.3 1.0
O A:HOH44 4.1 56.5 1.0
O4' A:DG3 4.2 36.2 1.0
C3' A:DG3 4.4 36.7 1.0
O A:HOH20 4.5 49.0 1.0
O A:HOH37 4.5 63.3 1.0
C5' A:DT2 4.5 24.8 1.0
C8 A:DG3 4.5 24.6 1.0
O5' A:DT2 4.8 22.3 1.0
C1' A:DT2 4.8 27.0 1.0
O4' A:DT2 5.0 30.1 1.0

Phosphorus binding site 3 out of 7 in 118d

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Phosphorus binding site 3 out of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:37.4
occ:1.00
P A:DC4 0.0 37.4 1.0
OP2 A:DC4 1.5 32.5 1.0
OP1 A:DC4 1.5 47.7 1.0
O5' A:DC4 1.6 31.0 1.0
O3' A:DG3 1.6 36.5 1.0
C5' A:DC4 2.6 29.3 1.0
C3' A:DG3 2.7 36.7 1.0
C2' A:DG3 3.2 32.1 1.0
O A:HOH47 3.3 71.6 1.0
C4' A:DC4 3.9 34.5 1.0
O A:HOH16 3.9 60.3 1.0
C4' A:DG3 4.0 35.0 1.0
O A:HOH45 4.1 59.2 1.0
O A:HOH49 4.2 67.7 1.0
O4' A:DC4 4.3 33.4 1.0
C3' A:DC4 4.3 32.8 1.0
C6 A:DC4 4.5 19.2 1.0
O A:HOH43 4.5 60.3 1.0
C1' A:DG3 4.6 31.6 1.0
C5' A:DG3 4.8 34.1 1.0
O4' A:DG3 4.9 36.2 1.0
O3' A:DC4 5.0 28.1 1.0

Phosphorus binding site 4 out of 7 in 118d

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Phosphorus binding site 4 out of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:27.9
occ:1.00
P A:DG5 0.0 27.9 1.0
OP2 A:DG5 1.4 26.8 1.0
OP1 A:DG5 1.5 32.4 1.0
O5' A:DG5 1.6 24.4 1.0
O3' A:DC4 1.6 28.1 1.0
C3' A:DC4 2.6 32.8 1.0
C5' A:DG5 2.6 19.6 1.0
C2' A:DC4 3.4 30.9 1.0
O A:HOH31 3.4 66.0 1.0
O A:HOH43 3.8 60.3 1.0
C4' A:DG5 3.9 20.2 1.0
C4' A:DC4 4.0 34.5 1.0
O A:HOH49 4.1 67.7 1.0
O4' A:DG5 4.1 23.1 1.0
C5' A:DC4 4.6 29.3 1.0
O5' A:DC4 4.7 31.0 1.0
C1' A:DC4 4.8 27.1 1.0
O4' A:DC4 5.0 33.4 1.0

Phosphorus binding site 5 out of 7 in 118d

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Phosphorus binding site 5 out of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:23.6
occ:1.00
P A:DC6 0.0 23.6 1.0
OP2 A:DC6 1.5 22.2 1.0
OP1 A:DC6 1.5 30.8 1.0
O3' A:DG5 1.6 24.5 1.0
O5' A:DC6 1.6 21.6 1.0
C3' A:DG5 2.6 21.9 1.0
C5' A:DC6 2.7 24.5 1.0
C2' A:DG5 3.6 19.0 1.0
O A:HOH39 3.6 62.3 1.0
O A:HOH26 3.6 44.3 1.0
O A:HOH34 3.7 88.4 1.0
O A:HOH46 3.8 72.6 1.0
C4' A:DG5 3.8 20.2 1.0
C4' A:DC6 3.9 25.2 1.0
C6 A:DC6 4.2 18.2 1.0
C5' A:DG5 4.3 19.6 1.0
O4' A:DC6 4.3 22.6 1.0
C3' A:DC6 4.4 25.1 1.0
O A:HOH40 4.4 90.9 1.0
O A:HOH22 4.7 30.8 1.0
C5 A:DC6 4.9 17.6 1.0
C1' A:DG5 4.9 18.0 1.0
O4' A:DG5 5.0 23.1 1.0

Phosphorus binding site 6 out of 7 in 118d

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Phosphorus binding site 6 out of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:27.4
occ:1.00
P A:DA7 0.0 27.4 1.0
OP1 A:DA7 1.5 32.3 1.0
OP2 A:DA7 1.5 26.7 1.0
O3' A:DC6 1.6 25.5 1.0
O5' A:DA7 1.6 23.6 1.0
C3' A:DC6 2.6 25.1 1.0
C5' A:DA7 2.7 23.3 1.0
O A:HOH48 3.3 67.7 1.0
C2' A:DC6 3.3 20.2 1.0
C4' A:DC6 3.9 25.2 1.0
C4' A:DA7 3.9 21.3 1.0
O A:HOH41 4.0 56.2 1.0
O A:HOH11 4.0 44.8 1.0
O A:HOH26 4.1 44.3 1.0
O4' A:DA7 4.3 23.7 1.0
C8 A:DA7 4.4 17.1 1.0
C3' A:DA7 4.5 19.6 1.0
O5' A:DC6 4.5 21.6 1.0
C5' A:DC6 4.5 24.5 1.0
C1' A:DC6 4.7 20.6 1.0
O4' A:DC6 4.9 22.6 1.0

Phosphorus binding site 7 out of 7 in 118d

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Phosphorus binding site 7 out of 7 in the Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:33.7
occ:1.00
P A:DC8 0.0 33.7 1.0
OP2 A:DC8 1.5 40.7 1.0
OP1 A:DC8 1.5 36.7 1.0
O5' A:DC8 1.6 29.9 1.0
O3' A:DA7 1.6 27.2 1.0
C5' A:DC8 2.6 36.4 1.0
C3' A:DA7 2.6 19.6 1.0
C2' A:DA7 3.4 20.0 1.0
O A:HOH42 3.8 52.6 1.0
O A:HOH41 3.8 56.2 1.0
C4' A:DC8 3.9 36.8 1.0
C4' A:DA7 3.9 21.3 1.0
O4' A:DC8 4.3 37.2 1.0
C3' A:DC8 4.3 39.7 1.0
C6 A:DC8 4.5 25.9 1.0
C5' A:DA7 4.5 23.3 1.0
O5' A:DA7 4.7 23.6 1.0
C1' A:DA7 4.8 21.5 1.0
C2' A:DC8 4.9 38.1 1.0
O4' A:DA7 5.0 23.7 1.0

Reference:

C.Bingman, X.Li, G.Zon, M.Sundaralingam. Crystal and Molecular Structure of D(Gtgcgcac): Investigation of the Effects of Base Sequence on the Conformation of Octamer Duplexes. Biochemistry V. 31 12803 1992.
ISSN: ISSN 0006-2960
PubMed: 1463751
DOI: 10.1021/BI00166A014
Page generated: Fri Sep 25 11:12:21 2020

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