Phosphorus in PDB 167d: The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps

Protein crystallography data

The structure of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps, PDB code: 167d was solved by D.S.Goodsell, M.Kaczor-Grzeskowiak, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 33.200, 33.200, 96.040, 90.00, 90.00, 120.00
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 The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps (pdb code 167d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps, PDB code: 167d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 167d

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Phosphorus binding site 1 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:45.3
occ:1.00
P A:DC2 0.0 45.3 1.0
OP1 A:DC2 1.5 50.9 1.0
OP2 A:DC2 1.5 50.2 1.0
O5' A:DC2 1.6 36.9 1.0
O3' A:DC1 1.7 48.6 1.0
C5' A:DC2 2.5 34.4 1.0
C3' A:DC1 2.7 38.1 1.0
C2' A:DC1 3.7 31.8 1.0
C4' A:DC2 3.8 35.8 1.0
C4' A:DC1 3.9 39.9 1.0
O A:HOH38 3.9 46.0 1.0
O A:HOH49 4.1 59.8 1.0
C3' A:DC2 4.3 36.3 1.0
O4' A:DC2 4.3 31.4 1.0
C1' A:DC1 4.5 19.8 1.0
C2' A:DC2 4.6 34.1 1.0
C5' A:DC1 4.7 38.3 1.0
O4' A:DC1 4.8 32.7 1.0

Phosphorus binding site 2 out of 18 in 167d

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Phosphorus binding site 2 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:42.9
occ:1.00
P A:DA3 0.0 42.9 1.0
OP1 A:DA3 1.5 39.6 1.0
OP2 A:DA3 1.5 38.9 1.0
O5' A:DA3 1.6 40.2 1.0
O3' A:DC2 1.7 47.2 1.0
C5' A:DA3 2.6 30.1 1.0
C3' A:DC2 2.9 36.3 1.0
C4' A:DA3 3.9 34.5 1.0
C2' A:DC2 3.9 34.1 1.0
C4' A:DC2 4.0 35.8 1.0
C2' A:DA3 4.2 34.5 1.0
C3' A:DA3 4.3 34.4 1.0
O4' A:DA3 4.5 32.9 1.0
C1' A:DC2 4.6 25.5 1.0
C8 A:DA3 4.7 25.3 1.0
C5' A:DC2 5.0 34.4 1.0
O4' A:DC2 5.0 31.4 1.0
C1' A:DA3 5.0 27.9 1.0

Phosphorus binding site 3 out of 18 in 167d

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Phosphorus binding site 3 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:43.3
occ:1.00
P A:DT4 0.0 43.3 1.0
OP1 A:DT4 1.5 46.9 1.0
OP2 A:DT4 1.5 38.9 1.0
O5' A:DT4 1.6 35.7 1.0
O3' A:DA3 1.7 47.4 1.0
C5' A:DT4 2.6 32.6 1.0
C3' A:DA3 2.7 34.4 1.0
C2' A:DA3 3.6 34.5 1.0
C4' A:DT4 3.8 33.9 1.0
O A:HOH63 3.9 57.3 1.0
C4' A:DA3 3.9 34.5 1.0
O4' A:DT4 4.1 31.4 1.0
C1' A:DA3 4.2 27.9 1.0
O A:HOH46 4.2 41.1 1.0
C3' A:DT4 4.3 34.6 1.0
O4' A:DA3 4.4 32.9 1.0
O A:HOH60 4.7 64.0 1.0
C2' A:DT4 4.7 33.2 1.0

Phosphorus binding site 4 out of 18 in 167d

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Phosphorus binding site 4 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:37.7
occ:1.00
P A:DT5 0.0 37.7 1.0
OP2 A:DT5 1.5 42.7 1.0
OP1 A:DT5 1.5 39.3 1.0
O3' A:DT4 1.6 46.5 1.0
O5' A:DT5 1.6 38.9 1.0
C5' A:DT5 2.6 26.1 1.0
C3' A:DT4 2.7 34.6 1.0
C2' A:DT4 3.3 33.2 1.0
C4' A:DT5 3.8 24.7 1.0
C4' A:DT4 4.0 33.9 1.0
O4' A:DT5 4.0 26.2 1.0
O A:HOH54 4.2 55.9 1.0
C1' A:DT4 4.2 21.5 1.0
O A:HOH55 4.2 53.1 1.0
C3' A:DT5 4.3 28.6 1.0
O4' A:DT4 4.8 31.4 1.0

Phosphorus binding site 5 out of 18 in 167d

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Phosphorus binding site 5 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:40.7
occ:1.00
P A:DA6 0.0 40.7 1.0
OP2 A:DA6 1.5 43.5 1.0
OP1 A:DA6 1.5 41.5 1.0
O3' A:DT5 1.6 31.5 1.0
O5' A:DA6 1.6 39.5 1.0
C3' A:DT5 2.7 28.6 1.0
C5' A:DA6 2.7 29.7 1.0
C2' A:DT5 3.4 30.9 1.0
C4' A:DA6 3.8 27.8 1.0
C4' A:DT5 3.9 24.7 1.0
O A:HOH59 4.0 62.5 1.0
O A:HOH41 4.2 47.9 1.0
O4' A:DA6 4.2 33.1 1.0
C1' A:DT5 4.5 18.1 1.0
O A:HOH64 4.6 55.2 1.0
C3' A:DA6 4.6 28.2 1.0
C5' A:DT5 4.7 26.1 1.0
O4' A:DT5 5.0 26.2 1.0

Phosphorus binding site 6 out of 18 in 167d

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Phosphorus binding site 6 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:44.4
occ:1.00
P A:DA7 0.0 44.4 1.0
OP1 A:DA7 1.4 44.9 1.0
OP2 A:DA7 1.5 36.8 1.0
O3' A:DA6 1.6 33.1 1.0
O5' A:DA7 1.6 37.8 1.0
C3' A:DA6 2.6 28.2 1.0
C5' A:DA7 2.6 22.3 1.0
C2' A:DA6 3.6 27.4 1.0
C4' A:DA6 3.6 27.8 1.0
C4' A:DA7 3.9 18.4 1.0
C3' A:DA7 4.2 25.6 1.0
C2' A:DA7 4.2 20.4 1.0
C5' A:DA6 4.3 29.7 1.0
O4' A:DA7 4.4 23.5 1.0
C1' A:DA6 4.4 25.8 1.0
O4' A:DA6 4.5 33.1 1.0
C8 A:DA7 4.9 14.6 1.0
C1' A:DA7 5.0 20.5 1.0

Phosphorus binding site 7 out of 18 in 167d

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Phosphorus binding site 7 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:39.6
occ:1.00
P A:DT8 0.0 39.6 1.0
OP1 A:DT8 1.5 40.6 1.0
OP2 A:DT8 1.5 47.9 1.0
O5' A:DT8 1.6 31.4 1.0
O3' A:DA7 1.7 41.4 1.0
C5' A:DT8 2.6 29.7 1.0
C3' A:DA7 2.7 25.6 1.0
C2' A:DA7 3.3 20.4 1.0
O A:HOH62 3.7 69.2 1.0
C1' A:DA7 3.9 20.5 1.0
C4' A:DT8 4.0 30.6 1.0
C4' A:DA7 4.0 18.4 1.0
C3' A:DT8 4.2 36.0 1.0
O4' A:DA7 4.6 23.5 1.0
O4' A:DT8 4.7 33.5 1.0
C2' A:DT8 4.8 33.6 1.0

Phosphorus binding site 8 out of 18 in 167d

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Phosphorus binding site 8 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:50.4
occ:1.00
P A:DG9 0.0 50.4 1.0
OP1 A:DG9 1.5 47.1 1.0
OP2 A:DG9 1.5 41.9 1.0
O5' A:DG9 1.6 36.5 1.0
O3' A:DT8 1.6 44.2 1.0
C3' A:DT8 2.7 36.0 1.0
C5' A:DG9 2.7 46.3 1.0
C2' A:DT8 3.4 33.6 1.0
C4' A:DT8 3.9 30.6 1.0
C4' A:DG9 3.9 47.2 1.0
C2' A:DG9 4.0 32.1 1.0
C3' A:DG9 4.3 45.8 1.0
C1' A:DT8 4.5 31.4 1.0
O4' A:DG9 4.6 42.3 1.0
C1' A:DG9 4.7 29.9 1.0
O4' A:DT8 4.8 33.5 1.0
C8 A:DG9 4.8 18.6 1.0
C5' A:DT8 4.9 29.7 1.0
O5' A:DT8 4.9 31.4 1.0

Phosphorus binding site 9 out of 18 in 167d

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Phosphorus binding site 9 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:57.0
occ:1.00
P A:DG10 0.0 57.0 1.0
OP1 A:DG10 1.5 43.9 1.0
OP2 A:DG10 1.5 50.6 1.0
O5' A:DG10 1.6 53.7 1.0
O3' A:DG9 1.7 54.9 1.0
C3' A:DG9 2.6 45.8 1.0
C5' A:DG10 2.7 33.3 1.0
C4' A:DG9 3.6 47.2 1.0
C2' A:DG9 3.8 32.1 1.0
O4' A:DG10 3.8 31.9 1.0
C4' A:DG10 3.8 24.9 1.0
C2' A:DG10 4.2 27.6 1.0
O A:HOH58 4.3 43.8 1.0
C3' A:DG10 4.3 29.7 1.0
C1' A:DG9 4.4 29.9 1.0
O4' A:DG9 4.4 42.3 1.0
C8 A:DG10 4.5 18.6 1.0
C1' A:DG10 4.6 24.6 1.0
C5' A:DG9 4.7 46.3 1.0
N9 A:DG10 4.9 18.2 1.0

Phosphorus binding site 10 out of 18 in 167d

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Phosphorus binding site 10 out of 18 in the The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Crystal Structure of C-C-A-T-T-A-A-T-G-G: Implications For Bending of B-Dna at T-A Steps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:55.4
occ:1.00
P B:DC12 0.0 55.4 1.0
OP1 B:DC12 1.5 52.3 1.0
OP2 B:DC12 1.5 53.3 1.0
O3' B:DC11 1.6 43.6 1.0
O5' B:DC12 1.6 57.9 1.0
C3' B:DC11 2.6 51.5 1.0
C5' B:DC12 2.6 56.4 1.0
C2' B:DC11 3.2 50.5 1.0
C4' B:DC12 3.9 45.6 1.0
C4' B:DC11 3.9 52.2 1.0
C1' B:DC11 4.1 37.0 1.0
O4' B:DC12 4.4 43.1 1.0
O4' B:DC11 4.4 53.9 1.0
C3' B:DC12 4.4 47.4 1.0
C2' B:DC12 4.9 39.5 1.0
O5' B:DC11 5.0 58.6 1.0

Reference:

D.S.Goodsell, M.Kaczor-Grzeskowiak, R.E.Dickerson. The Crystal Structure of C-C-A-T-T-A-A-T-G-G. Implications For Bending of B-Dna at T-A Steps. J.Mol.Biol. V. 239 79 1994.
ISSN: ISSN 0022-2836
PubMed: 8196049
DOI: 10.1006/JMBI.1994.1352
Page generated: Fri Sep 25 11:37:40 2020

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