Phosphorus in PDB 158d: Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna

Protein crystallography data

The structure of Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna, PDB code: 158d was solved by K.Grzeskowiak, D.S.Goodsell, M.Kaczor-Grzeskowiak, D.Cascio, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 53.080, 53.080, 34.320, 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 Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna (pdb code 158d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna, PDB code: 158d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 158d

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Phosphorus binding site 1 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:13.2
occ:1.00
P A:DC2 0.0 13.2 1.0
OP2 A:DC2 1.5 17.5 1.0
OP1 A:DC2 1.5 17.0 1.0
O5' A:DC2 1.6 14.4 1.0
O3' A:DC1 1.6 16.2 1.0
C3' A:DC1 2.7 11.4 1.0
C5' A:DC2 2.7 11.0 1.0
C2' A:DC1 3.5 11.2 1.0
O A:HOH69 3.8 39.0 1.0
C4' A:DC2 3.9 6.8 1.0
C4' A:DC1 3.9 13.1 1.0
C3' A:DC2 4.2 11.9 1.0
C2' A:DC2 4.3 10.3 1.0
O4' A:DC2 4.4 12.4 1.0
C1' A:DC1 4.4 9.6 1.0
O4' A:DC1 4.7 14.0 1.0
C1' A:DC2 5.0 10.2 1.0
C5' A:DC1 5.0 11.0 1.0
O5' A:DC1 5.0 14.1 1.0

Phosphorus binding site 2 out of 18 in 158d

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Phosphorus binding site 2 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:13.3
occ:1.00
P A:DA3 0.0 13.3 1.0
OP2 A:DA3 1.5 15.4 1.0
OP1 A:DA3 1.5 14.9 1.0
O3' A:DC2 1.6 10.4 1.0
O5' A:DA3 1.6 14.1 1.0
C3' A:DC2 2.6 11.9 1.0
C5' A:DA3 2.7 8.7 1.0
C4' A:DC2 3.6 6.8 1.0
C8 A:DA3 3.7 8.2 1.0
C2' A:DC2 3.8 10.3 1.0
C4' A:DA3 3.8 10.4 1.0
O4' A:DA3 4.1 11.9 1.0
O A:HOH69 4.2 39.0 1.0
N9 A:DA3 4.4 9.8 1.0
C1' A:DC2 4.4 10.2 1.0
N7 A:DA3 4.4 6.2 1.0
C3' A:DA3 4.4 7.2 1.0
C2' A:DA3 4.5 8.7 1.0
O4' A:DC2 4.5 12.4 1.0
C5' A:DC2 4.6 11.0 1.0
C1' A:DA3 4.6 9.3 1.0
O A:HOH40 4.7 13.6 1.0
O A:HOH91 4.7 37.6 1.0
O5' A:DC2 5.0 14.4 1.0

Phosphorus binding site 3 out of 18 in 158d

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Phosphorus binding site 3 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:13.6
occ:1.00
P A:DA4 0.0 13.6 1.0
OP2 A:DA4 1.5 14.5 1.0
OP1 A:DA4 1.5 15.3 1.0
O3' A:DA3 1.6 12.0 1.0
O5' A:DA4 1.6 7.0 1.0
C5' A:DA4 2.6 9.4 1.0
C3' A:DA3 2.6 7.2 1.0
C2' A:DA3 3.3 8.7 1.0
O A:HOH32 3.7 9.4 1.0
C4' A:DA4 3.9 8.5 1.0
C4' A:DA3 3.9 10.4 1.0
O A:HOH57 4.2 29.0 1.0
O4' A:DA4 4.2 9.6 1.0
C1' A:DA3 4.2 9.3 1.0
C3' A:DA4 4.4 8.8 1.0
C2' A:DA4 4.6 13.5 1.0
O4' A:DA3 4.6 11.9 1.0

Phosphorus binding site 4 out of 18 in 158d

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Phosphorus binding site 4 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:8.2
occ:1.00
P A:DG5 0.0 8.2 1.0
OP1 A:DG5 1.4 8.7 1.0
OP2 A:DG5 1.5 8.7 1.0
O3' A:DA4 1.6 12.8 1.0
O5' A:DG5 1.6 8.0 1.0
C5' A:DG5 2.6 5.0 1.0
C3' A:DA4 2.7 8.8 1.0
O A:HOH35 3.5 10.9 1.0
C4' A:DG5 3.7 7.4 1.0
C4' A:DA4 3.8 8.5 1.0
C2' A:DA4 3.8 13.5 1.0
O A:HOH29 3.9 11.4 1.0
O4' A:DG5 3.9 10.0 1.0
C3' A:DG5 4.3 8.0 1.0
C2' A:DG5 4.4 5.2 1.0
C1' A:DA4 4.5 7.9 1.0
C8 A:DG5 4.7 7.6 1.0
O4' A:DA4 4.7 9.6 1.0
C1' A:DG5 4.8 7.8 1.0
C5' A:DA4 4.8 9.4 1.0

Phosphorus binding site 5 out of 18 in 158d

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Phosphorus binding site 5 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:7.8
occ:1.00
P A:DC6 0.0 7.8 1.0
OP1 A:DC6 1.5 12.6 1.0
OP2 A:DC6 1.5 9.0 1.0
O3' A:DG5 1.6 4.9 1.0
O5' A:DC6 1.6 8.2 1.0
C5' A:DC6 2.6 8.6 1.0
C3' A:DG5 2.7 8.0 1.0
C2' A:DG5 3.3 5.2 1.0
O A:HOH25 3.7 11.1 1.0
C4' A:DC6 3.9 9.8 1.0
C4' A:DG5 3.9 7.4 1.0
C1' A:DG5 4.0 7.8 1.0
C3' A:DC6 4.3 8.8 1.0
O4' A:DC6 4.5 10.5 1.0
O4' A:DG5 4.6 10.0 1.0
C2' A:DC6 4.6 11.6 1.0
C6 A:DC6 4.9 5.9 1.0

Phosphorus binding site 6 out of 18 in 158d

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Phosphorus binding site 6 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:12.5
occ:1.00
P A:DT7 0.0 12.5 1.0
OP1 A:DT7 1.5 17.5 1.0
OP2 A:DT7 1.5 10.4 1.0
O3' A:DC6 1.6 13.2 1.0
O5' A:DT7 1.6 15.2 1.0
C3' A:DC6 2.7 8.8 1.0
C5' A:DT7 2.8 12.2 1.0
C2' A:DC6 3.3 11.6 1.0
O A:HOH81 3.8 31.7 1.0
C4' A:DC6 3.9 9.8 1.0
C4' A:DT7 4.0 11.1 1.0
C1' A:DC6 4.1 8.5 1.0
C3' A:DT7 4.4 11.2 1.0
O4' A:DT7 4.5 11.8 1.0
O4' A:DC6 4.6 10.5 1.0
C2' A:DT7 4.9 10.1 1.0

Phosphorus binding site 7 out of 18 in 158d

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Phosphorus binding site 7 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:17.2
occ:1.00
P A:DT8 0.0 17.2 1.0
OP2 A:DT8 1.5 15.6 1.0
OP1 A:DT8 1.5 16.7 1.0
O5' A:DT8 1.6 17.0 1.0
O3' A:DT7 1.6 15.0 1.0
C5' A:DT8 2.6 10.7 1.0
C3' A:DT7 2.7 11.2 1.0
C2' A:DT7 3.4 10.1 1.0
C4' A:DT8 3.8 10.0 1.0
C4' A:DT7 3.9 11.1 1.0
C3' A:DT8 4.2 12.1 1.0
O4' A:DT8 4.2 10.6 1.0
C1' A:DT7 4.3 8.2 1.0
C2' A:DT8 4.5 12.8 1.0
O4' A:DT7 4.8 11.8 1.0
C5' A:DT7 4.9 12.2 1.0

Phosphorus binding site 8 out of 18 in 158d

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Phosphorus binding site 8 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:12.7
occ:1.00
P A:DG9 0.0 12.7 1.0
OP1 A:DG9 1.5 15.4 1.0
OP2 A:DG9 1.5 17.0 1.0
O3' A:DT8 1.6 12.2 1.0
O5' A:DG9 1.6 10.2 1.0
C5' A:DG9 2.5 9.3 1.0
C3' A:DT8 2.7 12.1 1.0
C4' A:DT8 3.6 10.0 1.0
O A:HOH52 3.7 9.0 1.0
C4' A:DG9 3.8 10.2 1.0
C2' A:DT8 3.9 12.8 1.0
O4' A:DG9 4.1 12.6 1.0
C8 A:DG9 4.2 8.0 1.0
C3' A:DG9 4.3 12.3 1.0
C2' A:DG9 4.4 10.6 1.0
C1' A:DT8 4.6 10.3 1.0
C5' A:DT8 4.6 10.7 1.0
O4' A:DT8 4.7 10.6 1.0
N9 A:DG9 4.7 7.6 1.0
C1' A:DG9 4.7 8.2 1.0
N7 A:DG9 4.9 8.9 1.0

Phosphorus binding site 9 out of 18 in 158d

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Phosphorus binding site 9 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:16.1
occ:1.00
P A:DG10 0.0 16.1 1.0
OP1 A:DG10 1.5 23.5 1.0
OP2 A:DG10 1.5 17.2 1.0
O5' A:DG10 1.6 16.8 1.0
O3' A:DG9 1.6 12.8 1.0
C5' A:DG10 2.6 12.1 1.0
C3' A:DG9 2.7 12.3 1.0
C2' A:DG9 3.3 10.6 1.0
C4' A:DG10 3.9 12.8 1.0
O A:HOH76 3.9 34.1 0.5
C4' A:DG9 4.0 10.2 1.0
C1' A:DG9 4.1 8.2 1.0
C3' A:DG10 4.3 10.2 1.0
O4' A:DG10 4.3 17.4 1.0
O A:HOH75 4.5 38.6 1.0
O4' A:DG9 4.5 12.6 1.0
C2' A:DG10 4.6 15.1 1.0

Phosphorus binding site 10 out of 18 in 158d

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Phosphorus binding site 10 out of 18 in the Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna


Mono view


Stereo pair view

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

b:15.1
occ:1.00
P B:DC12 0.0 15.1 1.0
OP2 B:DC12 1.5 10.4 1.0
OP1 B:DC12 1.5 17.6 1.0
O3' B:DC11 1.6 13.8 1.0
O5' B:DC12 1.6 13.4 1.0
C3' B:DC11 2.6 17.6 1.0
C5' B:DC12 2.7 14.3 1.0
C2' B:DC11 3.4 13.1 1.0
O B:HOH62 3.8 18.9 1.0
C4' B:DC11 3.9 19.2 1.0
C4' B:DC12 3.9 11.5 1.0
C3' B:DC12 4.3 8.6 1.0
C1' B:DC11 4.4 13.7 1.0
O4' B:DC12 4.5 10.8 1.0
C2' B:DC12 4.5 10.3 1.0
O4' B:DC11 4.7 17.2 1.0
O5' B:DC11 4.7 23.1 1.0
C5' B:DC11 4.9 21.4 1.0

Reference:

K.Grzeskowiak, D.S.Goodsell, M.Kaczor-Grzeskowiak, D.Cascio, R.E.Dickerson. Crystallographic Analysis of C-C-A-A-G-C-T-T-G-G and Its Implications For Bending in B-Dna. Biochemistry V. 32 8923 1993.
ISSN: ISSN 0006-2960
PubMed: 8364037
DOI: 10.1021/BI00085A025
Page generated: Fri Sep 25 11:34:36 2020

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