Phosphorus in PDB 131d: The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove

Protein crystallography data

The structure of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove, PDB code: 131d was solved by D.Bancroft, L.D.Williams, A.Rich, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 1.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 18.265, 30.690, 42.460, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove (pdb code 131d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 10 binding sites of Phosphorus where determined in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove, PDB code: 131d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 10 in 131d

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Phosphorus binding site 1 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:9.3
occ:1.00
P A:DG2 0.0 9.3 1.0
OP2 A:DG2 1.4 10.6 1.0
OP1 A:DG2 1.5 10.8 1.0
O5' A:DG2 1.6 8.3 1.0
O3' A:DC1 1.6 8.1 1.0
C5' A:DG2 2.6 7.1 1.0
C3' A:DC1 2.7 8.3 1.0
C4' A:DC1 3.5 8.0 1.0
C2' A:DC1 3.9 8.0 1.0
C4' A:DG2 3.9 6.8 1.0
O4' A:DG2 4.2 7.0 1.0
O A:HOH64 4.4 21.8 1.0
C5' A:DC1 4.5 8.8 1.0
O4' A:DC1 4.6 7.5 1.0
C1' A:DC1 4.6 6.8 1.0
O A:HOH32 4.9 10.3 1.0

Phosphorus binding site 2 out of 10 in 131d

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Phosphorus binding site 2 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:5.8
occ:1.00
P A:DC3 0.0 5.8 1.0
OP1 A:DC3 1.4 6.5 1.0
OP2 A:DC3 1.4 7.7 1.0
O3' A:DG2 1.6 6.1 1.0
O5' A:DC3 1.6 6.9 1.0
C3' A:DG2 2.7 6.2 1.0
C5' A:DC3 2.7 6.9 1.0
C4' A:DG2 3.6 6.8 1.0
N1 A:SPM13 3.7 7.2 1.0
O A:HOH31 3.8 9.4 1.0
C2' A:DG2 3.8 6.8 1.0
C4' A:DC3 3.8 7.5 1.0
O A:HOH64 4.0 21.8 1.0
O A:HOH32 4.0 10.3 1.0
C5' A:DG2 4.0 7.1 1.0
C3 A:SPM13 4.1 7.5 1.0
C3' A:DC3 4.1 7.3 1.0
C2 A:SPM13 4.1 7.1 1.0
C2' A:DC3 4.3 6.7 1.0
O4' A:DC3 4.4 7.4 1.0
C6 A:DC3 4.8 6.3 1.0
O4' A:DG2 4.9 7.0 1.0
C4 A:SPM13 5.0 8.6 1.0
C1' A:DC3 5.0 6.5 1.0

Phosphorus binding site 3 out of 10 in 131d

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Phosphorus binding site 3 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:9.6
occ:1.00
P A:DG4 0.0 9.6 1.0
OP2 A:DG4 1.4 11.7 1.0
OP1 A:DG4 1.5 9.3 1.0
O5' A:DG4 1.6 9.3 1.0
O3' A:DC3 1.6 8.4 1.0
C5' A:DG4 2.6 8.1 1.0
C3' A:DC3 2.6 7.3 1.0
C4' A:DC3 3.4 7.5 1.0
O A:HOH67 3.6 31.1 1.0
C4' A:DG4 3.9 7.5 1.0
C2' A:DC3 3.9 6.7 1.0
O A:HOH71 4.1 39.2 1.0
O B:HOH63 4.2 45.3 1.0
O A:HOH28 4.2 21.5 1.0
O4' A:DG4 4.2 8.3 1.0
O4' A:DC3 4.4 7.4 1.0
C1' A:DC3 4.4 6.5 1.0
C5' A:DC3 4.5 6.9 1.0
O A:HOH55 4.8 20.7 1.0
O A:HOH58 4.8 43.4 1.0
O A:HOH73 4.9 42.5 1.0

Phosphorus binding site 4 out of 10 in 131d

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Phosphorus binding site 4 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:11.4
occ:1.00
P A:DC5 0.0 11.4 1.0
OP2 A:DC5 1.4 15.1 1.0
OP1 A:DC5 1.5 14.2 1.0
O3' A:DG4 1.5 10.6 1.0
O5' A:DC5 1.6 8.3 1.0
C5' A:DC5 2.7 7.4 1.0
C3' A:DG4 2.7 8.4 1.0
NA A:NA16 2.9 28.3 1.0
O A:HOH21 3.3 26.7 1.0
C4' A:DG4 3.7 7.5 1.0
C2' A:DG4 3.7 7.7 1.0
O A:HOH19 3.8 12.7 1.0
O A:HOH66 3.8 23.3 1.0
C4' A:DC5 3.9 6.9 1.0
C5' A:DG4 4.0 8.1 1.0
O A:HOH24 4.1 33.6 1.0
C3' A:DC5 4.1 7.3 1.0
NA A:NA15 4.1 22.8 1.0
O A:HOH18 4.1 30.1 1.0
O4' A:DC5 4.4 6.9 1.0
O A:HOH72 4.6 37.2 1.0
C2' A:DC5 4.6 7.0 1.0
O A:HOH60 4.8 28.3 1.0
O4' A:DG4 4.9 8.3 1.0
C1' A:DG4 5.0 6.9 1.0

Phosphorus binding site 5 out of 10 in 131d

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Phosphorus binding site 5 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:10.1
occ:1.00
P A:DG6 0.0 10.1 1.0
OP2 A:DG6 1.4 11.3 1.0
OP1 A:DG6 1.5 11.9 1.0
O3' A:DC5 1.5 8.5 1.0
O5' A:DG6 1.6 9.7 1.0
C3' A:DC5 2.5 7.3 1.0
C5' A:DG6 2.6 8.5 1.0
C4' A:DC5 3.4 6.9 1.0
C2' A:DC5 3.8 7.0 1.0
O A:HOH27 3.9 20.1 1.0
C4' A:DG6 3.9 6.8 1.0
O A:HOH66 4.0 23.3 1.0
C5' A:DC5 4.2 7.4 1.0
O A:HOH68 4.3 33.0 1.0
O4' A:DG6 4.4 7.1 1.0
C1' A:DC5 4.5 6.6 1.0
C11 B:SPM14 4.6 34.0 1.0
O4' A:DC5 4.6 6.9 1.0
C12 B:SPM14 4.6 34.3 1.0
C9 B:SPM14 4.7 34.3 1.0
O5' A:DC5 4.9 8.3 1.0
O A:HOH28 4.9 21.5 1.0
OP2 A:DC5 5.0 15.1 1.0

Phosphorus binding site 6 out of 10 in 131d

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Phosphorus binding site 6 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:8.8
occ:1.00
P B:DG8 0.0 8.8 1.0
OP1 B:DG8 1.4 9.5 1.0
OP2 B:DG8 1.5 9.8 1.0
O5' B:DG8 1.6 8.1 1.0
O3' B:DC7 1.6 7.7 1.0
C5' B:DG8 2.5 7.8 1.0
C3' B:DC7 2.6 7.4 1.0
C4' B:DC7 3.5 8.3 1.0
O B:HOH77 3.7 53.1 1.0
O B:HOH61 3.8 25.1 1.0
O B:HOH51 3.8 23.0 1.0
C4' B:DG8 3.9 7.6 1.0
C2' B:DC7 3.9 6.9 1.0
O B:HOH56 4.0 35.5 1.0
O4' B:DG8 4.3 6.9 1.0
C1' B:DC7 4.4 6.5 1.0
O5' B:DC7 4.5 14.0 1.0
O4' B:DC7 4.5 7.5 1.0
O B:HOH78 4.6 41.0 1.0
N1 B:SPM14 4.6 35.2 1.0
C5' B:DC7 4.7 10.4 1.0
C6 B:SPM14 4.9 34.4 1.0

Phosphorus binding site 7 out of 10 in 131d

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Phosphorus binding site 7 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:17.3
occ:1.00
P B:DC9 0.0 17.3 1.0
OP1 B:DC9 1.4 17.5 1.0
OP2 B:DC9 1.5 16.3 1.0
O3' B:DG8 1.5 11.2 1.0
O5' B:DC9 1.6 11.8 1.0
C5' B:DC9 2.6 9.3 1.0
C3' B:DG8 2.6 8.2 1.0
C2' B:DG8 3.5 7.7 1.0
C4' B:DG8 3.8 7.6 1.0
O B:HOH57 3.9 46.2 1.0
C4' B:DC9 3.9 7.7 1.0
O4' B:DC9 4.2 7.2 1.0
C6 B:DC9 4.4 6.2 1.0
C3' B:DC9 4.4 7.5 1.0
C5' B:DG8 4.5 7.8 1.0
C2' B:DC9 4.5 6.8 1.0
C1' B:DG8 4.8 7.1 1.0
O4' B:DG8 4.9 6.9 1.0
C1' B:DC9 4.9 7.1 1.0

Phosphorus binding site 8 out of 10 in 131d

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Phosphorus binding site 8 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:8.8
occ:1.00
P B:DG10 0.0 8.8 1.0
OP1 B:DG10 1.4 9.7 1.0
OP2 B:DG10 1.5 10.3 1.0
O3' B:DC9 1.6 8.3 1.0
O5' B:DG10 1.6 8.2 1.0
C5' B:DG10 2.6 6.4 1.0
C3' B:DC9 2.6 7.5 1.0
C4' B:DC9 3.4 7.7 1.0
O B:HOH53 3.6 32.4 1.0
C2' B:DC9 3.8 6.8 1.0
C4' B:DG10 3.9 6.7 1.0
N14 B:SPM14 3.9 35.1 1.0
C12 B:SPM14 4.0 34.3 1.0
C13 B:SPM14 4.1 34.5 1.0
O4' B:DG10 4.3 6.2 1.0
C5' B:DC9 4.4 9.3 1.0
O4' B:DC9 4.5 7.2 1.0
C1' B:DC9 4.5 7.1 1.0
O B:HOH34 4.9 10.2 1.0
O B:HOH51 5.0 23.0 1.0

Phosphorus binding site 9 out of 10 in 131d

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Phosphorus binding site 9 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:7.4
occ:1.00
P B:DC11 0.0 7.4 1.0
OP1 B:DC11 1.4 9.2 1.0
OP2 B:DC11 1.5 8.8 1.0
O5' B:DC11 1.6 8.6 1.0
O3' B:DG10 1.6 7.3 1.0
C3' B:DG10 2.6 6.3 1.0
C5' B:DC11 2.7 6.7 1.0
C2' B:DG10 3.6 6.4 1.0
C4' B:DG10 3.7 6.7 1.0
C4' B:DC11 3.8 6.9 1.0
C3' B:DC11 3.9 7.1 1.0
O B:HOH34 4.0 10.2 1.0
C5' B:DG10 4.2 6.4 1.0
C2' B:DC11 4.3 6.7 1.0
O4' B:DC11 4.4 6.5 1.0
C1' B:DG10 4.9 5.5 1.0
O4' B:DG10 5.0 6.2 1.0

Phosphorus binding site 10 out of 10 in 131d

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Phosphorus binding site 10 out of 10 in the The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:8.5
occ:1.00
P B:DG12 0.0 8.5 1.0
OP1 B:DG12 1.4 8.7 1.0
OP2 B:DG12 1.5 10.3 1.0
O3' B:DC11 1.6 7.8 1.0
O5' B:DG12 1.6 8.7 1.0
C5' B:DG12 2.6 8.3 1.0
C3' B:DC11 2.7 7.1 1.0
C4' B:DC11 3.5 6.9 1.0
O B:HOH30 3.8 13.0 1.0
C4' B:DG12 3.9 7.8 1.0
C2' B:DC11 3.9 6.7 1.0
O B:HOH63 4.3 45.3 1.0
O4' B:DG12 4.3 6.7 1.0
C5' B:DC11 4.4 6.7 1.0
C1' B:DC11 4.5 6.5 1.0
O4' B:DC11 4.5 6.5 1.0

Reference:

D.Bancroft, L.D.Williams, A.Rich, M.Egli. The Low-Temperature Crystal Structure of the Pure-Spermine Form of Z-Dna Reveals Binding of A Spermine Molecule in the Minor Groove. Biochemistry V. 33 1073 1994.
ISSN: ISSN 0006-2960
PubMed: 8110738
DOI: 10.1021/BI00171A005
Page generated: Fri Sep 25 11:18:27 2020

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