Phosphorus in PDB 127d: Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258

Protein crystallography data

The structure of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258, PDB code: 127d was solved by M.Sriram, G.A.Van Der Marel, H.L.P.F.Roelen, J.H.Van Boom, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.230, 40.580, 66.080, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 (pdb code 127d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258, PDB code: 127d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 127d

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Phosphorus binding site 1 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:22.6
occ:1.00
P A:DG2 0.0 22.6 1.0
OP1 A:DG2 1.5 23.0 1.0
OP2 A:DG2 1.5 23.1 1.0
O3' A:DC1 1.6 20.6 1.0
O5' A:DG2 1.6 16.8 1.0
C5' A:DG2 2.6 15.5 1.0
C3' A:DC1 2.7 20.5 1.0
C2' A:DC1 3.2 20.4 1.0
O A:HOH93 3.7 17.4 1.0
C1' A:DC1 3.8 20.2 1.0
O A:HOH135 3.8 59.6 1.0
C4' A:DC1 3.9 20.6 1.0
C4' A:DG2 3.9 15.1 1.0
O4' A:DC1 3.9 20.6 1.0
O4' A:DG2 4.3 14.6 1.0
C8 A:DG2 4.5 13.4 1.0
C3' A:DG2 4.6 14.8 1.0
O A:HOH138 4.7 25.3 1.0
O A:HOH114 4.7 53.4 1.0
C2' A:DG2 4.9 14.6 1.0
O A:HOH96 4.9 26.4 1.0
O A:HOH125 4.9 34.8 1.0

Phosphorus binding site 2 out of 22 in 127d

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Phosphorus binding site 2 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:17.8
occ:1.00
P A:DC3 0.0 17.8 1.0
OP2 A:DC3 1.5 18.5 1.0
OP1 A:DC3 1.5 16.7 1.0
O3' A:DG2 1.6 15.2 1.0
O5' A:DC3 1.6 12.4 1.0
C5' A:DC3 2.6 11.6 1.0
C3' A:DG2 2.7 14.8 1.0
C2' A:DG2 3.4 14.6 1.0
C4' A:DC3 3.9 11.2 1.0
C4' A:DG2 4.0 15.1 1.0
C1' A:DG2 4.5 14.2 1.0
C3' A:DC3 4.5 11.2 1.0
C2' A:DC3 4.7 10.9 1.0
O4' A:DG2 4.8 14.6 1.0
O4' A:DC3 4.8 10.8 1.0
C5' A:DG2 4.9 15.5 1.0

Phosphorus binding site 3 out of 22 in 127d

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Phosphorus binding site 3 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:15.2
occ:1.00
P A:DG4 0.0 15.2 1.0
OP2 A:DG4 1.5 13.3 1.0
OP1 A:DG4 1.5 13.9 1.0
O5' A:DG4 1.6 15.5 1.0
O3' A:DC3 1.6 11.8 1.0
C5' A:DG4 2.6 16.5 1.0
C3' A:DC3 2.6 11.2 1.0
C2' A:DC3 3.3 10.9 1.0
C8 A:DG4 3.8 16.7 1.0
C4' A:DG4 3.8 16.5 1.0
C4' A:DC3 4.0 11.2 1.0
O4' A:DG4 4.0 16.5 1.0
C1' A:DC3 4.1 10.4 1.0
O A:HOH123 4.2 46.9 1.0
C2' A:DG4 4.2 16.5 1.0
C3' A:DG4 4.4 16.6 1.0
N9 A:DG4 4.4 16.7 1.0
C1' A:DG4 4.5 16.7 1.0
O4' A:DC3 4.5 10.8 1.0
N7 A:DG4 4.7 16.8 1.0

Phosphorus binding site 4 out of 22 in 127d

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Phosphorus binding site 4 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:18.5
occ:1.00
P A:DA5 0.0 18.5 1.0
OP2 A:DA5 1.5 18.6 1.0
OP1 A:DA5 1.5 18.6 1.0
O3' A:DG4 1.6 16.6 1.0
O5' A:DA5 1.6 16.1 1.0
C5' A:DA5 2.6 15.3 1.0
C3' A:DG4 2.7 16.6 1.0
C2' A:DG4 3.5 16.5 1.0
C4' A:DA5 3.8 15.2 1.0
C4' A:DG4 3.9 16.5 1.0
O4' A:DA5 4.1 15.0 1.0
C3' A:DA5 4.3 15.1 1.0
C1' A:DG4 4.3 16.7 1.0
O A:HOH82 4.4 43.7 1.0
C2' A:DA5 4.4 14.9 1.0
O A:HOH95 4.4 15.1 1.0
O A:HOH90 4.6 7.0 1.0
O4' A:DG4 4.6 16.5 1.0
C8 A:DA5 4.7 14.3 1.0
C1' A:DA5 4.9 14.7 1.0

Phosphorus binding site 5 out of 22 in 127d

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Phosphorus binding site 5 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:16.8
occ:1.00
P A:DA6 0.0 16.8 1.0
OP1 A:DA6 1.5 16.4 1.0
OP2 A:DA6 1.5 15.5 1.0
O5' A:DA6 1.6 14.0 1.0
O3' A:DA5 1.6 15.0 1.0
C5' A:DA6 2.6 13.5 1.0
C3' A:DA5 2.6 15.1 1.0
C2' A:DA5 3.5 14.9 1.0
O A:HOH110 3.8 57.9 1.0
C4' A:DA6 3.9 13.4 1.0
C4' A:DA5 3.9 15.2 1.0
O A:HOH134 4.0 12.2 1.0
C1' A:DA5 4.3 14.7 1.0
C3' A:DA6 4.6 13.3 1.0
O A:HOH90 4.7 7.0 1.0
O4' A:DA5 4.8 15.0 1.0
C5' A:DA5 4.9 15.3 1.0
C8 A:DA6 4.9 12.8 1.0
C2' A:DA6 4.9 13.2 1.0
O4' A:DA6 5.0 13.5 1.0

Phosphorus binding site 6 out of 22 in 127d

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Phosphorus binding site 6 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:12.7
occ:1.00
P A:DT7 0.0 12.7 1.0
OP2 A:DT7 1.5 10.4 1.0
OP1 A:DT7 1.5 10.0 1.0
O5' A:DT7 1.6 12.0 1.0
O3' A:DA6 1.6 13.3 1.0
C5' A:DT7 2.6 12.1 1.0
C3' A:DA6 2.6 13.3 1.0
C2' A:DA6 3.1 13.2 1.0
C4' A:DT7 3.9 12.1 1.0
C1' A:DA6 3.9 13.1 1.0
C4' A:DA6 4.0 13.4 1.0
C3' A:DT7 4.2 12.0 1.0
O4' A:DA6 4.2 13.5 1.0
C2' A:DT7 4.5 12.0 1.0
O4' A:DT7 4.6 11.9 1.0

Phosphorus binding site 7 out of 22 in 127d

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Phosphorus binding site 7 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:15.4
occ:1.00
P A:DT8 0.0 15.4 1.0
OP2 A:DT8 1.5 15.6 1.0
OP1 A:DT8 1.5 15.5 1.0
O3' A:DT7 1.6 12.6 1.0
O5' A:DT8 1.6 15.5 1.0
C5' A:DT8 2.6 15.8 1.0
C3' A:DT7 2.7 12.0 1.0
C2' A:DT7 3.6 12.0 1.0
C4' A:DT8 3.8 16.0 1.0
C4' A:DT7 3.9 12.1 1.0
O A:HOH111 4.0 41.0 1.0
C1' A:DT7 4.3 11.8 1.0
O A:HOH68 4.4 22.6 1.0
O4' A:DT7 4.7 11.9 1.0
C3' A:DT8 4.7 16.2 1.0
O4' A:DT8 4.8 15.8 1.0
C10 B:HT25 4.9 34.8 1.0

Phosphorus binding site 8 out of 22 in 127d

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Phosphorus binding site 8 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:21.5
occ:1.00
P A:DC9 0.0 21.5 1.0
OP2 A:DC9 1.5 21.4 1.0
OP1 A:DC9 1.5 21.4 1.0
O5' A:DC9 1.6 19.2 1.0
O3' A:DT8 1.6 16.6 1.0
C5' A:DC9 2.6 19.4 1.0
O A:HOH28 2.6 53.3 1.0
C3' A:DT8 2.6 16.2 1.0
C2' A:DT8 3.4 16.0 1.0
C4' A:DC9 3.8 19.4 1.0
C4' A:DT8 4.0 16.0 1.0
C3' A:DC9 4.3 19.4 1.0
O4' A:DC9 4.3 19.2 1.0
C1' A:DT8 4.3 15.7 1.0
O4' A:DT8 4.5 15.8 1.0

Phosphorus binding site 9 out of 22 in 127d

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Phosphorus binding site 9 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:21.6
occ:1.00
P A:DG10 0.0 21.6 1.0
OP2 A:DG10 1.5 21.2 1.0
OP1 A:DG10 1.5 20.4 1.0
O5' A:DG10 1.6 19.0 1.0
O3' A:DC9 1.6 20.1 1.0
C5' A:DG10 2.6 18.7 1.0
C3' A:DC9 2.7 19.4 1.0
C2' A:DC9 3.5 19.4 1.0
C4' A:DG10 3.7 18.4 1.0
C4' A:DC9 4.0 19.4 1.0
O4' A:DG10 4.0 18.2 1.0
C8 A:DG10 4.2 17.4 1.0
C3' A:DG10 4.3 18.4 1.0
C2' A:DG10 4.6 18.2 1.0
C5' A:DC9 4.7 19.4 1.0
C1' A:DC9 4.7 19.1 1.0
O5' A:DC9 4.7 19.2 1.0
C1' A:DG10 4.8 17.9 1.0
N9 A:DG10 4.8 17.5 1.0
O4' A:DC9 5.0 19.2 1.0

Phosphorus binding site 10 out of 22 in 127d

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Phosphorus binding site 10 out of 22 in the Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Dna (5'-D(*Cp*Gp*Cp*Gp*Ap*Ap*Tp*Tp*Cp*Gp*Cp*G)-3') Complexed with Hoechst 33258 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:21.5
occ:1.00
P A:DC11 0.0 21.5 1.0
OP2 A:DC11 1.5 20.1 1.0
OP1 A:DC11 1.5 20.5 1.0
O3' A:DG10 1.6 18.7 1.0
O5' A:DC11 1.6 19.8 1.0
C5' A:DC11 2.6 20.0 1.0
C3' A:DG10 2.7 18.4 1.0
C2' A:DG10 3.3 18.2 1.0
O A:HOH141 3.5 33.0 1.0
C4' A:DC11 3.8 19.9 1.0
C4' A:DG10 3.8 18.4 1.0
C2' A:DC11 3.9 19.7 1.0
C6 A:DC11 4.0 19.1 1.0
C1' A:DG10 4.1 17.9 1.0
C3' A:DC11 4.1 20.0 1.0
O A:HOH118 4.2 20.3 1.0
O A:HOH115 4.2 42.2 1.0
O4' A:DC11 4.3 19.8 1.0
O4' A:DG10 4.5 18.2 1.0
C1' A:DC11 4.6 19.4 1.0
N1 A:DC11 4.7 19.1 1.0
O A:HOH139 4.8 20.9 1.0
C5 A:DC11 4.8 19.0 1.0

Reference:

M.Sriram, G.A.Van Der Marel, H.L.Roelen, J.H.Van Boom, A.H.Wang. Conformation of B-Dna Containing O6-Ethyl-G-C Base Pairs Stabilized By Minor Groove Binding Drugs: Molecular Structure of D(Cgc[E6G]Aattcgcg Complexed with Hoechst 33258 or Hoechst 33342. Embo J. V. 11 225 1992.
ISSN: ISSN 0261-4189
PubMed: 1371249
Page generated: Fri Sep 25 11:16:09 2020

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