Phosphorus in PDB 154d: Dna Distortion in Bis-Intercalated Complexes

Protein crystallography data

The structure of Dna Distortion in Bis-Intercalated Complexes, PDB code: 154d was solved by M.E.Peek, L.A.Lipscomb, J.A.Bertrand, Q.Gao, B.P.Roques, C.Garbay-Jaureguiberry, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.10 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 27.090, 27.090, 81.890, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Dna Distortion in Bis-Intercalated Complexes (pdb code 154d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Dna Distortion in Bis-Intercalated Complexes, PDB code: 154d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 154d

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Phosphorus binding site 1 out of 6 in the Dna Distortion in Bis-Intercalated Complexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Dna Distortion in Bis-Intercalated Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:23.3
occ:1.00
P A:DG2 0.0 23.3 1.0
OP2 A:DG2 1.4 22.9 1.0
OP1 A:DG2 1.5 23.2 1.0
O3' A:CBR1 1.6 22.9 1.0
O5' A:DG2 1.7 22.3 1.0
C5' A:DG2 2.5 20.3 1.0
C3' A:CBR1 2.6 22.2 1.0
C2' A:CBR1 3.6 21.7 1.0
C4' A:CBR1 3.8 21.8 1.0
C4' A:DG2 3.8 18.3 1.0
C3' A:DG2 4.0 18.5 1.0
O A:HOH26 4.1 49.7 1.0
C2' A:DG2 4.2 16.6 1.0
C5' A:CBR1 4.3 21.6 1.0
O4' A:DG2 4.6 16.5 1.0
C4 B:FLD9 4.8 4.7 1.0
O4' A:CBR1 4.9 21.6 1.0
C1' A:CBR1 4.9 20.9 1.0

Phosphorus binding site 2 out of 6 in 154d

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Phosphorus binding site 2 out of 6 in the Dna Distortion in Bis-Intercalated Complexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Dna Distortion in Bis-Intercalated Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:22.1
occ:1.00
P A:DC3 0.0 22.1 1.0
OP1 A:DC3 1.4 21.8 1.0
OP2 A:DC3 1.5 21.7 1.0
O3' A:DG2 1.6 20.6 1.0
O5' A:DC3 1.7 20.8 1.0
C5' A:DC3 2.5 19.3 1.0
C3' A:DG2 2.7 18.5 1.0
O4' A:DC3 3.4 16.7 1.0
C4' A:DC3 3.5 17.9 1.0
C2' A:DG2 3.7 16.6 1.0
C4' A:DG2 3.9 18.3 1.0
C1' A:DG2 4.3 13.9 1.0
C3' A:DC3 4.4 17.9 1.0
O4' A:DG2 4.6 16.5 1.0
C1' A:DC3 4.8 14.7 1.0

Phosphorus binding site 3 out of 6 in 154d

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Phosphorus binding site 3 out of 6 in the Dna Distortion in Bis-Intercalated Complexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Dna Distortion in Bis-Intercalated Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:20.1
occ:1.00
P A:DG4 0.0 20.1 1.0
OP2 A:DG4 1.4 19.5 1.0
OP1 A:DG4 1.5 20.1 1.0
O3' A:DC3 1.6 19.0 1.0
O5' A:DG4 1.6 18.1 1.0
C5' A:DG4 2.6 14.9 1.0
C3' A:DC3 2.7 17.9 1.0
O A:HOH12 3.4 50.9 1.0
C2' A:DC3 3.5 16.9 1.0
C4' A:DG4 3.9 12.4 1.0
C4' A:DC3 3.9 17.9 1.0
O A:HOH17 3.9 34.3 1.0
C3' A:DG4 4.1 11.6 1.0
C2' A:DG4 4.3 10.3 1.0
O A:HOH18 4.3 47.4 1.0
C5' A:DC3 4.4 19.3 1.0
O5' A:DC3 4.8 20.8 1.0
C1' A:DC3 4.9 14.7 1.0
O4' A:DC3 4.9 16.7 1.0

Phosphorus binding site 4 out of 6 in 154d

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Phosphorus binding site 4 out of 6 in the Dna Distortion in Bis-Intercalated Complexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Dna Distortion in Bis-Intercalated Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P6

b:16.9
occ:1.00
P B:DG6 0.0 16.9 1.0
OP1 B:DG6 1.4 17.1 1.0
OP2 B:DG6 1.5 17.1 1.0
O3' B:CBR5 1.6 17.0 1.0
O5' B:DG6 1.6 16.3 1.0
C5' B:DG6 2.5 15.1 1.0
C3' B:CBR5 2.6 16.5 1.0
O B:HOH11 3.5 24.4 1.0
C4' B:CBR5 3.7 16.2 1.0
C2' B:CBR5 3.8 16.0 1.0
C4' B:DG6 3.8 14.3 1.0
C5' B:CBR5 3.9 16.8 1.0
C3' B:DG6 4.2 14.5 1.0
C2' B:DG6 4.4 13.1 1.0
O B:HOH36 4.4 52.1 1.0
O4' B:DG6 4.5 13.3 1.0
C4X B:FLD9 4.8 6.0 1.0
O4' B:CBR5 4.8 15.6 1.0
O5' B:CBR5 4.8 17.2 1.0
C1' B:CBR5 4.9 15.1 1.0

Phosphorus binding site 5 out of 6 in 154d

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Phosphorus binding site 5 out of 6 in the Dna Distortion in Bis-Intercalated Complexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Dna Distortion in Bis-Intercalated Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P7

b:17.0
occ:1.00
P B:DC7 0.0 17.0 1.0
OP1 B:DC7 1.4 17.2 1.0
OP2 B:DC7 1.5 17.0 1.0
O3' B:DG6 1.6 16.1 1.0
O5' B:DC7 1.6 16.6 1.0
C5' B:DC7 2.5 16.3 1.0
C3' B:DG6 2.7 14.5 1.0
C4' B:DC7 3.6 15.7 1.0
O4' B:DC7 3.7 14.7 1.0
C4' B:DG6 3.7 14.3 1.0
O B:HOH25 3.9 46.8 1.0
C2' B:DG6 3.9 13.1 1.0
O B:HOH21 3.9 57.0 1.0
O B:HOH22 4.1 42.8 1.0
C3' B:DC7 4.3 16.0 1.0
C1' B:DG6 4.5 11.6 1.0
O4' B:DG6 4.7 13.3 1.0
C5' B:DG6 4.7 15.1 1.0

Phosphorus binding site 6 out of 6 in 154d

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Phosphorus binding site 6 out of 6 in the Dna Distortion in Bis-Intercalated Complexes


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Dna Distortion in Bis-Intercalated Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:18.8
occ:1.00
P B:DG8 0.0 18.8 1.0
OP1 B:DG8 1.4 18.8 1.0
OP2 B:DG8 1.5 18.8 1.0
O3' B:DC7 1.6 17.8 1.0
O5' B:DG8 1.6 17.6 1.0
C5' B:DG8 2.6 16.2 1.0
C3' B:DC7 2.7 16.0 1.0
C2' B:DC7 3.2 14.5 1.0
C4' B:DG8 3.8 15.0 1.0
C4' B:DC7 3.9 15.7 1.0
C2' B:DG8 4.0 13.5 1.0
C3' B:DG8 4.0 14.6 1.0
C1' B:DC7 4.5 12.2 1.0
O4' B:DG8 4.6 13.8 1.0
C8 B:DG8 4.6 10.6 1.0
C5' B:DC7 4.7 16.3 1.0
C1' B:DG8 4.8 12.1 1.0
O4' B:DC7 4.9 14.7 1.0
O5' B:DC7 4.9 16.6 1.0
N9 B:DG8 5.0 11.0 1.0

Reference:

M.E.Peek, L.A.Lipscomb, J.A.Bertrand, Q.Gao, B.P.Roques, C.Garbay-Jaureguiberry, L.D.Williams. Dna Distortion in Bis-Intercalated Complexes. Biochemistry V. 33 3794 1994.
ISSN: ISSN 0006-2960
PubMed: 8142381
DOI: 10.1021/BI00179A002
Page generated: Fri Sep 25 11:32:28 2020

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