Phosphorus in PDB 1agl: Structure of A Dna-Bisdaunomycin Complex

Protein crystallography data

The structure of Structure of A Dna-Bisdaunomycin Complex, PDB code: 1agl was solved by G.G.Hu, X.Shui, F.Leng, W.Priebe, J.B.Chaires, L.D.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 28.270, 28.270, 53.770, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 31.4

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Structure of A Dna-Bisdaunomycin Complex (pdb code 1agl). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 5 binding sites of Phosphorus where determined in the Structure of A Dna-Bisdaunomycin Complex, PDB code: 1agl:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5;

Phosphorus binding site 1 out of 5 in 1agl

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Phosphorus binding site 1 out of 5 in the Structure of A Dna-Bisdaunomycin Complex


Mono view


Stereo pair view

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

b:26.1
occ:1.00
P A:DG2 0.0 26.1 1.0
OP1 A:DG2 1.5 26.9 1.0
OP2 A:DG2 1.5 28.4 1.0
O3' A:DC1 1.6 23.8 1.0
O5' A:DG2 1.6 27.6 1.0
C3' A:DC1 2.6 18.8 1.0
C5' A:DG2 2.7 24.6 1.0
C2' A:DC1 3.7 15.1 1.0
C4' A:DC1 3.7 18.8 1.0
C4' A:DG2 4.1 23.6 1.0
C3' A:DG2 4.5 21.9 1.0
C5' A:DC1 4.6 16.6 1.0
O4' A:DG2 4.6 22.3 1.0
C1' A:DC1 4.7 12.9 1.0
O4' A:DC1 4.8 12.8 1.0
C2' A:DG2 4.9 19.2 1.0

Phosphorus binding site 2 out of 5 in 1agl

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Phosphorus binding site 2 out of 5 in the Structure of A Dna-Bisdaunomycin Complex


Mono view


Stereo pair view

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

b:31.5
occ:1.00
P A:DA3 0.0 31.5 1.0
OP2 A:DA3 1.5 29.0 1.0
OP1 A:DA3 1.5 31.1 1.0
O5' A:DA3 1.6 30.2 1.0
O3' A:DG2 1.6 27.2 1.0
C5' A:DA3 2.6 23.2 1.0
C3' A:DG2 2.7 21.9 1.0
C4' A:DG2 3.7 23.6 1.0
C4' A:DA3 3.8 18.8 1.0
C2' A:DG2 3.8 19.2 1.0
O4' A:DA3 4.0 16.5 1.0
C8 A:DA3 4.2 14.1 1.0
C3' A:DA3 4.4 15.7 1.0
C5' A:DG2 4.6 24.6 1.0
C1' A:DG2 4.6 15.6 1.0
C2' A:DA3 4.6 15.6 1.0
O4' A:DG2 4.8 22.3 1.0
C1' A:DA3 4.9 16.1 1.0
N9 A:DA3 4.9 14.7 1.0

Phosphorus binding site 3 out of 5 in 1agl

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Phosphorus binding site 3 out of 5 in the Structure of A Dna-Bisdaunomycin Complex


Mono view


Stereo pair view

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

b:18.8
occ:1.00
P A:DT4 0.0 18.8 1.0
OP1 A:DT4 1.5 21.1 1.0
OP2 A:DT4 1.5 13.7 1.0
O5' A:DT4 1.6 16.6 1.0
O3' A:DA3 1.6 16.9 1.0
C5' A:DT4 2.6 15.9 1.0
C3' A:DA3 2.6 15.7 1.0
C2' A:DA3 3.3 15.6 1.0
C4' A:DA3 3.9 18.8 1.0
C4' A:DT4 3.9 13.9 1.0
O4' A:DT4 4.2 15.6 1.0
C1' A:DA3 4.2 16.1 1.0
C3' A:DT4 4.5 11.5 1.0
O A:HOH13 4.7 40.3 1.0
O4' A:DA3 4.7 16.5 1.0
C5' A:DA3 4.9 23.2 1.0

Phosphorus binding site 4 out of 5 in 1agl

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Phosphorus binding site 4 out of 5 in the Structure of A Dna-Bisdaunomycin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Structure of A Dna-Bisdaunomycin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:24.7
occ:1.00
P A:DC5 0.0 24.7 1.0
OP1 A:DC5 1.5 27.1 1.0
OP2 A:DC5 1.5 25.2 1.0
O5' A:DC5 1.6 22.4 1.0
O3' A:DT4 1.6 17.8 1.0
C5' A:DC5 2.6 17.6 1.0
C3' A:DT4 2.7 11.5 1.0
C2' A:DT4 3.6 9.9 1.0
C4' A:DT4 3.8 13.9 1.0
C4' A:DC5 3.9 16.5 1.0
O4' A:DC5 4.1 12.4 1.0
C5' A:DT4 4.3 15.9 1.0
C3' A:DC5 4.6 14.0 1.0
O5' A:DT4 4.8 16.6 1.0
C1' A:DT4 4.8 12.5 1.0
C2' A:DC5 4.9 10.6 1.0
O4' A:DT4 5.0 15.6 1.0

Phosphorus binding site 5 out of 5 in 1agl

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Phosphorus binding site 5 out of 5 in the Structure of A Dna-Bisdaunomycin Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Structure of A Dna-Bisdaunomycin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:22.9
occ:1.00
P A:DG6 0.0 22.9 1.0
OP2 A:DG6 1.5 14.8 1.0
OP1 A:DG6 1.5 18.1 1.0
O3' A:DC5 1.6 17.7 1.0
O5' A:DG6 1.6 16.0 1.0
C3' A:DC5 2.6 14.0 1.0
C5' A:DG6 2.6 15.7 1.0
C4' A:DC5 3.6 16.5 1.0
C2' A:DC5 3.7 10.6 1.0
C4' A:DG6 4.0 13.8 1.0
C3' A:DG6 4.4 12.0 1.0
C8 A:DG6 4.5 7.0 1.0
C1' A:DC5 4.5 11.7 1.0
C5' A:DC5 4.6 17.6 1.0
O4' A:DG6 4.6 14.1 1.0
C2' A:DG6 4.6 9.1 1.0
O4' A:DC5 4.7 12.4 1.0

Reference:

G.G.Hu, X.Shui, F.Leng, W.Priebe, J.B.Chaires, L.D.Williams. Structure of A Dna-Bisdaunomycin Complex. Biochemistry V. 36 5940 1997.
ISSN: ISSN 0006-2960
PubMed: 9166763
DOI: 10.1021/BI9705218
Page generated: Fri Sep 25 12:51:55 2020

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