Phosphorus in PDB 121d: Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin

Protein crystallography data

The structure of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin, PDB code: 121d was solved by L.Tabernero, N.Verdaguer, M.Coll, I.Fita, G.A.Van Der Marel, J.H.Van Boom, A.Rich, J.Aymami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.650, 42.030, 65.330, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 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 Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin (pdb code 121d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin, PDB code: 121d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 121d

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Phosphorus binding site 1 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:28.5
occ:1.00
P A:DG2 0.0 28.5 1.0
OP1 A:DG2 1.5 26.9 1.0
OP2 A:DG2 1.5 28.4 1.0
O5' A:DG2 1.6 22.3 1.0
O3' A:DC1 1.6 23.2 1.0
C5' A:DG2 2.5 18.8 1.0
C3' A:DC1 2.7 19.5 1.0
C2' A:DC1 3.2 20.7 1.0
C4' A:DG2 3.9 18.0 1.0
C4' A:DC1 4.0 19.5 1.0
C1' A:DC1 4.2 22.0 1.0
C8 A:DG2 4.3 23.2 1.0
O4' A:DC1 4.4 18.1 1.0
O4' A:DG2 4.5 18.3 1.0
C3' A:DG2 4.6 17.3 1.0
C2' A:DG2 4.9 17.8 1.0
N9 A:DG2 5.0 22.0 1.0

Phosphorus binding site 2 out of 22 in 121d

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Phosphorus binding site 2 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:24.4
occ:1.00
P A:DC3 0.0 24.4 1.0
OP1 A:DC3 1.5 22.6 1.0
OP2 A:DC3 1.5 20.4 1.0
O3' A:DG2 1.5 21.6 1.0
O5' A:DC3 1.6 24.0 1.0
C3' A:DG2 2.5 17.3 1.0
C5' A:DC3 2.6 24.1 1.0
C2' A:DG2 3.1 17.8 1.0
C4' A:DG2 3.7 18.0 1.0
C4' A:DC3 3.9 27.8 1.0
O4' A:DC3 4.1 30.2 1.0
C1' A:DG2 4.1 19.9 1.0
O4' A:DG2 4.4 18.3 1.0
C3' A:DC3 4.5 30.2 1.0
C6 A:DC3 4.7 41.1 1.0
C5' A:DG2 4.8 18.8 1.0

Phosphorus binding site 3 out of 22 in 121d

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Phosphorus binding site 3 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:35.3
occ:1.00
P A:DA4 0.0 35.3 1.0
OP1 A:DA4 1.5 36.6 1.0
OP2 A:DA4 1.5 35.4 1.0
O3' A:DC3 1.6 33.3 1.0
O5' A:DA4 1.6 34.0 1.0
C3' A:DC3 2.6 30.2 1.0
C5' A:DA4 2.6 32.6 1.0
C2' A:DC3 3.2 31.4 1.0
C4' A:DC3 3.9 27.8 1.0
C4' A:DA4 3.9 32.8 1.0
C3' A:DA4 4.2 33.5 1.0
C8 A:DA4 4.3 31.5 1.0
C2' A:DA4 4.3 32.9 1.0
O4' A:DA4 4.4 30.5 1.0
C1' A:DC3 4.5 33.5 1.0
O A:HOH43 4.6 28.6 1.0
O4' A:DC3 4.8 30.2 1.0
C5' A:DC3 4.9 24.1 1.0
C1' A:DA4 4.9 30.4 1.0

Phosphorus binding site 4 out of 22 in 121d

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Phosphorus binding site 4 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:39.2
occ:1.00
P A:DA5 0.0 39.2 1.0
OP1 A:DA5 1.5 40.2 1.0
OP2 A:DA5 1.5 39.9 1.0
O3' A:DA4 1.6 37.1 1.0
O5' A:DA5 1.6 36.7 1.0
C5' A:DA5 2.6 33.0 1.0
C3' A:DA4 2.6 33.5 1.0
C2' A:DA4 3.2 32.9 1.0
C4' A:DA4 3.9 32.8 1.0
C4' A:DA5 3.9 31.5 1.0
C1' A:DA4 4.1 30.4 1.0
O4' A:DA5 4.1 32.7 1.0
C2' A:DA5 4.4 30.3 1.0
O4' A:DA4 4.5 30.5 1.0
C3' A:DA5 4.5 29.2 1.0
C8 A:DA5 4.7 35.4 1.0
C1' A:DA5 4.8 32.9 1.0
C5' A:DA4 5.0 32.6 1.0

Phosphorus binding site 5 out of 22 in 121d

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Phosphorus binding site 5 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:18.9
occ:1.00
P A:DA6 0.0 18.9 1.0
OP1 A:DA6 1.5 15.9 1.0
OP2 A:DA6 1.5 19.5 1.0
O5' A:DA6 1.6 18.7 1.0
O3' A:DA5 1.6 24.4 1.0
C5' A:DA6 2.6 16.7 1.0
C3' A:DA5 2.8 29.2 1.0
C2' A:DA5 3.8 30.3 1.0
C4' A:DA6 3.8 15.2 1.0
C4' A:DA5 4.0 31.5 1.0
O4' A:DA6 4.3 16.2 1.0
C3' A:DA6 4.4 12.2 1.0
C2' A:DA6 4.5 14.2 1.0
C1' A:DA5 4.5 32.9 1.0
O A:HOH60 4.7 12.1 1.0
O4' A:DA5 4.9 32.7 1.0

Phosphorus binding site 6 out of 22 in 121d

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Phosphorus binding site 6 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:14.7
occ:1.00
P A:DT7 0.0 14.7 1.0
OP1 A:DT7 1.5 9.4 1.0
OP2 A:DT7 1.5 9.3 1.0
O3' A:DA6 1.6 12.9 1.0
O5' A:DT7 1.6 12.5 1.0
C3' A:DA6 2.6 12.2 1.0
C5' A:DT7 2.6 14.8 1.0
C2' A:DA6 3.3 14.2 1.0
C4' A:DA6 3.8 15.2 1.0
C4' A:DT7 3.9 15.5 1.0
C1' A:DA6 4.1 16.9 1.0
O4' A:DT7 4.3 17.3 1.0
C3' A:DT7 4.5 16.8 1.0
O4' A:DA6 4.6 16.2 1.0
N10 A:NT25 4.8 46.2 1.0
C5' A:DA6 4.9 16.7 1.0
C2' A:DT7 4.9 20.2 1.0

Phosphorus binding site 7 out of 22 in 121d

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Phosphorus binding site 7 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:15.3
occ:1.00
P A:DT8 0.0 15.3 1.0
OP2 A:DT8 1.5 13.3 1.0
OP1 A:DT8 1.5 8.3 1.0
O5' A:DT8 1.6 11.8 1.0
O3' A:DT7 1.6 15.6 1.0
C3' A:DT7 2.6 16.8 1.0
C5' A:DT8 2.6 13.2 1.0
C4' A:DT7 3.4 15.5 1.0
C2' A:DT7 3.7 20.2 1.0
O4' A:DT8 3.8 16.9 1.0
C4' A:DT8 3.8 14.4 1.0
C5' A:DT7 4.2 14.8 1.0
C1' A:DT7 4.4 25.0 1.0
O4' A:DT7 4.6 17.3 1.0
C3' A:DT8 4.7 15.3 1.0

Phosphorus binding site 8 out of 22 in 121d

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Phosphorus binding site 8 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:18.5
occ:1.00
P A:DT9 0.0 18.5 1.0
OP2 A:DT9 1.5 20.8 1.0
OP1 A:DT9 1.5 15.7 1.0
O3' A:DT8 1.6 15.1 1.0
O5' A:DT9 1.6 20.5 1.0
C5' A:DT9 2.5 28.7 1.0
C3' A:DT8 2.6 15.3 1.0
C2' A:DT8 3.2 17.6 1.0
C4' A:DT8 3.8 14.4 1.0
C4' A:DT9 3.9 32.5 1.0
C3' A:DT9 4.2 34.8 1.0
C1' A:DT8 4.5 19.8 1.0
O4' A:DT9 4.6 32.7 1.0
C5' A:DT8 4.7 13.2 1.0
O4' A:DT8 4.8 16.9 1.0
C2' A:DT9 4.8 34.4 1.0

Phosphorus binding site 9 out of 22 in 121d

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Phosphorus binding site 9 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:41.1
occ:1.00
P A:DG10 0.0 41.1 1.0
OP1 A:DG10 1.5 43.3 1.0
OP2 A:DG10 1.5 41.9 1.0
O5' A:DG10 1.6 41.2 1.0
O3' A:DT9 1.6 38.7 1.0
C3' A:DT9 2.7 34.8 1.0
C5' A:DG10 2.8 40.4 1.0
C4' A:DG10 3.3 40.0 1.0
C2' A:DT9 3.6 34.4 1.0
O4' A:DG10 3.7 39.6 1.0
C4' A:DT9 3.9 32.5 1.0
C1' A:DT9 4.5 35.1 1.0
C5' A:DT9 4.7 28.7 1.0
C3' A:DG10 4.8 40.5 1.0
O4' A:DT9 4.9 32.7 1.0

Phosphorus binding site 10 out of 22 in 121d

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Phosphorus binding site 10 out of 22 in the Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:44.3
occ:1.00
P A:DC11 0.0 44.3 1.0
OP1 A:DC11 1.5 44.7 1.0
OP2 A:DC11 1.5 44.1 1.0
O5' A:DC11 1.6 45.0 1.0
O3' A:DG10 1.6 42.4 1.0
C3' A:DG10 2.6 40.5 1.0
C5' A:DC11 2.6 42.6 1.0
C2' A:DG10 3.2 39.6 1.0
C4' A:DC11 3.9 40.3 1.0
C4' A:DG10 4.0 40.0 1.0
O4' A:DC11 4.2 38.4 1.0
C1' A:DG10 4.3 39.7 1.0
C6 A:DC11 4.4 41.1 1.0
C3' A:DC11 4.4 41.3 1.0
O4' A:DG10 4.7 39.6 1.0
C2' A:DC11 4.8 41.3 1.0
C5' A:DG10 4.9 40.4 1.0

Reference:

L.Tabernero, N.Verdaguer, M.Coll, I.Fita, G.A.Van Der Marel, J.H.Van Boom, A.Rich, J.Aymami. Molecular Structure of the A-Tract Dna Dodecamer D(Cgcaaatttgcg) Complexed with the Minor Groove Binding Drug Netropsin. Biochemistry V. 32 8403 1993.
ISSN: ISSN 0006-2960
PubMed: 8395202
DOI: 10.1021/BI00084A004
Page generated: Fri Sep 25 11:13:00 2020

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