Phosphorus in PDB 182d: Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin

Protein crystallography data

The structure of Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin, PDB code: 182d was solved by C.K.Smith, G.J.Davies, E.J.Dodson, M.H.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 37.200, 37.200, 70.100, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin (pdb code 182d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 10 binding sites of Phosphorus where determined in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin, PDB code: 182d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 10 in 182d

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Phosphorus binding site 1 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

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

b:33.5
occ:1.00
 P A:DG2 0.0 33.5 1.0
OP2 A:DG2 1.4 32.3 1.0
OP1 A:DG2 1.6 34.7 1.0
O5' A:DG2 1.7 33.2 1.0
O3' A:DT1 1.7 29.3 1.0
C3' A:DT1 2.6 27.6 1.0
C5' A:DG2 2.7 31.0 1.0
C2' A:DT1 3.5 26.2 1.0
C4' A:DT1 3.8 26.1 1.0
C4' A:DG2 3.9 30.9 1.0
O A:HOH42 4.0 48.2 1.0
C3' A:DG2 4.4 30.4 1.0
O A:HOH31 4.4 65.7 1.0
C5' A:DT1 4.5 25.6 1.0
O4' A:DG2 4.5 27.1 1.0
O A:HOH44 4.5 57.7 1.0
O A:HOH30 4.6 40.3 1.0
C2' A:DG2 4.7 28.2 1.0
C1' A:DT1 4.8 23.9 1.0
O4' A:DT1 4.9 25.5 1.0
O A:HOH21 5.0 27.6 1.0
O A:HOH45 5.0 91.5 1.0

Phosphorus binding site 2 out of 10 in 182d

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Phosphorus binding site 2 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

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

b:32.5
occ:1.00
 P A:DA3 0.0 32.5 1.0
OP2 A:DA3 1.4 37.3 1.0
OP1 A:DA3 1.6 36.7 1.0
O5' A:DA3 1.6 31.6 1.0
O3' A:DG2 1.7 34.9 1.0
C5' A:DA3 2.6 28.6 1.0
C3' A:DG2 2.8 30.4 1.0
C4' A:DG2 3.8 30.9 1.0
C4' A:DA3 3.8 28.5 1.0
C2' A:DG2 3.8 28.2 1.0
O A:HOH59 4.0 68.7 1.0
O A:HOH54 4.1 55.9 1.0
O4' A:DA3 4.1 26.8 1.0
C3' A:DA3 4.3 29.3 1.0
O A:HOH87 4.3 73.6 1.0
C1' A:DG2 4.4 25.8 1.0
O A:HOH43 4.4 47.2 1.0
C8 A:DA3 4.6 19.3 1.0
O4' A:DG2 4.6 27.1 1.0
C2' A:DA3 4.7 27.5 1.0
C5' A:DG2 4.9 31.0 1.0
C1' A:DA3 4.9 23.9 1.0
O A:HOH45 5.0 91.5 1.0
O A:HOH88 5.0 55.5 1.0

Phosphorus binding site 3 out of 10 in 182d

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Phosphorus binding site 3 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

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

b:34.5
occ:1.00
 P A:DT4 0.0 34.5 1.0
OP2 A:DT4 1.5 35.6 1.0
OP1 A:DT4 1.6 36.4 1.0
O5' A:DT4 1.6 33.5 1.0
O3' A:DA3 1.7 34.8 1.0
C5' A:DT4 2.6 27.6 1.0
C3' A:DA3 2.7 29.3 1.0
C2' A:DA3 3.4 27.5 1.0
C4' A:DT4 3.8 25.9 1.0
O A:HOH65 3.8 49.6 1.0
C4' A:DA3 3.9 28.5 1.0
O4' A:DT4 4.1 23.9 1.0
O A:HOH56 4.2 74.3 1.0
O A:HOH70 4.2 47.1 1.0
C1' A:DA3 4.4 23.9 1.0
C3' A:DT4 4.4 27.2 1.0
O A:HOH69 4.6 53.4 1.0
O A:HOH55 4.7 51.8 1.0
O4' A:DA3 4.7 26.8 1.0
O A:HOH88 4.8 55.5 1.0
C5' A:DA3 4.9 28.6 1.0

Phosphorus binding site 4 out of 10 in 182d

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Phosphorus binding site 4 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

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

b:32.2
occ:1.00
 P A:DC5 0.0 32.2 1.0
OP2 A:DC5 1.5 29.9 1.0
OP1 A:DC5 1.6 32.8 1.0
O5' A:DC5 1.6 30.4 1.0
O3' A:DT4 1.7 29.7 1.0
C5' A:DC5 2.6 30.7 1.0
C3' A:DT4 2.7 27.2 1.0
C2' A:DT4 3.4 25.3 1.0
O A:HOH66 3.8 70.0 1.0
C4' A:DC5 3.9 24.6 1.0
C4' A:DT4 3.9 25.9 1.0
O4' A:DC5 4.2 22.8 1.0
C3' A:DC5 4.5 25.1 1.0
C5' A:DT4 4.5 27.6 1.0
C1' A:DT4 4.7 23.3 1.0
C2' A:DC5 4.7 22.9 1.0
O A:HOH67 4.9 71.3 1.0
O5' A:DT4 4.9 33.5 1.0
O4' A:DT4 4.9 23.9 1.0

Phosphorus binding site 5 out of 10 in 182d

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Phosphorus binding site 5 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

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

b:26.7
occ:1.00
 P A:DA6 0.0 26.7 1.0
OP1 A:DA6 1.5 31.3 1.0
OP2 A:DA6 1.5 25.2 1.0
O5' A:DA6 1.6 25.2 1.0
O3' A:DC5 1.7 24.6 1.0
C5' A:DA6 2.6 24.4 1.0
C3' A:DC5 2.7 25.1 1.0
C4' A:DC5 3.5 24.6 1.0
C4' A:DA6 3.8 23.1 1.0
C2' A:DC5 3.9 22.9 1.0
O4' A:DA6 4.0 21.0 1.0
O A:HOH20 4.0 42.3 1.0
C8 A:DA6 4.1 16.6 1.0
O A:HOH82 4.1 73.8 1.0
C3' A:DA6 4.4 22.9 1.0
C5' A:DC5 4.5 30.7 1.0
C2' A:DA6 4.5 21.3 1.0
C1' A:DC5 4.6 21.9 1.0
O4' A:DC5 4.6 22.8 1.0
C1' A:DA6 4.7 20.5 1.0
C29 B:NGM13 4.8 16.7 1.0
N9 A:DA6 4.8 15.9 1.0
N7 A:DA6 5.0 15.9 1.0

Phosphorus binding site 6 out of 10 in 182d

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Phosphorus binding site 6 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:41.7
occ:1.00
 P B:DG8 0.0 41.7 1.0
OP2 B:DG8 1.5 42.9 1.0
OP1 B:DG8 1.6 42.0 1.0
O5' B:DG8 1.6 36.7 1.0
O3' B:DT7 1.7 39.7 1.0
C5' B:DG8 2.5 33.2 1.0
C3' B:DT7 2.7 37.8 1.0
C2' B:DT7 3.7 34.2 1.0
C4' B:DG8 3.7 28.9 1.0
C4' B:DT7 3.8 39.3 1.0
O B:HOH92 3.9 46.6 1.0
C3' B:DG8 4.1 30.0 1.0
O4' B:DG8 4.1 25.6 1.0
O5' B:DT7 4.4 40.4 1.0
O B:HOH90 4.5 54.2 1.0
O4' B:DT7 4.7 36.4 1.0
C2' B:DG8 4.7 25.3 1.0
C5' B:DT7 4.8 41.3 1.0
C1' B:DT7 4.8 29.4 1.0

Phosphorus binding site 7 out of 10 in 182d

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Phosphorus binding site 7 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:36.3
occ:1.00
 P B:DA9 0.0 36.3 1.0
OP2 B:DA9 1.4 37.9 1.0
O5' B:DA9 1.6 33.4 1.0
OP1 B:DA9 1.6 39.7 1.0
O3' B:DG8 1.7 35.8 1.0
C5' B:DA9 2.6 31.8 1.0
C3' B:DG8 2.8 30.0 1.0
C2' B:DG8 3.5 25.3 1.0
C4' B:DA9 3.8 31.8 1.0
C4' B:DG8 3.8 28.9 1.0
O4' B:DA9 3.9 28.6 1.0
O B:HOH58 4.1 46.0 1.0
C1' B:DG8 4.3 23.5 1.0
C3' B:DA9 4.4 33.2 1.0
C5' B:DG8 4.7 33.2 1.0
C8 B:DA9 4.7 20.2 1.0
C2' B:DA9 4.8 30.1 1.0
O4' B:DG8 4.8 25.6 1.0
O B:HOH38 4.8 81.6 1.0
O B:HOH40 4.9 68.4 1.0
C1' B:DA9 4.9 26.4 1.0

Phosphorus binding site 8 out of 10 in 182d

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Phosphorus binding site 8 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:42.2
occ:1.00
 P B:DT10 0.0 42.2 1.0
OP2 B:DT10 1.5 40.2 1.0
OP1 B:DT10 1.6 42.3 1.0
O5' B:DT10 1.6 37.1 1.0
O3' B:DA9 1.7 39.7 1.0
C5' B:DT10 2.5 34.0 1.0
C3' B:DA9 2.6 33.2 1.0
C2' B:DA9 3.3 30.1 1.0
O B:HOH105 3.4 62.1 1.0
C4' B:DT10 3.8 31.7 1.0
C4' B:DA9 3.9 31.8 1.0
O B:HOH34 4.0 78.8 1.0
O4' B:DT10 4.1 28.3 1.0
C3' B:DT10 4.3 32.3 1.0
C1' B:DA9 4.3 26.4 1.0
O B:HOH39 4.6 64.5 1.0
O4' B:DA9 4.7 28.6 1.0
C5' B:DA9 4.9 31.8 1.0
O B:HOH26 5.0 43.3 1.0

Phosphorus binding site 9 out of 10 in 182d

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Phosphorus binding site 9 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:39.0
occ:1.00
 P B:DC11 0.0 39.0 1.0
OP2 B:DC11 1.5 38.2 1.0
O5' B:DC11 1.6 35.2 1.0
OP1 B:DC11 1.6 41.0 1.0
O3' B:DT10 1.7 36.4 1.0
C5' B:DC11 2.7 31.7 1.0
C3' B:DT10 2.7 32.3 1.0
C2' B:DT10 3.3 29.6 1.0
C4' B:DC11 3.8 29.5 1.0
O B:HOH125 3.8 66.8 1.0
C4' B:DT10 3.9 31.7 1.0
O4' B:DC11 4.0 27.0 1.0
C3' B:DC11 4.2 30.0 1.0
O B:HOH86 4.3 48.2 1.0
C2' B:DC11 4.3 29.4 1.0
O B:HOH26 4.5 43.3 1.0
C1' B:DT10 4.6 27.4 1.0
C5' B:DT10 4.8 34.0 1.0
C1' B:DC11 4.8 26.1 1.0
O4' B:DT10 4.9 28.3 1.0
O B:HOH101 4.9 64.2 1.0

Phosphorus binding site 10 out of 10 in 182d

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Phosphorus binding site 10 out of 10 in the Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:36.3
occ:1.00
 P B:DA12 0.0 36.3 1.0
OP2 B:DA12 1.5 38.6 1.0
OP1 B:DA12 1.6 38.4 1.0
O3' B:DC11 1.7 33.3 1.0
C5' B:DA12 2.6 32.5 1.0
C3' B:DC11 2.7 30.0 1.0
C4' B:DC11 3.6 29.5 1.0
C4' B:DA12 3.9 32.7 1.0
C2' B:DC11 3.9 29.4 1.0
O B:HOH25 4.0 69.4 1.0
C8 B:DA12 4.2 17.7 1.0
O4' B:DA12 4.4 28.7 1.0
C5' B:DC11 4.5 31.7 1.0
C3' B:DA12 4.5 32.5 1.0
O B:HOH19 4.6 56.3 1.0
O A:HOH107 4.6 90.3 1.0
C2' B:DA12 4.6 31.0 1.0
C1' B:DC11 4.7 26.1 1.0
O4' B:DC11 4.7 27.0 1.0
C29 A:NGM14 4.8 22.5 1.0
C1' B:DA12 4.9 26.4 1.0
N9 B:DA12 5.0 21.6 1.0
O5' B:DC11 5.0 35.2 1.0

Reference:

C.K.Smith, G.J.Davies, E.J.Dodson, M.H.Moore. Dna-Nogalamycin Interactions: the Crystal Structure of D(Tgatca) Complexed with Nogalamycin. Biochemistry V. 34 415 1995.
ISSN: ISSN 0006-2960
PubMed: 7819233
DOI: 10.1021/BI00002A005
Page generated: Fri Sep 25 11:46:22 2020

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