Phosphorus in PDB 196d: Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction

Protein crystallography data

The structure of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction, PDB code: 196d was solved by D.S.Goodsell, K.Grzeskowiak, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.230, 24.320, 40.830, 90.00, 126.78, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction (pdb code 196d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction, PDB code: 196d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 196d

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Phosphorus binding site 1 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:23.4
occ:1.00
P A:DT2 0.0 23.4 1.0
OP2 A:DT2 1.5 23.1 1.0
OP1 A:DT2 1.5 32.1 1.0
O5' A:DT2 1.6 21.5 1.0
O3' A:DC1 1.6 25.7 1.0
C3' A:DC1 2.7 20.1 1.0
C5' A:DT2 2.7 24.0 1.0
C2' A:DC1 3.3 19.7 1.0
O A:HOH66 3.7 29.2 1.0
O A:HOH59 3.9 37.0 1.0
C4' A:DT2 4.0 14.7 1.0
C4' A:DC1 4.0 19.8 1.0
C6 A:DT2 4.2 13.5 1.0
O4' A:DT2 4.4 14.5 1.0
C3' A:DT2 4.4 22.5 1.0
C2' A:DT2 4.6 18.5 1.0
C5' A:DC1 4.6 21.2 1.0
O5' A:DC1 4.7 25.8 1.0
C1' A:DC1 4.7 14.6 1.0
C7 A:DT2 4.8 15.0 1.0
C1' A:DT2 4.9 12.4 1.0
O4' A:DC1 4.9 16.0 1.0
C5 A:DT2 5.0 15.8 1.0
N1 A:DT2 5.0 16.4 1.0
O A:HOH93 5.0 41.5 1.0

Phosphorus binding site 2 out of 18 in 196d

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Phosphorus binding site 2 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction 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 1.5 27.1 1.0
OP2 A:DC3 1.5 21.9 1.0
O5' A:DC3 1.6 17.1 1.0
O3' A:DT2 1.6 26.8 1.0
C5' A:DC3 2.6 16.7 1.0
C3' A:DT2 2.7 22.5 1.0
C2' A:DT2 3.3 18.5 1.0
O A:HOH47 3.5 20.6 1.0
C4' A:DC3 3.8 19.1 1.0
C4' A:DT2 4.0 14.7 1.0
C3' A:DC3 4.2 15.8 1.0
C1' A:DT2 4.2 12.4 1.0
O4' A:DC3 4.2 15.7 1.0
O A:HOH93 4.4 41.5 1.0
O4' A:DT2 4.6 14.5 1.0
C2' A:DC3 4.8 17.2 1.0
C6 A:DC3 4.9 11.0 1.0

Phosphorus binding site 3 out of 18 in 196d

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Phosphorus binding site 3 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:17.4
occ:1.00
P A:DT4 0.0 17.4 1.0
OP1 A:DT4 1.5 18.9 1.0
O3' A:DC3 1.5 13.1 1.0
OP2 A:DT4 1.5 14.8 1.0
O5' A:DT4 1.6 16.6 1.0
C3' A:DC3 2.6 15.8 1.0
C5' A:DT4 2.6 13.2 1.0
C2' A:DC3 3.2 17.2 1.0
O A:HOH49 3.8 22.4 1.0
C4' A:DT4 3.8 11.7 1.0
C4' A:DC3 3.9 19.1 1.0
O4' A:DT4 4.2 14.9 1.0
O A:HOH85 4.2 42.2 1.0
C1' A:DC3 4.3 17.4 1.0
C3' A:DT4 4.3 12.2 1.0
O A:HOH116 4.4 23.9 1.0
C2' A:DT4 4.8 16.7 1.0
O4' A:DC3 4.8 15.7 1.0
C6 A:DT4 4.9 14.8 1.0
C5' A:DC3 4.9 16.7 1.0

Phosphorus binding site 4 out of 18 in 196d

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Phosphorus binding site 4 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:15.2
occ:1.00
P A:DC5 0.0 15.2 1.0
OP2 A:DC5 1.4 13.1 1.0
OP1 A:DC5 1.5 15.9 1.0
O3' A:DT4 1.6 14.4 1.0
O5' A:DC5 1.7 12.3 1.0
C5' A:DC5 2.7 8.5 1.0
C3' A:DT4 2.7 12.2 1.0
CA A:CA22 3.4 21.3 1.0
C2' A:DT4 3.5 16.7 1.0
O A:HOH78 3.6 21.8 1.0
O A:HOH119 3.6 23.4 1.0
O A:HOH117 3.9 26.6 1.0
C4' A:DC5 3.9 10.1 1.0
C4' A:DT4 3.9 11.7 1.0
O A:HOH120 4.0 31.2 1.0
O A:HOH116 4.2 23.9 1.0
O4' A:DC5 4.3 9.7 1.0
C3' A:DC5 4.4 11.3 1.0
O A:HOH37 4.4 20.1 1.0
C1' A:DT4 4.4 16.4 1.0
C2' A:DC5 4.6 15.6 1.0
O4' A:DT4 4.8 14.9 1.0
C5' A:DT4 4.8 13.2 1.0
O A:HOH118 4.9 24.5 1.0

Phosphorus binding site 5 out of 18 in 196d

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Phosphorus binding site 5 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:20.7
occ:1.00
P A:DG6 0.0 20.7 1.0
OP1 A:DG6 1.4 25.4 1.0
OP2 A:DG6 1.5 23.3 1.0
O3' A:DC5 1.6 20.6 1.0
O5' A:DG6 1.6 22.3 1.0
C5' A:DG6 2.6 19.7 1.0
C3' A:DC5 2.7 11.3 1.0
C4' A:DC5 3.7 10.1 1.0
C2' A:DC5 3.8 15.6 1.0
C4' A:DG6 3.8 17.7 1.0
O4' A:DG6 4.1 12.4 1.0
C8 A:DG6 4.2 12.1 1.0
C3' A:DG6 4.4 11.7 1.0
C2' A:DG6 4.4 11.7 1.0
C1' A:DC5 4.5 7.8 1.0
C1' A:DG6 4.6 11.8 1.0
O A:HOH101 4.7 43.2 1.0
O4' A:DC5 4.7 9.7 1.0
C5' A:DC5 4.7 8.5 1.0
N9 A:DG6 4.8 13.7 1.0

Phosphorus binding site 6 out of 18 in 196d

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Phosphorus binding site 6 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:16.2
occ:1.00
P A:DA7 0.0 16.2 1.0
OP2 A:DA7 1.4 13.9 1.0
OP1 A:DA7 1.5 27.5 1.0
O5' A:DA7 1.6 12.4 1.0
O3' A:DG6 1.6 17.2 1.0
C5' A:DA7 2.6 14.8 1.0
C3' A:DG6 2.7 11.7 1.0
C2' A:DG6 3.3 11.7 1.0
C4' A:DA7 3.9 13.5 1.0
C4' A:DG6 4.0 17.7 1.0
C1' A:DG6 4.1 11.8 1.0
C3' A:DA7 4.2 13.6 1.0
O4' A:DA7 4.5 9.8 1.0
C2' A:DA7 4.6 12.9 1.0
O4' A:DG6 4.6 12.4 1.0
C8 A:DA7 4.7 11.8 1.0

Phosphorus binding site 7 out of 18 in 196d

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Phosphorus binding site 7 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:14.7
occ:1.00
P A:DG8 0.0 14.7 1.0
OP2 A:DG8 1.4 10.6 1.0
OP1 A:DG8 1.5 17.1 1.0
O3' A:DA7 1.6 17.7 1.0
O5' A:DG8 1.6 17.8 1.0
C5' A:DG8 2.6 14.2 1.0
C3' A:DA7 2.6 13.6 1.0
C2' A:DA7 3.3 12.9 1.0
O A:HOH28 3.7 15.3 1.0
C4' A:DG8 3.9 21.9 1.0
C4' A:DA7 3.9 13.5 1.0
C1' A:DA7 4.2 8.6 1.0
O4' A:DG8 4.3 19.5 1.0
C3' A:DG8 4.4 26.4 1.0
C2' A:DG8 4.6 22.7 1.0
O4' A:DA7 4.6 9.8 1.0
O A:HOH113 4.6 19.0 1.0
O A:HOH31 4.7 44.6 1.0
C5' A:DA7 5.0 14.8 1.0

Phosphorus binding site 8 out of 18 in 196d

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Phosphorus binding site 8 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:28.7
occ:1.00
P A:DA9 0.0 28.7 1.0
OP2 A:DA9 1.5 19.8 1.0
OP1 A:DA9 1.5 38.1 1.0
O5' A:DA9 1.6 25.8 1.0
O3' A:DG8 1.6 28.2 1.0
C5' A:DA9 2.6 25.5 1.0
C3' A:DG8 2.7 26.4 1.0
C2' A:DG8 3.3 22.7 1.0
C4' A:DA9 3.9 25.6 1.0
C4' A:DG8 4.0 21.9 1.0
C1' A:DG8 4.1 24.2 1.0
C3' A:DA9 4.2 28.9 1.0
O A:HOH104 4.3 35.5 1.0
C2' A:DA9 4.4 19.2 1.0
O4' A:DA9 4.5 24.3 1.0
O4' A:DG8 4.7 19.5 1.0
C8 A:DA9 4.9 15.9 1.0

Phosphorus binding site 9 out of 18 in 196d

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Phosphorus binding site 9 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:33.1
occ:1.00
P A:DG10 0.0 33.1 1.0
OP2 A:DG10 1.5 27.7 1.0
OP1 A:DG10 1.5 26.6 1.0
O3' A:DA9 1.6 29.2 1.0
O5' A:DG10 1.6 22.0 1.0
C5' A:DG10 2.6 19.5 1.0
C3' A:DA9 2.7 28.9 1.0
C2' A:DA9 3.4 19.2 1.0
C4' A:DG10 3.8 16.3 1.0
C4' A:DA9 4.0 25.6 1.0
O4' A:DG10 4.1 19.7 1.0
C3' A:DG10 4.2 20.4 1.0
C1' A:DA9 4.2 17.5 1.0
C2' A:DG10 4.5 14.8 1.0
O4' A:DA9 4.6 24.3 1.0
C1' A:DG10 4.8 17.9 1.0
C8 A:DG10 4.8 17.6 1.0

Phosphorus binding site 10 out of 18 in 196d

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Phosphorus binding site 10 out of 18 in the Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Crystal Structure of C-T-C-T-C-G-A-G-A-G: Implications For the Structure of the Holliday Junction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:30.7
occ:1.00
P B:DT12 0.0 30.7 1.0
OP1 B:DT12 1.5 30.4 1.0
OP2 B:DT12 1.5 24.6 1.0
O5' B:DT12 1.6 26.7 1.0
O3' B:DC11 1.6 25.1 1.0
C3' B:DC11 2.6 18.2 1.0
C5' B:DT12 2.7 14.7 1.0
C2' B:DC11 3.3 16.8 1.0
O B:HOH65 3.3 44.1 1.0
O B:HOH35 3.8 15.0 1.0
O B:HOH60 3.8 24.7 1.0
C4' B:DC11 3.9 19.1 1.0
C4' B:DT12 3.9 23.3 1.0
C6 B:DT12 4.2 14.9 1.0
O4' B:DT12 4.4 18.2 1.0
C3' B:DT12 4.4 24.0 1.0
C2' B:DT12 4.4 16.4 1.0
C5' B:DC11 4.6 17.8 1.0
C1' B:DC11 4.6 19.9 1.0
C7 B:DT12 4.7 13.0 1.0
O5' B:DC11 4.8 16.9 1.0
O4' B:DC11 4.9 23.0 1.0
C5 B:DT12 4.9 18.7 1.0
C1' B:DT12 4.9 14.4 1.0
O B:HOH62 4.9 40.8 1.0

Reference:

D.S.Goodsell, K.Grzeskowiak, R.E.Dickerson. Crystal Structure of C-T-C-T-C-G-A-G-A-G. Implications For the Structure of the Holliday Junction. Biochemistry V. 34 1022 1995.
ISSN: ISSN 0006-2960
PubMed: 7827018
DOI: 10.1021/BI00003A037
Page generated: Fri Sep 25 11:52:20 2020

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