Phosphorus in PDB 1a73: Intron-Encoded Endonuclease I-Ppoi Complexed with Dna

Protein crystallography data

The structure of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna, PDB code: 1a73 was solved by K.E.Flick, R.J.Monnat Junior, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.700, 113.700, 88.400, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 29.7

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Phosphorus atom in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna (pdb code 1a73). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 40 binding sites of Phosphorus where determined in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna, PDB code: 1a73:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 40 in 1a73

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Phosphorus binding site 1 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P2

b:20.3
occ:1.00
 P C:DT2 0.0 20.3 1.0
OP2 C:DT2 1.5 18.9 1.0
OP1 C:DT2 1.5 21.8 1.0
O5' C:DT2 1.6 20.5 1.0
O3' C:DT1 1.6 21.6 1.0
C5' C:DT2 2.6 24.1 1.0
C3' C:DT1 2.6 20.3 1.0
C2' C:DT1 3.3 18.7 1.0
O C:HOH557 3.6 20.4 1.0
O C:HOH553 3.8 18.8 1.0
C4' C:DT2 3.9 22.1 1.0
O A:HOH382 3.9 18.0 1.0
C4' C:DT1 3.9 20.6 1.0
C1' C:DT1 4.2 19.2 1.0
NH2 A:ARG66 4.3 13.3 1.0
C3' C:DT2 4.4 23.2 1.0
O4' C:DT1 4.6 21.1 1.0
CZ A:ARG66 4.7 14.9 1.0
NH1 A:ARG66 4.9 17.1 1.0
O4' C:DT2 4.9 23.9 1.0

Phosphorus binding site 2 out of 40 in 1a73

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Phosphorus binding site 2 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P3

b:23.2
occ:1.00
 P C:DG3 0.0 23.2 1.0
OP1 C:DG3 1.5 23.4 1.0
OP2 C:DG3 1.5 22.6 1.0
O5' C:DG3 1.6 22.3 1.0
O3' C:DT2 1.6 23.0 1.0
C5' C:DG3 2.6 18.3 1.0
C3' C:DT2 2.6 23.2 1.0
C2' C:DT2 3.1 21.7 1.0
O A:HOH561 3.8 24.9 1.0
N A:GLY53 3.8 11.8 1.0
O C:HOH622 3.8 47.6 1.0
C4' C:DG3 3.9 17.6 1.0
C4' C:DT2 3.9 22.1 1.0
O C:HOH648 4.1 38.3 1.0
O A:HOH525 4.2 19.9 1.0
C1' C:DT2 4.2 20.7 1.0
C3' C:DG3 4.4 16.6 1.0
O4' C:DG3 4.4 18.1 1.0
CA A:VAL52 4.5 12.8 1.0
CA A:GLY53 4.6 11.6 1.0
O4' C:DT2 4.6 23.9 1.0
C A:VAL52 4.7 12.7 1.0
CG1 A:VAL52 4.7 12.7 1.0
C2' C:DG3 4.7 16.9 1.0
C8 C:DG3 4.7 15.2 1.0
NH2 A:ARG66 4.8 13.3 1.0

Phosphorus binding site 3 out of 40 in 1a73

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Phosphorus binding site 3 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P4

b:19.9
occ:1.00
 P C:DA4 0.0 19.9 1.0
OP1 C:DA4 1.5 17.2 1.0
OP2 C:DA4 1.5 20.1 1.0
O5' C:DA4 1.6 20.2 1.0
O3' C:DG3 1.6 16.9 1.0
C3' C:DG3 2.6 16.6 1.0
C5' C:DA4 2.6 19.3 1.0
C2' C:DG3 3.3 16.9 1.0
O C:HOH436 3.7 14.0 1.0
C4' C:DG3 3.9 17.6 1.0
CB A:ALA48 3.9 18.6 1.0
C4' C:DA4 3.9 18.4 1.0
O C:HOH396 4.0 31.0 1.0
O C:HOH468 4.0 12.4 1.0
CB A:PRO49 4.1 18.5 1.0
CA A:PRO49 4.1 17.7 1.0
C1' C:DG3 4.2 16.9 1.0
C3' C:DA4 4.4 18.4 1.0
O4' C:DA4 4.5 18.1 1.0
O4' C:DG3 4.6 18.1 1.0
N A:PRO49 4.7 18.4 1.0
C2' C:DA4 4.7 17.5 1.0
O C:HOH648 4.9 38.3 1.0
CA A:ALA48 4.9 18.2 1.0

Phosphorus binding site 4 out of 40 in 1a73

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Phosphorus binding site 4 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P5

b:19.7
occ:1.00
 P C:DC5 0.0 19.7 1.0
OP2 C:DC5 1.5 19.3 1.0
OP1 C:DC5 1.5 20.0 1.0
O5' C:DC5 1.6 18.6 1.0
O3' C:DA4 1.6 18.9 1.0
C3' C:DA4 2.6 18.4 1.0
C5' C:DC5 2.6 18.5 1.0
C2' C:DA4 3.5 17.5 1.0
C4' C:DC5 3.7 19.1 1.0
C4' C:DA4 3.8 18.4 1.0
O C:HOH347 4.0 25.8 1.0
O4' C:DC5 4.0 17.4 1.0
O C:HOH470 4.1 16.0 1.0
C1' C:DA4 4.4 17.3 1.0
CB A:ALA48 4.7 18.6 1.0
O4' C:DA4 4.7 18.1 1.0
C5' C:DA4 4.8 19.3 1.0

Phosphorus binding site 5 out of 40 in 1a73

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Phosphorus binding site 5 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P6

b:21.0
occ:1.00
 P C:DT6 0.0 21.0 1.0
OP1 C:DT6 1.5 23.0 1.0
OP2 C:DT6 1.5 22.3 1.0
O5' C:DT6 1.6 20.7 1.0
O3' C:DC5 1.6 20.8 1.0
C3' C:DC5 2.6 18.8 1.0
C5' C:DT6 2.6 20.6 1.0
C2' C:DC5 3.4 17.6 1.0
C4' C:DC5 3.9 19.1 1.0
C4' C:DT6 3.9 19.8 1.0
O C:HOH388 4.1 23.8 1.0
O C:HOH612 4.1 33.1 1.0
O4' C:DT6 4.4 18.2 1.0
C5' C:DC5 4.4 18.5 1.0
C3' C:DT6 4.4 21.9 1.0
C6 C:DT6 4.5 17.5 1.0
C7 C:DT6 4.7 13.9 1.0
C1' C:DC5 4.8 16.5 1.0
O4' C:DC5 4.9 17.4 1.0

Phosphorus binding site 6 out of 40 in 1a73

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Phosphorus binding site 6 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P7

b:26.3
occ:1.00
 P C:DC7 0.0 26.3 1.0
OP2 C:DC7 1.5 26.2 1.0
OP1 C:DC7 1.5 28.6 1.0
O5' C:DC7 1.6 25.0 1.0
O3' C:DT6 1.6 24.8 1.0
C5' C:DC7 2.6 25.6 1.0
C3' C:DT6 2.6 21.9 1.0
C2' C:DT6 3.4 19.9 1.0
C4' C:DC7 3.9 25.8 1.0
C4' C:DT6 4.0 19.8 1.0
O C:HOH612 4.2 33.1 1.0
O4' C:DC7 4.3 26.1 1.0
C3' C:DC7 4.5 26.8 1.0
C5' C:DT6 4.6 20.6 1.0
O5' C:DT6 4.7 20.7 1.0
C6 C:DC7 4.8 18.5 1.0
C1' C:DT6 4.8 18.0 1.0
O4' C:DT6 5.0 18.2 1.0

Phosphorus binding site 7 out of 40 in 1a73

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Phosphorus binding site 7 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P8

b:29.3
occ:1.00
 P C:DT8 0.0 29.3 1.0
OP1 C:DT8 1.5 29.6 1.0
OP2 C:DT8 1.5 28.8 1.0
O5' C:DT8 1.6 27.3 1.0
O3' C:DC7 1.6 28.3 1.0
C5' C:DT8 2.6 24.2 1.0
C3' C:DC7 2.6 26.8 1.0
C2' C:DC7 3.4 25.5 1.0
C4' C:DT8 3.9 23.5 1.0
C4' C:DC7 3.9 25.8 1.0
O4' C:DT8 4.4 22.9 1.0
C3' C:DT8 4.4 22.1 1.0
C6 C:DT8 4.4 16.1 1.0
C5' C:DC7 4.6 25.6 1.0
C2' C:DT8 4.6 21.8 1.0
C1' C:DC7 4.8 24.3 1.0
O5' C:DC7 4.9 25.0 1.0
C7 C:DT8 4.9 15.3 1.0
O4' C:DC7 5.0 26.1 1.0

Phosphorus binding site 8 out of 40 in 1a73

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Phosphorus binding site 8 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P9

b:24.3
occ:1.00
 P C:DC9 0.0 24.3 1.0
OP2 C:DC9 1.5 24.0 1.0
OP1 C:DC9 1.5 24.0 1.0
O5' C:DC9 1.6 22.4 1.0
O3' C:DT8 1.6 23.1 1.0
C3' C:DT8 2.6 22.1 1.0
C5' C:DC9 2.6 21.2 1.0
C2' C:DT8 3.1 21.8 1.0
C4' C:DT8 3.9 23.5 1.0
C4' C:DC9 3.9 21.1 1.0
C1' C:DT8 4.1 21.1 1.0
C3' C:DC9 4.4 21.2 1.0
O4' C:DC9 4.5 22.0 1.0
O4' C:DT8 4.6 22.9 1.0
C2' C:DC9 4.8 19.4 1.0

Phosphorus binding site 9 out of 40 in 1a73

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Phosphorus binding site 9 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P10

b:23.5
occ:1.00
 P C:DT10 0.0 23.5 1.0
OP2 C:DT10 1.5 23.4 1.0
OP1 C:DT10 1.5 23.0 1.0
O5' C:DT10 1.6 22.2 1.0
O3' C:DC9 1.6 21.8 1.0
C5' C:DT10 2.6 18.9 1.0
C3' C:DC9 2.6 21.2 1.0
C2' C:DC9 3.2 19.4 1.0
O C:HOH595 3.6 25.8 1.0
C4' C:DT10 3.9 17.1 1.0
C4' C:DC9 3.9 21.1 1.0
C1' C:DC9 4.2 17.2 1.0
C3' C:DT10 4.2 16.5 1.0
O4' C:DT10 4.6 15.9 1.0
O4' C:DC9 4.7 22.0 1.0
C2' C:DT10 4.8 15.3 1.0

Phosphorus binding site 10 out of 40 in 1a73

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Phosphorus binding site 10 out of 40 in the Intron-Encoded Endonuclease I-Ppoi Complexed with Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Intron-Encoded Endonuclease I-Ppoi Complexed with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P11

b:18.8
occ:1.00
 P C:DT11 0.0 18.8 1.0
OP1 C:DT11 1.5 18.4 1.0
OP2 C:DT11 1.5 19.7 1.0
O5' C:DT11 1.6 19.9 1.0
O3' C:DT10 1.6 17.3 1.0
C5' C:DT11 2.6 21.4 1.0
C3' C:DT10 2.6 16.5 1.0
C2' C:DT10 3.4 15.3 1.0
C4' C:DT11 3.8 15.7 1.0
C4' C:DT10 3.9 17.1 1.0
O C:HOH684 4.1 33.2 1.0
C1' C:DT10 4.4 14.2 1.0
C3' C:DT11 4.5 16.3 1.0
O4' C:DT10 4.8 15.9 1.0
O4' C:DT11 4.9 14.8 1.0
C5' C:DT10 4.9 18.9 1.0

Reference:

K.E.Flick, M.S.Jurica, R.J.Monnat Jr., B.L.Stoddard. Dna Binding and Cleavage By the Nuclear Intron-Encoded Homing Endonuclease I-Ppoi. Nature V. 394 96 1998.
ISSN: ISSN 0028-0836
PubMed: 9665136
DOI: 10.1038/27952
Page generated: Fri Sep 25 12:21:59 2020

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