Phosphorus in PDB 1a74: I-Ppol Homing Endonuclease/Dna Complex

Protein crystallography data

The structure of I-Ppol Homing Endonuclease/Dna Complex, PDB code: 1a74 was solved by B.L.Jurica, K.E.Flick, R.J.Monnat Junior, M.S.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.400, 113.400, 88.200, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 26.5

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 I-Ppol Homing Endonuclease/Dna Complex (pdb code 1a74). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 40 binding sites of Phosphorus where determined in the I-Ppol Homing Endonuclease/Dna Complex, PDB code: 1a74:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 40 in 1a74

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Phosphorus binding site 1 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P402

b:24.9
occ:1.00
 P C:DT402 0.0 24.9 1.0
OP2 C:DT402 1.5 20.2 1.0
OP1 C:DT402 1.5 28.2 1.0
O5' C:DT402 1.6 24.5 1.0
O3' C:DT401 1.6 24.1 1.0
C5' C:DT402 2.6 28.4 1.0
C3' C:DT401 2.6 24.3 1.0
C2' C:DT401 3.3 23.0 1.0
O C:HOH208 3.5 23.4 1.0
O C:HOH90 3.8 20.1 1.0
O C:HOH107 3.9 28.6 1.0
C4' C:DT402 3.9 27.5 1.0
C4' C:DT401 3.9 23.6 1.0
C1' C:DT401 4.3 23.2 1.0
NH2 A:ARG66 4.3 13.4 1.0
C3' C:DT402 4.5 27.2 1.0
CZ A:ARG66 4.6 16.8 1.0
NH1 A:ARG66 4.6 17.6 1.0
O4' C:DT401 4.7 25.0 1.0
O4' C:DT402 5.0 27.9 1.0

Phosphorus binding site 2 out of 40 in 1a74

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Phosphorus binding site 2 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P403

b:26.1
occ:1.00
 P C:DG403 0.0 26.1 1.0
OP1 C:DG403 1.5 29.2 1.0
OP2 C:DG403 1.5 28.1 1.0
O5' C:DG403 1.6 26.4 1.0
O3' C:DT402 1.6 27.6 1.0
C3' C:DT402 2.6 27.2 1.0
C5' C:DG403 2.6 17.5 1.0
C2' C:DT402 3.2 25.4 1.0
O A:HOH645 3.7 28.2 1.0
N A:GLY53 3.9 17.1 1.0
C4' C:DG403 3.9 17.2 1.0
C4' C:DT402 3.9 27.5 1.0
C1' C:DT402 4.3 23.6 1.0
O4' C:DG403 4.4 19.9 1.0
C3' C:DG403 4.4 15.7 1.0
CA A:VAL52 4.5 17.2 1.0
C2' C:DG403 4.6 16.0 1.0
CA A:GLY53 4.6 14.9 1.0
O4' C:DT402 4.7 27.9 1.0
C8 C:DG403 4.7 14.5 1.0
CG1 A:VAL52 4.7 12.8 1.0
C A:VAL52 4.7 17.7 1.0
NH2 A:ARG66 4.8 13.4 1.0

Phosphorus binding site 3 out of 40 in 1a74

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Phosphorus binding site 3 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P404

b:18.8
occ:1.00
 P C:DA404 0.0 18.8 1.0
OP2 C:DA404 1.5 20.1 1.0
OP1 C:DA404 1.5 20.9 1.0
O5' C:DA404 1.6 23.1 1.0
O3' C:DG403 1.6 17.5 1.0
C5' C:DA404 2.6 22.4 1.0
C3' C:DG403 2.6 15.7 1.0
C2' C:DG403 3.3 16.0 1.0
O C:HOH29 3.7 11.4 1.0
CB A:ALA48 3.8 18.8 1.0
C4' C:DG403 3.9 17.2 1.0
C4' C:DA404 3.9 19.3 1.0
CA A:PRO49 4.0 21.3 1.0
CB A:PRO49 4.0 23.2 1.0
O C:HOH101 4.1 14.4 1.0
C1' C:DG403 4.2 15.7 1.0
C3' C:DA404 4.4 20.1 1.0
O4' C:DA404 4.5 19.7 1.0
N A:PRO49 4.6 21.9 1.0
O4' C:DG403 4.7 19.9 1.0
C2' C:DA404 4.7 19.6 1.0
CA A:ALA48 4.8 20.9 1.0
C A:ALA48 4.9 21.5 1.0

Phosphorus binding site 4 out of 40 in 1a74

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Phosphorus binding site 4 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P405

b:24.1
occ:1.00
 P C:DC405 0.0 24.1 1.0
OP2 C:DC405 1.5 20.9 1.0
OP1 C:DC405 1.5 26.1 1.0
O5' C:DC405 1.6 21.2 1.0
O3' C:DA404 1.6 22.2 1.0
C3' C:DA404 2.6 20.1 1.0
C5' C:DC405 2.7 21.6 1.0
C2' C:DA404 3.5 19.6 1.0
C4' C:DC405 3.7 20.1 1.0
C4' C:DA404 3.9 19.3 1.0
O C:HOH213 4.0 33.6 1.0
O4' C:DC405 4.0 18.1 1.0
O C:HOH118 4.1 27.4 1.0
C1' C:DA404 4.4 17.0 1.0
CB A:ALA48 4.7 18.8 1.0
O4' C:DA404 4.8 19.7 1.0
C5' C:DA404 4.8 22.4 1.0

Phosphorus binding site 5 out of 40 in 1a74

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Phosphorus binding site 5 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P406

b:23.6
occ:1.00
 P C:DT406 0.0 23.6 1.0
OP1 C:DT406 1.5 25.5 1.0
OP2 C:DT406 1.5 24.9 1.0
O5' C:DT406 1.6 23.0 1.0
O3' C:DC405 1.6 23.2 1.0
C3' C:DC405 2.6 20.2 1.0
C5' C:DT406 2.6 24.9 1.0
C2' C:DC405 3.4 17.3 1.0
C4' C:DC405 3.9 20.1 1.0
C4' C:DT406 3.9 22.2 1.0
C3' C:DT406 4.4 24.8 1.0
O4' C:DT406 4.4 22.9 1.0
C6 C:DT406 4.5 22.0 1.0
C5' C:DC405 4.5 21.6 1.0
C7 C:DT406 4.6 13.0 1.0
C1' C:DC405 4.8 18.7 1.0
O4' C:DC405 5.0 18.1 1.0

Phosphorus binding site 6 out of 40 in 1a74

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Phosphorus binding site 6 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P407

b:28.2
occ:1.00
 P C:DC407 0.0 28.2 1.0
OP2 C:DC407 1.5 25.6 1.0
OP1 C:DC407 1.5 31.4 1.0
O5' C:DC407 1.6 24.4 1.0
O3' C:DT406 1.6 27.4 1.0
C3' C:DT406 2.6 24.8 1.0
C5' C:DC407 2.6 25.4 1.0
C2' C:DT406 3.4 24.3 1.0
C4' C:DT406 3.9 22.2 1.0
C4' C:DC407 3.9 26.1 1.0
O4' C:DC407 4.4 28.3 1.0
C3' C:DC407 4.5 27.7 1.0
C5' C:DT406 4.5 24.9 1.0
O C:HOH168 4.6 50.6 1.0
O5' C:DT406 4.7 23.0 1.0
C6 C:DC407 4.7 21.1 1.0
C1' C:DT406 4.8 22.4 1.0
O4' C:DT406 5.0 22.9 1.0

Phosphorus binding site 7 out of 40 in 1a74

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Phosphorus binding site 7 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P408

b:30.6
occ:1.00
 P C:DT408 0.0 30.6 1.0
OP1 C:DT408 1.5 32.0 1.0
OP2 C:DT408 1.5 29.9 1.0
O5' C:DT408 1.6 26.0 1.0
O3' C:DC407 1.6 31.2 1.0
C3' C:DC407 2.6 27.7 1.0
C5' C:DT408 2.6 23.5 1.0
C2' C:DC407 3.3 26.8 1.0
C4' C:DC407 3.9 26.1 1.0
C4' C:DT408 3.9 23.2 1.0
O4' C:DT408 4.4 26.5 1.0
C3' C:DT408 4.5 24.4 1.0
C6 C:DT408 4.5 16.2 1.0
C5' C:DC407 4.6 25.4 1.0
C1' C:DC407 4.8 26.5 1.0
C2' C:DT408 4.8 22.1 1.0
O5' C:DC407 4.9 24.4 1.0
O4' C:DC407 5.0 28.3 1.0

Phosphorus binding site 8 out of 40 in 1a74

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Phosphorus binding site 8 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P409

b:30.2
occ:1.00
 P C:DC409 0.0 30.2 1.0
OP1 C:DC409 1.5 31.0 1.0
OP2 C:DC409 1.5 29.8 1.0
O5' C:DC409 1.6 30.8 1.0
O3' C:DT408 1.6 28.6 1.0
C5' C:DC409 2.6 27.0 1.0
C3' C:DT408 2.6 24.4 1.0
C2' C:DT408 3.1 22.1 1.0
C4' C:DC409 3.9 24.4 1.0
C4' C:DT408 3.9 23.2 1.0
C1' C:DT408 4.0 23.1 1.0
C3' C:DC409 4.3 23.7 1.0
O4' C:DT408 4.5 26.5 1.0
O4' C:DC409 4.6 23.0 1.0
C2' C:DC409 4.7 22.0 1.0

Phosphorus binding site 9 out of 40 in 1a74

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Phosphorus binding site 9 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P410

b:28.0
occ:1.00
 P C:DT410 0.0 28.0 1.0
OP1 C:DT410 1.5 28.7 1.0
OP2 C:DT410 1.5 27.5 1.0
O5' C:DT410 1.6 27.1 1.0
O3' C:DC409 1.6 25.6 1.0
C5' C:DT410 2.6 25.6 1.0
C3' C:DC409 2.6 23.7 1.0
C2' C:DC409 3.2 22.0 1.0
O C:HOH74 3.3 19.2 1.0
C4' C:DT410 3.9 23.8 1.0
C4' C:DC409 3.9 24.4 1.0
C1' C:DC409 4.1 18.4 1.0
C3' C:DT410 4.2 23.0 1.0
O4' C:DC409 4.6 23.0 1.0
O4' C:DT410 4.7 24.5 1.0
C2' C:DT410 4.7 20.8 1.0

Phosphorus binding site 10 out of 40 in 1a74

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Phosphorus binding site 10 out of 40 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P411

b:18.7
occ:1.00
 P C:DT411 0.0 18.7 1.0
OP1 C:DT411 1.5 22.4 1.0
OP2 C:DT411 1.5 23.3 1.0
O5' C:DT411 1.6 21.0 1.0
O3' C:DT410 1.6 21.8 1.0
C5' C:DT411 2.6 24.0 1.0
C3' C:DT410 2.6 23.0 1.0
C2' C:DT410 3.4 20.8 1.0
C4' C:DT411 3.8 18.3 1.0
C4' C:DT410 3.9 23.8 1.0
C1' C:DT410 4.4 20.1 1.0
C3' C:DT411 4.5 19.5 1.0
O4' C:DT410 4.8 24.5 1.0
O4' C:DT411 4.9 19.9 1.0
C5' C:DT410 5.0 25.6 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 12:22:14 2020

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