Phosphorus in PDB 1a0a: Phosphate System Positive Regulatory Protein PHO4/Dna Complex

Protein crystallography data

The structure of Phosphate System Positive Regulatory Protein PHO4/Dna Complex, PDB code: 1a0a was solved by T.Shimizu, A.Toumoto, K.Ihara, M.Shimizu, Y.Kyogoku, N.Ogawa, Y.Oshima, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.510, 68.300, 108.770, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 28.4

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Phosphorus atom in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex (pdb code 1a0a). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 32 binding sites of Phosphorus where determined in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex, PDB code: 1a0a:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 32 in 1a0a

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Phosphorus binding site 1 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P2

b:36.2
occ:1.00
P C:DT2 0.0 36.2 1.0
OP2 C:DT2 1.5 34.0 1.0
OP1 C:DT2 1.5 33.1 1.0
O5' C:DT2 1.6 40.7 1.0
O3' C:DC1 1.6 38.8 1.0
C3' C:DC1 2.6 38.7 1.0
C5' C:DT2 2.7 37.5 1.0
C2' C:DC1 3.2 37.3 1.0
C4' C:DT2 3.4 33.8 1.0
C2' C:DT2 3.5 36.4 1.0
C3' C:DT2 3.6 37.9 1.0
O4' C:DT2 3.7 21.9 1.0
C4' C:DC1 4.0 35.4 1.0
C6 C:DT2 4.1 42.5 1.0
C1' C:DT2 4.1 34.5 1.0
C1' C:DC1 4.3 32.1 1.0
N1 C:DT2 4.5 36.9 1.0
NZ A:LYS1 4.6 5.9 1.0
O4' C:DC1 4.6 39.1 1.0
O3' C:DT2 5.0 31.1 1.0

Phosphorus binding site 2 out of 32 in 1a0a

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Phosphorus binding site 2 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P3

b:29.5
occ:1.00
P C:DC3 0.0 29.5 1.0
OP1 C:DC3 1.5 24.6 1.0
OP2 C:DC3 1.5 29.0 1.0
O5' C:DC3 1.6 19.6 1.0
O3' C:DT2 1.6 31.1 1.0
C5' C:DC3 2.6 24.8 1.0
C3' C:DT2 2.7 37.9 1.0
C2' C:DT2 2.9 36.4 1.0
C1' C:DT2 3.6 34.5 1.0
C4' C:DC3 3.6 32.2 1.0
C3' C:DC3 3.7 36.8 1.0
C4' C:DT2 3.9 33.8 1.0
O4' C:DT2 4.4 21.9 1.0
C2' C:DC3 4.4 37.2 1.0
O C:HOH34 4.5 31.6 1.0
C6 C:DC3 4.7 31.3 1.0
O4' C:DC3 4.7 30.4 1.0
O3' C:DC3 4.8 35.0 1.0
N1 C:DT2 4.8 36.9 1.0

Phosphorus binding site 3 out of 32 in 1a0a

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Phosphorus binding site 3 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P4

b:34.7
occ:1.00
P C:DA4 0.0 34.7 1.0
OP1 C:DA4 1.5 22.3 1.0
OP2 C:DA4 1.5 30.0 1.0
O5' C:DA4 1.6 28.5 1.0
O3' C:DC3 1.6 35.0 1.0
C5' C:DA4 2.6 26.3 1.0
C3' C:DC3 2.7 36.8 1.0
C2' C:DC3 3.0 37.2 1.0
C4' C:DA4 3.5 29.2 1.0
C2' C:DA4 3.6 28.8 1.0
CD A:ARG12 3.6 33.9 1.0
C3' C:DA4 3.7 36.5 1.0
NE A:ARG12 3.7 29.4 1.0
O4' C:DA4 3.7 27.6 1.0
O B:ALA38 3.9 42.0 1.0
C4' C:DC3 4.0 32.2 1.0
C1' C:DC3 4.1 36.4 1.0
C1' C:DA4 4.2 28.1 1.0
C8 C:DA4 4.3 28.9 1.0
CG A:ARG12 4.3 38.2 1.0
CB B:ALA39 4.4 45.2 1.0
O4' C:DC3 4.6 30.4 1.0
N9 C:DA4 4.7 31.6 1.0
C B:ALA38 4.7 45.6 1.0
CB B:ALA38 4.8 46.0 1.0
CZ A:ARG12 5.0 31.5 1.0

Phosphorus binding site 4 out of 32 in 1a0a

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Phosphorus binding site 4 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P5

b:54.8
occ:1.00
P C:DC5 0.0 54.8 1.0
OP1 C:DC5 1.5 49.9 1.0
OP2 C:DC5 1.5 54.6 1.0
O5' C:DC5 1.6 54.2 1.0
O3' C:DA4 1.6 50.2 1.0
C5' C:DC5 2.6 52.1 1.0
C3' C:DA4 2.7 36.5 1.0
C2' C:DA4 2.9 28.8 1.0
OG B:SER41 3.5 31.5 1.0
C1' C:DA4 3.5 28.1 1.0
C3' C:DC5 3.5 42.8 1.0
C4' C:DC5 3.6 47.1 1.0
C2' C:DC5 3.7 46.1 1.0
CB B:SER41 3.9 39.9 1.0
C4' C:DA4 3.9 29.2 1.0
NH2 A:ARG12 4.3 28.7 1.0
O4' C:DA4 4.3 27.6 1.0
O4' C:DC5 4.4 48.2 1.0
C6 C:DC5 4.6 48.1 1.0
C1' C:DC5 4.6 47.2 1.0
N9 C:DA4 4.7 31.6 1.0
O3' C:DC5 4.9 32.3 1.0

Phosphorus binding site 5 out of 32 in 1a0a

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Phosphorus binding site 5 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P6

b:30.6
occ:1.00
P C:DA6 0.0 30.6 1.0
OP1 C:DA6 1.5 27.8 1.0
OP2 C:DA6 1.5 23.5 1.0
O5' C:DA6 1.6 17.4 1.0
O3' C:DC5 1.6 32.3 1.0
C3' C:DC5 2.6 42.8 1.0
C5' C:DA6 2.6 14.7 1.0
C2' C:DC5 3.4 46.1 1.0
C4' C:DA6 3.7 13.7 1.0
O4' C:DA6 3.7 2.0 1.0
C8 C:DA6 3.8 25.6 1.0
C4' C:DC5 3.9 47.1 1.0
O C:HOH32 4.1 51.1 1.0
C1' C:DC5 4.3 47.2 1.0
N9 C:DA6 4.5 21.5 1.0
C3' C:DA6 4.5 7.1 1.0
C2' C:DA6 4.5 3.2 1.0
C1' C:DA6 4.5 10.4 1.0
OP1 C:DC5 4.5 49.9 1.0
O4' C:DC5 4.6 48.2 1.0
N7 C:DA6 4.7 32.8 1.0
NZ B:LYS42 5.0 26.6 1.0
C5' C:DC5 5.0 52.1 1.0

Phosphorus binding site 6 out of 32 in 1a0a

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Phosphorus binding site 6 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P7

b:27.2
occ:1.00
P C:DC7 0.0 27.2 1.0
OP2 C:DC7 1.5 32.2 1.0
OP1 C:DC7 1.5 18.6 1.0
O5' C:DC7 1.6 20.0 1.0
O3' C:DA6 1.6 18.1 1.0
C5' C:DC7 2.6 27.8 1.0
C3' C:DA6 2.6 7.1 1.0
C2' C:DA6 3.1 3.2 1.0
C4' C:DC7 3.9 23.9 1.0
C6 C:DC7 3.9 39.4 1.0
C4' C:DA6 4.0 13.7 1.0
C1' C:DA6 4.1 10.4 1.0
O4' C:DC7 4.3 24.5 1.0
C3' C:DC7 4.4 22.2 1.0
C5 C:DC7 4.5 45.3 1.0
C2' C:DC7 4.6 24.4 1.0
O4' C:DA6 4.6 2.0 1.0
CG B:GLN10 4.7 22.7 1.0
N1 C:DC7 4.9 34.7 1.0
C1' C:DC7 4.9 28.6 1.0

Phosphorus binding site 7 out of 32 in 1a0a

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Phosphorus binding site 7 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P8

b:27.9
occ:1.00
P C:DG8 0.0 27.9 1.0
OP2 C:DG8 1.5 22.4 1.0
OP1 C:DG8 1.5 24.5 1.0
O5' C:DG8 1.6 19.9 1.0
O3' C:DC7 1.6 26.1 1.0
C3' C:DC7 2.6 22.2 1.0
C5' C:DG8 2.7 20.6 1.0
C2' C:DC7 3.0 24.4 1.0
O C:HOH35 3.2 2.1 1.0
C8 C:DG8 3.6 30.7 1.0
CE B:LYS6 3.7 2.0 1.0
C4' C:DG8 3.7 12.3 1.0
C2' C:DG8 3.7 9.4 1.0
C3' C:DG8 3.8 11.6 1.0
C4' C:DC7 3.9 23.9 1.0
C1' C:DC7 3.9 28.6 1.0
NZ B:LYS6 4.3 2.0 1.0
O4' C:DG8 4.4 10.5 1.0
N9 C:DG8 4.4 26.9 1.0
C1' C:DG8 4.4 20.9 1.0
O4' C:DC7 4.5 24.5 1.0
N7 C:DG8 4.5 31.9 1.0
CB B:LYS6 4.9 18.8 1.0
CD B:LYS6 5.0 12.9 1.0

Phosphorus binding site 8 out of 32 in 1a0a

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Phosphorus binding site 8 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P9

b:2.4
occ:1.00
P C:DT9 0.0 2.4 1.0
OP2 C:DT9 1.5 6.9 1.0
OP1 C:DT9 1.5 2.1 1.0
O5' C:DT9 1.6 12.7 1.0
O3' C:DG8 1.6 14.8 1.0
C5' C:DT9 2.6 4.9 1.0
C3' C:DG8 2.7 11.6 1.0
C2' C:DG8 2.9 9.4 1.0
C3' C:DT9 3.1 23.2 1.0
C2' C:DT9 3.2 19.8 1.0
C1' C:DG8 3.2 20.9 1.0
C4' C:DT9 3.5 21.1 1.0
C4' C:DG8 3.6 12.3 1.0
O4' C:DG8 3.7 10.5 1.0
C6 C:DT9 3.8 33.6 1.0
NZ B:LYS6 3.9 2.0 1.0
O4' C:DT9 4.1 18.8 1.0
C1' C:DT9 4.1 26.1 1.0
O3' C:DT9 4.4 22.4 1.0
CE B:LYS6 4.4 2.0 1.0
N1 C:DT9 4.5 34.3 1.0
N9 C:DG8 4.6 26.9 1.0
CD B:LYS6 4.6 12.9 1.0
C5 C:DT9 4.7 34.0 1.0
OP1 C:DG10 4.7 25.0 1.0
C7 C:DT9 4.7 28.8 1.0
OP2 C:DG10 4.8 22.2 1.0
P C:DG10 4.9 27.3 1.0

Phosphorus binding site 9 out of 32 in 1a0a

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Phosphorus binding site 9 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P10

b:27.3
occ:1.00
P C:DG10 0.0 27.3 1.0
OP1 C:DG10 1.5 25.0 1.0
OP2 C:DG10 1.5 22.2 1.0
O5' C:DG10 1.6 29.2 1.0
O3' C:DT9 1.6 22.4 1.0
C3' C:DT9 2.6 23.2 1.0
C5' C:DG10 2.6 36.0 1.0
C2' C:DT9 3.2 19.8 1.0
C4' C:DG10 3.5 40.3 1.0
O4' C:DG10 3.5 28.5 1.0
OP1 C:DT9 3.9 2.1 1.0
C4' C:DT9 3.9 21.1 1.0
C3' C:DG10 4.2 40.9 1.0
C8 C:DG10 4.2 40.2 1.0
C2' C:DG10 4.3 35.2 1.0
C1' C:DT9 4.3 26.1 1.0
C1' C:DG10 4.4 37.1 1.0
N9 C:DG10 4.7 37.3 1.0
O4' C:DT9 4.7 18.8 1.0
C5' C:DT9 4.9 4.9 1.0
P C:DT9 4.9 2.4 1.0

Phosphorus binding site 10 out of 32 in 1a0a

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Phosphorus binding site 10 out of 32 in the Phosphate System Positive Regulatory Protein PHO4/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Phosphate System Positive Regulatory Protein PHO4/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P11

b:45.8
occ:1.00
P C:DG11 0.0 45.8 1.0
OP2 C:DG11 1.5 44.6 1.0
OP1 C:DG11 1.5 35.7 1.0
O5' C:DG11 1.6 51.1 1.0
O3' C:DG10 1.6 42.7 1.0
C5' C:DG11 2.6 52.6 1.0
C3' C:DG10 2.7 40.9 1.0
C2' C:DG10 3.1 35.2 1.0
C4' C:DG11 3.8 55.5 1.0
C3' C:DG11 3.8 56.0 1.0
C1' C:DG10 3.9 37.1 1.0
C4' C:DG10 4.0 40.3 1.0
C2' C:DG11 4.4 59.8 1.0
OP2 C:DG12 4.5 43.1 1.0
O4' C:DG10 4.6 28.5 1.0
O4' C:DG11 4.8 57.6 1.0

Reference:

T.Shimizu, A.Toumoto, K.Ihara, M.Shimizu, Y.Kyogoku, N.Ogawa, Y.Oshima, T.Hakoshima. Crystal Structure of PHO4 Bhlh Domain-Dna Complex: Flanking Base Recognition. Embo J. V. 16 4689 1997.
ISSN: ISSN 0261-4189
PubMed: 9303313
DOI: 10.1093/EMBOJ/16.15.4689
Page generated: Fri Sep 25 11:56:02 2020

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