Phosphorus in PDB 1a1j: Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)

Protein crystallography data

The structure of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site), PDB code: 1a1j was solved by M.Elrod-Erickson, T.E.Benson, C.O.Pabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 42.300, 55.900, 133.600, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.2

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Phosphorus atom in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) (pdb code 1a1j). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site), PDB code: 1a1j:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1a1j

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Phosphorus binding site 1 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P2

b:32.1
occ:1.00
P B:DG2 0.0 32.1 1.0
OP1 B:DG2 1.5 32.6 1.0
OP2 B:DG2 1.5 32.0 1.0
O5' B:DG2 1.6 30.1 1.0
O3' B:DA1 1.6 31.6 1.0
C5' B:DG2 2.6 30.1 1.0
C3' B:DA1 2.6 30.7 1.0
C2' B:DA1 3.3 29.3 1.0
O B:HOH361 3.7 47.6 1.0
C4' B:DG2 3.9 30.8 1.0
C4' B:DA1 3.9 30.2 1.0
O B:HOH360 4.1 51.0 1.0
C1' B:DA1 4.2 27.9 1.0
C3' B:DG2 4.3 31.9 1.0
O A:HOH398 4.4 31.5 1.0
O A:HOH399 4.5 32.4 1.0
O4' B:DG2 4.5 29.6 1.0
O4' B:DA1 4.6 29.8 1.0
C2' B:DG2 4.7 30.9 1.0
O A:HOH362 4.8 29.7 1.0
NH2 A:ARG170 4.9 28.4 1.0
O B:HOH363 4.9 33.6 1.0

Phosphorus binding site 2 out of 20 in 1a1j

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Phosphorus binding site 2 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P3

b:35.4
occ:1.00
P B:DC3 0.0 35.4 1.0
OP1 B:DC3 1.5 34.0 1.0
OP2 B:DC3 1.5 35.4 1.0
O5' B:DC3 1.6 32.2 1.0
O3' B:DG2 1.6 33.0 1.0
C5' B:DC3 2.6 30.0 1.0
C3' B:DG2 2.6 31.9 1.0
C2' B:DG2 3.1 30.9 1.0
CG2 A:THR156 3.7 25.8 1.0
CB A:THR156 3.9 26.5 1.0
C4' B:DC3 3.9 28.7 1.0
C4' B:DG2 3.9 30.8 1.0
C1' B:DG2 4.0 29.8 1.0
O B:HOH356 4.1 51.6 1.0
C3' B:DC3 4.4 28.1 1.0
O4' B:DG2 4.6 29.6 1.0
O4' B:DC3 4.6 27.6 1.0
O A:HOH355 4.7 33.5 1.0
CA A:THR156 4.7 27.1 1.0
C2' B:DC3 4.9 27.7 1.0

Phosphorus binding site 3 out of 20 in 1a1j

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Phosphorus binding site 3 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P4

b:30.6
occ:1.00
P B:DG4 0.0 30.6 1.0
OP1 B:DG4 1.5 32.4 1.0
OP2 B:DG4 1.5 29.9 1.0
O5' B:DG4 1.6 30.2 1.0
O3' B:DC3 1.6 29.6 1.0
C3' B:DC3 2.6 28.1 1.0
C5' B:DG4 2.6 28.6 1.0
C2' B:DC3 3.6 27.7 1.0
ND1 A:HIS153 3.6 25.9 1.0
C4' B:DC3 3.8 28.7 1.0
O A:HOH352 3.8 22.9 1.0
C4' B:DG4 3.8 28.1 1.0
O A:HOH353 4.1 24.8 1.0
O4' B:DG4 4.1 28.1 1.0
C8 B:DG4 4.2 25.0 1.0
CB A:HIS153 4.3 25.4 1.0
C1' B:DC3 4.3 26.9 1.0
C3' B:DG4 4.3 27.7 1.0
CG A:HIS153 4.4 26.0 1.0
C2' B:DG4 4.5 26.8 1.0
CA A:HIS153 4.5 25.6 1.0
CE1 A:HIS153 4.6 26.1 1.0
O4' B:DC3 4.7 27.6 1.0
C5' B:DC3 4.8 30.0 1.0
C1' B:DG4 4.8 25.8 1.0
CG2 A:THR156 4.9 25.8 1.0
CE1 A:PHE144 4.9 27.0 1.0
N9 B:DG4 4.9 25.8 1.0
O A:HOH402 5.0 33.1 1.0

Phosphorus binding site 4 out of 20 in 1a1j

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Phosphorus binding site 4 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


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Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P5

b:26.7
occ:1.00
P B:DT5 0.0 26.7 1.0
OP1 B:DT5 1.5 27.4 1.0
OP2 B:DT5 1.5 26.4 1.0
O5' B:DT5 1.6 27.9 1.0
O3' B:DG4 1.6 27.5 1.0
C3' B:DG4 2.6 27.7 1.0
C5' B:DT5 2.6 27.7 1.0
C2' B:DG4 3.3 26.8 1.0
O B:HOH349 3.6 26.7 1.0
O A:HOH403 3.7 25.1 1.0
O A:HOH324 3.7 46.3 1.0
NH2 A:ARG142 3.7 26.9 1.0
O B:HOH347 3.7 25.4 1.0
O B:HOH351 3.8 25.6 1.0
O B:HOH404 3.9 33.2 1.0
C4' B:DG4 3.9 28.1 1.0
C4' B:DT5 3.9 27.3 1.0
C1' B:DG4 4.3 25.8 1.0
C3' B:DT5 4.3 28.5 1.0
O B:HOH348 4.5 27.6 1.0
O4' B:DT5 4.5 26.3 1.0
O A:HOH325 4.5 36.2 1.0
O4' B:DG4 4.7 28.1 1.0
CZ A:ARG142 4.7 26.1 1.0
C2' B:DT5 4.8 26.5 1.0
CD1 A:PHE144 4.9 27.4 1.0
NZ A:LYS133 4.9 37.4 1.0
C5' B:DG4 4.9 28.6 1.0

Phosphorus binding site 5 out of 20 in 1a1j

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Phosphorus binding site 5 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P6

b:32.4
occ:1.00
P B:DG6 0.0 32.4 1.0
OP1 B:DG6 1.5 33.2 1.0
OP2 B:DG6 1.5 32.6 1.0
O5' B:DG6 1.6 32.7 1.0
O3' B:DT5 1.6 31.9 1.0
C5' B:DG6 2.6 33.5 1.0
C3' B:DT5 2.6 28.5 1.0
C2' B:DT5 3.4 26.5 1.0
O B:HOH411 3.4 27.9 1.0
OG A:SER145 3.6 27.5 1.0
O B:HOH348 3.8 27.6 1.0
C4' B:DG6 3.8 33.5 1.0
C4' B:DT5 3.9 27.3 1.0
O B:HOH345 4.0 50.6 1.0
O4' B:DG6 4.0 32.3 1.0
C8 B:DG6 4.1 28.1 1.0
O A:HOH409 4.1 34.0 1.0
C1' B:DT5 4.3 26.0 1.0
C3' B:DG6 4.4 34.5 1.0
O A:HOH410 4.5 26.1 1.0
C2' B:DG6 4.5 33.3 1.0
CG1 A:ILE128 4.5 35.3 1.0
CB A:SER145 4.6 28.7 1.0
C1' B:DG6 4.7 31.4 1.0
O4' B:DT5 4.7 26.3 1.0
N9 B:DG6 4.8 29.5 1.0
C5' B:DT5 4.9 27.7 1.0
CD1 A:ILE128 4.9 34.4 1.0

Phosphorus binding site 6 out of 20 in 1a1j

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Phosphorus binding site 6 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P7

b:37.1
occ:1.00
P B:DG7 0.0 37.1 1.0
OP1 B:DG7 1.5 36.5 1.0
OP2 B:DG7 1.5 36.5 1.0
O5' B:DG7 1.6 35.2 1.0
O3' B:DG6 1.6 36.7 1.0
C5' B:DG7 2.6 32.8 1.0
C3' B:DG6 2.6 34.5 1.0
C2' B:DG6 3.3 33.3 1.0
ND1 A:HIS125 3.6 35.0 1.0
C4' B:DG7 3.9 32.8 1.0
C4' B:DG6 3.9 33.5 1.0
CD1 A:ILE128 4.0 34.4 1.0
C1' B:DG6 4.3 31.4 1.0
CZ A:PHE116 4.3 36.6 1.0
CE1 A:HIS125 4.3 34.6 1.0
C3' B:DG7 4.4 33.2 1.0
O4' B:DG7 4.4 32.2 1.0
CG A:HIS125 4.6 34.2 1.0
C2' B:DG7 4.7 32.0 1.0
O4' B:DG6 4.7 32.3 1.0
O A:HOH442 4.8 28.2 1.0
CB A:HIS125 4.9 33.6 1.0
C8 B:DG7 4.9 31.7 1.0
CD A:ARG114 4.9 47.3 1.0
C5' B:DG6 5.0 33.5 1.0
CE2 A:PHE116 5.0 36.5 1.0

Phosphorus binding site 7 out of 20 in 1a1j

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Phosphorus binding site 7 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:32.3
occ:1.00
P B:DG8 0.0 32.3 1.0
OP2 B:DG8 1.5 33.7 1.0
OP1 B:DG8 1.5 33.4 1.0
O5' B:DG8 1.6 32.0 1.0
O3' B:DG7 1.6 33.5 1.0
C5' B:DG8 2.6 30.4 1.0
C3' B:DG7 2.6 33.2 1.0
C2' B:DG7 3.2 32.0 1.0
O A:HOH337 3.6 40.4 1.0
O A:HOH443 3.7 34.9 1.0
O A:HOH444 3.8 27.2 1.0
C4' B:DG8 3.9 30.4 1.0
C4' B:DG7 3.9 32.8 1.0
NH1 A:ARG103 4.0 51.9 1.0
C1' B:DG7 4.1 32.0 1.0
NH2 A:ARG103 4.3 51.6 1.0
C3' B:DG8 4.3 31.3 1.0
O4' B:DG8 4.5 30.0 1.0
CZ A:ARG103 4.6 51.5 1.0
O4' B:DG7 4.6 32.2 1.0
NH1 A:ARG114 4.7 50.9 1.0
CE2 A:PHE116 4.7 36.5 1.0
C2' B:DG8 4.7 29.7 1.0
CD2 A:PHE116 4.9 36.8 1.0

Phosphorus binding site 8 out of 20 in 1a1j

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Phosphorus binding site 8 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:35.6
occ:1.00
P B:DC9 0.0 35.6 1.0
OP2 B:DC9 1.5 37.0 1.0
OP1 B:DC9 1.5 35.0 1.0
O5' B:DC9 1.6 35.9 1.0
O3' B:DG8 1.6 32.7 1.0
C3' B:DG8 2.6 31.3 1.0
C5' B:DC9 2.6 34.7 1.0
C2' B:DG8 3.2 29.7 1.0
NH2 A:ARG118 3.6 21.9 0.5
O B:HOH446 3.7 39.8 1.0
C4' B:DC9 3.9 34.1 1.0
C4' B:DG8 3.9 30.4 1.0
NH1 A:ARG118 4.1 22.6 0.5
C1' B:DG8 4.1 29.0 1.0
CZ A:ARG118 4.3 22.7 0.5
C3' B:DC9 4.4 33.7 1.0
O4' B:DC9 4.5 32.4 1.0
O4' B:DG8 4.6 30.0 1.0
C2' B:DC9 4.8 32.9 1.0

Phosphorus binding site 9 out of 20 in 1a1j

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Phosphorus binding site 9 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:34.0
occ:1.00
P B:DG10 0.0 34.0 1.0
OP1 B:DG10 1.5 34.9 1.0
OP2 B:DG10 1.5 36.0 1.0
O5' B:DG10 1.6 34.3 1.0
O3' B:DC9 1.6 34.2 1.0
C3' B:DC9 2.6 33.7 1.0
C5' B:DG10 2.6 31.3 1.0
C4' B:DC9 3.6 34.1 1.0
C2' B:DC9 3.7 32.9 1.0
C4' B:DG10 3.8 30.8 1.0
O4' B:DG10 4.0 29.9 1.0
C8 B:DG10 4.2 28.2 1.0
C1' B:DC9 4.4 31.7 1.0
C3' B:DG10 4.4 30.3 1.0
C2' B:DG10 4.5 29.3 1.0
C5' B:DC9 4.6 34.7 1.0
O4' B:DC9 4.6 32.4 1.0
C1' B:DG10 4.7 29.0 1.0
N9 B:DG10 4.9 28.8 1.0

Phosphorus binding site 10 out of 20 in 1a1j

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Phosphorus binding site 10 out of 20 in the Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site)


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Radr (ZIF268 Variant) Zinc Finger-Dna Complex (Gcgt Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:30.1
occ:1.00
P B:DT11 0.0 30.1 1.0
OP1 B:DT11 1.5 29.8 1.0
OP2 B:DT11 1.5 29.6 1.0
O5' B:DT11 1.6 30.2 1.0
O3' B:DG10 1.6 30.5 1.0
C5' B:DT11 2.6 29.5 1.0
C3' B:DG10 2.6 30.3 1.0
C2' B:DG10 3.3 29.3 1.0
O B:HOH422 3.5 24.3 1.0
C4' B:DT11 3.9 30.1 1.0
C4' B:DG10 3.9 30.8 1.0
C1' B:DG10 4.2 29.0 1.0
C3' B:DT11 4.4 30.4 1.0
O4' B:DT11 4.5 30.0 1.0
C2' B:DT11 4.6 30.6 1.0
O4' B:DG10 4.7 29.9 1.0
O B:HOH427 5.0 43.2 1.0

Reference:

M.Elrod-Erickson, T.E.Benson, C.O.Pabo. High-Resolution Structures of Variant ZIF268-Dna Complexes: Implications For Understanding Zinc Finger-Dna Recognition. Structure V. 6 451 1998.
ISSN: ISSN 0969-2126
PubMed: 9562555
DOI: 10.1016/S0969-2126(98)00047-1
Page generated: Fri Sep 25 11:59:29 2020

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