Phosphorus in PDB 1a1f: Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site)

Protein crystallography data

The structure of Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site), PDB code: 1a1f 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 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 43.000, 55.900, 128.400, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27

Phosphorus Binding Sites:

Pages:

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

Binding sites:

The binding sites of Phosphorus atom in the Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site) (pdb code 1a1f). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site), PDB code: 1a1f:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 1a1f

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Phosphorus binding site 1 out of 20 in the Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc 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 Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P2

b:38.4
occ:1.00
P B:DG2 0.0 38.4 1.0
OP2 B:DG2 1.5 38.1 1.0
OP1 B:DG2 1.5 39.1 1.0
O5' B:DG2 1.6 38.1 1.0
O3' B:DA1 1.6 37.7 1.0
C3' B:DA1 2.6 35.4 1.0
C5' B:DG2 2.6 36.8 1.0
C2' B:DA1 3.2 34.7 1.0
O B:HOH326 3.8 31.4 1.0
C4' B:DG2 3.9 34.8 1.0
C4' B:DA1 3.9 33.5 1.0
O B:HOH325 4.0 35.0 1.0
C1' B:DA1 4.0 31.0 1.0
C3' B:DG2 4.2 34.6 1.0
NH2 A:ARG170 4.3 44.0 1.0
O4' B:DA1 4.6 33.8 1.0
O4' B:DG2 4.6 34.9 1.0
C2' B:DG2 4.6 33.5 1.0
O A:HOH321 4.9 35.0 1.0

Phosphorus binding site 2 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:37.3
occ:1.00
P B:DC3 0.0 37.3 1.0
OP1 B:DC3 1.5 34.3 1.0
OP2 B:DC3 1.5 36.5 1.0
O5' B:DC3 1.6 34.4 1.0
O3' B:DG2 1.6 37.3 1.0
C3' B:DG2 2.6 34.6 1.0
C5' B:DC3 2.6 31.9 1.0
C2' B:DG2 3.2 33.5 1.0
CG2 A:THR156 3.7 32.0 1.0
C4' B:DC3 3.9 29.8 1.0
C4' B:DG2 3.9 34.8 1.0
O A:HOH320 4.0 38.8 1.0
C1' B:DG2 4.1 31.8 1.0
CB A:THR156 4.2 32.8 1.0
C3' B:DC3 4.3 29.8 1.0
O4' B:DC3 4.5 29.5 1.0
O4' B:DG2 4.6 34.9 1.0
C2' B:DC3 4.7 28.7 1.0
O B:HOH322 4.8 37.7 1.0
CA A:THR156 4.8 34.0 1.0

Phosphorus binding site 3 out of 20 in 1a1f

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Phosphorus binding site 3 out of 20 in the Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc 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 Dsnr (ZIF268 Variant) Zinc Finger-Dna Complex (Gacc Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P4

b:27.4
occ:1.00
P B:DG4 0.0 27.4 1.0
OP2 B:DG4 1.5 31.0 1.0
OP1 B:DG4 1.5 28.7 1.0
O5' B:DG4 1.6 30.0 1.0
O3' B:DC3 1.6 29.7 1.0
C3' B:DC3 2.6 29.8 1.0
C5' B:DG4 2.6 30.9 1.0
C2' B:DC3 3.5 28.7 1.0
O A:HOH317 3.7 24.2 1.0
C4' B:DG4 3.8 31.7 1.0
C4' B:DC3 3.8 29.8 1.0
O B:HOH318 3.9 32.6 1.0
C8 B:DG4 3.9 27.4 1.0
ND1 A:HIS153 4.0 28.8 1.0
O4' B:DG4 4.0 33.8 1.0
C1' B:DC3 4.3 29.0 1.0
C3' B:DG4 4.4 32.8 1.0
CB A:HIS153 4.4 27.9 1.0
C2' B:DG4 4.4 31.9 1.0
CA A:HIS153 4.6 29.9 1.0
C1' B:DG4 4.7 30.1 1.0
CG A:HIS153 4.7 27.0 1.0
O4' B:DC3 4.7 29.5 1.0
N9 B:DG4 4.7 27.7 1.0
CE2 A:PHE144 4.8 33.8 1.0
C5' B:DC3 4.9 31.9 1.0
CG2 A:THR156 4.9 32.0 1.0
N7 B:DG4 4.9 26.7 1.0

Phosphorus binding site 4 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:36.7
occ:1.00
P B:DT5 0.0 36.7 1.0
OP2 B:DT5 1.5 36.9 1.0
OP1 B:DT5 1.5 36.0 1.0
O5' B:DT5 1.6 38.3 1.0
O3' B:DG4 1.6 37.3 1.0
C3' B:DG4 2.6 32.8 1.0
C5' B:DT5 2.6 37.9 1.0
C2' B:DG4 3.3 31.9 1.0
C4' B:DT5 3.9 39.8 1.0
C4' B:DG4 3.9 31.7 1.0
O B:HOH315 4.0 20.1 1.0
C1' B:DG4 4.2 30.1 1.0
C3' B:DT5 4.3 40.7 1.0
NH1 A:ARG142 4.4 45.1 1.0
O4' B:DT5 4.6 39.4 1.0
O4' B:DG4 4.7 33.8 1.0
C2' B:DT5 4.8 39.7 1.0
C5' B:DG4 5.0 30.9 1.0

Phosphorus binding site 5 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:47.9
occ:1.00
P B:DG6 0.0 47.9 1.0
OP1 B:DG6 1.5 45.3 1.0
OP2 B:DG6 1.5 47.0 1.0
O5' B:DG6 1.6 45.5 1.0
O3' B:DT5 1.6 44.1 1.0
C3' B:DT5 2.6 40.7 1.0
C5' B:DG6 2.6 41.9 1.0
C2' B:DT5 3.3 39.7 1.0
C4' B:DG6 3.9 40.2 1.0
C4' B:DT5 3.9 39.8 1.0
C1' B:DT5 4.2 36.4 1.0
O4' B:DG6 4.3 37.6 1.0
CG1 A:ILE128 4.3 41.5 1.0
C8 B:DG6 4.3 25.1 1.0
C3' B:DG6 4.3 41.5 1.0
CD1 A:ILE128 4.4 41.4 1.0
O A:HOH352 4.4 30.6 1.0
C2' B:DG6 4.6 39.2 1.0
O4' B:DT5 4.7 39.4 1.0
C1' B:DG6 4.9 35.1 1.0
OG A:SER145 4.9 41.9 1.0
C5' B:DT5 4.9 37.9 1.0

Phosphorus binding site 6 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:46.7
occ:1.00
P B:DG7 0.0 46.7 1.0
OP1 B:DG7 1.5 47.7 1.0
OP2 B:DG7 1.5 45.1 1.0
O5' B:DG7 1.6 45.0 1.0
O3' B:DG6 1.6 45.5 1.0
C5' B:DG7 2.6 44.1 1.0
C3' B:DG6 2.6 41.5 1.0
C2' B:DG6 3.2 39.2 1.0
ND1 A:HIS125 3.7 32.5 1.0
NH1 A:ARG114 3.9 64.2 1.0
C4' B:DG7 3.9 42.1 1.0
C4' B:DG6 4.0 40.2 1.0
C1' B:DG6 4.2 35.1 1.0
CZ A:PHE116 4.2 41.9 1.0
O A:HOH374 4.2 29.7 1.0
CE2 A:PHE116 4.3 41.5 1.0
C3' B:DG7 4.3 42.3 1.0
CD1 A:ILE128 4.4 41.4 1.0
CZ A:ARG114 4.5 61.5 1.0
CE1 A:HIS125 4.5 30.1 1.0
O4' B:DG7 4.5 40.3 1.0
C2' B:DG7 4.6 39.9 1.0
O4' B:DG6 4.7 37.6 1.0
CD A:ARG114 4.7 58.4 1.0
CG A:HIS125 4.7 30.0 1.0
NE A:ARG114 4.8 60.8 1.0
CB A:HIS125 4.8 29.8 1.0
C8 B:DG7 5.0 31.3 1.0

Phosphorus binding site 7 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:48.3
occ:1.00
P B:DG8 0.0 48.3 1.0
OP1 B:DG8 1.5 48.9 1.0
OP2 B:DG8 1.5 47.5 1.0
O5' B:DG8 1.6 46.2 1.0
O3' B:DG7 1.6 46.8 1.0
C5' B:DG8 2.6 41.1 1.0
C3' B:DG7 2.6 42.3 1.0
O B:HOH375 3.2 34.2 1.0
O B:HOH335 3.2 37.1 1.0
C2' B:DG7 3.4 39.9 1.0
NH1 A:ARG103 3.8 64.4 1.0
C4' B:DG7 3.9 42.1 1.0
NH2 A:ARG103 3.9 66.0 1.0
C4' B:DG8 3.9 39.3 1.0
CZ A:ARG103 4.0 63.2 1.0
O B:HOH334 4.0 43.4 1.0
C1' B:DG7 4.3 37.2 1.0
C3' B:DG8 4.4 39.9 1.0
O4' B:DG7 4.7 40.3 1.0
NH2 A:ARG114 4.7 60.4 1.0
CD2 A:PHE116 4.8 41.2 1.0
NE A:ARG103 4.9 59.5 1.0
CE2 A:PHE116 4.9 41.5 1.0
C5' B:DG7 5.0 44.1 1.0
O4' B:DG8 5.0 37.5 1.0
O A:HOH386 5.0 33.0 1.0

Phosphorus binding site 8 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:40.8
occ:1.00
P B:DA9 0.0 40.8 1.0
OP2 B:DA9 1.5 43.1 1.0
OP1 B:DA9 1.5 41.3 1.0
O5' B:DA9 1.6 41.5 1.0
O3' B:DG8 1.6 41.9 1.0
C3' B:DG8 2.6 39.9 1.0
C5' B:DA9 2.6 36.3 1.0
C2' B:DG8 3.0 38.0 1.0
C1' B:DG8 3.9 34.9 1.0
C4' B:DA9 3.9 37.4 1.0
C4' B:DG8 3.9 39.3 1.0
C3' B:DA9 4.2 38.7 1.0
O4' B:DG8 4.3 37.5 1.0
O4' B:DA9 4.6 36.1 1.0
C2' B:DA9 4.6 36.6 1.0

Phosphorus binding site 9 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:45.3
occ:1.00
P B:DC10 0.0 45.3 1.0
OP2 B:DC10 1.5 50.4 1.0
OP1 B:DC10 1.5 48.1 1.0
O5' B:DC10 1.6 47.3 1.0
O3' B:DA9 1.6 43.3 1.0
C5' B:DC10 2.6 46.1 1.0
C3' B:DA9 2.6 38.7 1.0
C2' B:DA9 3.0 36.6 1.0
O B:HOH379 3.7 46.2 1.0
C1' B:DA9 3.9 32.5 1.0
C4' B:DA9 3.9 37.4 1.0
C4' B:DC10 3.9 43.2 1.0
O B:HOH383 4.3 40.7 1.0
C3' B:DC10 4.3 41.6 1.0
O4' B:DA9 4.5 36.1 1.0
O4' B:DC10 4.6 39.2 1.0
C2' B:DC10 4.7 40.0 1.0

Phosphorus binding site 10 out of 20 in 1a1f

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


Mono view


Stereo pair view

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

b:39.2
occ:1.00
P B:DC11 0.0 39.2 1.0
OP1 B:DC11 1.5 39.3 1.0
OP2 B:DC11 1.5 40.4 1.0
O5' B:DC11 1.6 40.3 1.0
O3' B:DC10 1.6 40.7 1.0
C3' B:DC10 2.6 41.6 1.0
C5' B:DC11 2.6 38.2 1.0
C2' B:DC10 3.4 40.0 1.0
O B:HOH381 3.5 44.5 1.0
C4' B:DC10 3.9 43.2 1.0
C4' B:DC11 3.9 37.7 1.0
O B:HOH380 4.2 51.6 1.0
C1' B:DC10 4.3 37.2 1.0
O4' B:DC11 4.4 36.6 1.0
C3' B:DC11 4.4 35.4 1.0
C2' B:DC11 4.7 33.8 1.0
O4' B:DC10 4.7 39.2 1.0
C5' B:DC10 4.9 46.1 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 11:57:41 2020

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