Phosphorus in PDB 1aay: ZIF268 Zinc Finger-Dna Complex

Protein crystallography data

The structure of ZIF268 Zinc Finger-Dna Complex, PDB code: 1aay was solved by M.Elrod-Erickson, M.A.Rould, C.O.Pabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 45.400, 56.200, 130.800, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.2

Phosphorus Binding Sites:

Pages:

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

Binding sites:

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

Phosphorus binding site 1 out of 20 in 1aay

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Phosphorus binding site 1 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:31.8
occ:1.00
 P B:DG2 0.0 31.8 1.0
OP1 B:DG2 1.5 32.4 1.0
OP2 B:DG2 1.5 31.8 1.0
O5' B:DG2 1.6 29.1 1.0
O3' B:DA1 1.6 29.5 1.0
C3' B:DA1 2.6 27.3 1.0
C5' B:DG2 2.6 25.4 1.0
C2' B:DA1 3.4 25.1 1.0
NH2 A:ARG170 3.5 46.8 1.0
O A:HOH279 3.7 29.8 1.0
C4' B:DA1 3.9 26.9 1.0
C4' B:DG2 3.9 24.7 1.0
O A:HOH265 4.1 52.2 1.0
C3' B:DG2 4.4 24.6 1.0
O4' B:DG2 4.4 23.3 1.0
C1' B:DA1 4.4 24.4 1.0
CZ A:ARG170 4.8 45.8 1.0
O4' B:DA1 4.8 26.4 1.0
C5' B:DA1 4.9 25.9 1.0
C2' B:DG2 4.9 22.8 1.0

Phosphorus binding site 2 out of 20 in 1aay

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Phosphorus binding site 2 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:25.0
occ:1.00
 P B:DC3 0.0 25.0 1.0
OP2 B:DC3 1.5 22.5 1.0
OP1 B:DC3 1.5 26.0 1.0
O5' B:DC3 1.6 22.7 1.0
O3' B:DG2 1.6 24.0 1.0
C5' B:DC3 2.6 21.2 1.0
C3' B:DG2 2.7 24.6 1.0
C2' B:DG2 3.3 22.8 1.0
O B:HOH264 3.8 60.2 1.0
CG2 A:THR156 3.8 23.7 1.0
O B:HOH214 3.8 20.6 1.0
C4' B:DG2 3.9 24.7 1.0
C4' B:DC3 4.0 19.9 1.0
CB A:THR156 4.2 23.1 1.0
C1' B:DG2 4.3 21.9 1.0
O4' B:DC3 4.4 20.1 1.0
C3' B:DC3 4.4 19.7 1.0
CA A:THR156 4.7 23.1 1.0
C2' B:DC3 4.7 18.9 1.0
O4' B:DG2 4.7 23.3 1.0
C5' B:DG2 4.9 25.4 1.0

Phosphorus binding site 3 out of 20 in 1aay

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Phosphorus binding site 3 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:19.1
occ:1.00
 P B:DG4 0.0 19.1 1.0
OP1 B:DG4 1.5 19.6 1.0
OP2 B:DG4 1.5 18.9 1.0
O5' B:DG4 1.6 20.5 1.0
O3' B:DC3 1.6 20.1 1.0
C3' B:DC3 2.6 19.7 1.0
C5' B:DG4 2.6 20.0 1.0
C2' B:DC3 3.6 18.9 1.0
O B:HOH262 3.7 45.3 1.0
C4' B:DC3 3.8 19.9 1.0
ND1 A:HIS153 3.8 17.1 1.0
O A:HOH210 3.9 20.8 1.0
C4' B:DG4 3.9 21.3 1.0
O B:HOH211 4.0 19.3 1.0
C8 B:DG4 4.1 18.5 1.0
O4' B:DG4 4.2 21.4 1.0
CB A:HIS153 4.3 17.5 1.0
C1' B:DC3 4.3 18.8 1.0
C3' B:DG4 4.4 21.9 1.0
C2' B:DG4 4.4 20.2 1.0
CA A:HIS153 4.5 19.1 1.0
CG A:HIS153 4.5 18.1 1.0
C5' B:DC3 4.7 21.2 1.0
O4' B:DC3 4.7 20.1 1.0
CG2 A:THR156 4.7 23.7 1.0
C1' B:DG4 4.8 19.3 1.0
N9 B:DG4 4.9 19.9 1.0
CE1 A:HIS153 4.9 18.1 1.0
CE2 A:PHE144 5.0 29.0 1.0

Phosphorus binding site 4 out of 20 in 1aay

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Phosphorus binding site 4 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:23.7
occ:1.00
 P B:DT5 0.0 23.7 1.0
OP2 B:DT5 1.5 23.3 1.0
OP1 B:DT5 1.5 24.5 1.0
O5' B:DT5 1.6 23.6 1.0
O3' B:DG4 1.6 23.7 1.0
C3' B:DG4 2.6 21.9 1.0
C5' B:DT5 2.7 23.4 1.0
C2' B:DG4 3.3 20.2 1.0
O B:HOH254 3.4 31.6 1.0
O B:HOH208 3.7 28.2 1.0
O B:HOH330 3.7 48.5 1.0
NH2 A:ARG142 3.8 36.5 1.0
C4' B:DG4 3.9 21.3 1.0
C4' B:DT5 3.9 25.4 1.0
O B:HOH209 3.9 27.5 1.0
C1' B:DG4 4.2 19.3 1.0
O4' B:DT5 4.3 25.2 1.0
C3' B:DT5 4.3 27.8 1.0
O4' B:DG4 4.6 21.4 1.0
CZ A:ARG142 4.7 36.3 1.0
C2' B:DT5 4.8 26.3 1.0
O B:HOH329 4.8 36.3 1.0
NZ A:LYS133 4.9 44.3 1.0
C5' B:DG4 4.9 20.0 1.0
NE A:ARG142 5.0 36.2 1.0

Phosphorus binding site 5 out of 20 in 1aay

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Phosphorus binding site 5 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:36.2
occ:1.00
 P B:DG6 0.0 36.2 1.0
OP1 B:DG6 1.5 35.8 1.0
OP2 B:DG6 1.5 35.6 1.0
O5' B:DG6 1.6 32.8 1.0
O3' B:DT5 1.6 33.2 1.0
C3' B:DT5 2.7 27.8 1.0
C5' B:DG6 2.7 28.1 1.0
C2' B:DT5 3.6 26.3 1.0
O B:HOH329 3.7 36.3 1.0
O A:HOH242 3.7 48.6 1.0
C4' B:DT5 3.8 25.4 1.0
C4' B:DG6 3.9 27.1 1.0
CG2 A:ILE128 4.0 35.4 1.0
OG A:SER145 4.0 31.1 1.0
O4' B:DG6 4.1 25.1 1.0
C8 B:DG6 4.3 23.7 1.0
C3' B:DG6 4.4 28.1 1.0
C1' B:DT5 4.5 24.1 1.0
C2' B:DG6 4.6 26.3 1.0
O A:HOH239 4.6 33.2 1.0
C5' B:DT5 4.7 23.4 1.0
O A:HOH223 4.8 42.8 1.0
C1' B:DG6 4.8 25.1 1.0
O4' B:DT5 4.9 25.2 1.0
CB A:SER145 4.9 29.5 1.0
N9 B:DG6 5.0 23.5 1.0

Phosphorus binding site 6 out of 20 in 1aay

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Phosphorus binding site 6 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:31.6
occ:1.00
 P B:DG7 0.0 31.6 1.0
OP2 B:DG7 1.5 32.5 1.0
OP1 B:DG7 1.5 34.6 1.0
O5' B:DG7 1.6 31.4 1.0
O3' B:DG6 1.6 30.8 1.0
C5' B:DG7 2.5 30.1 1.0
C3' B:DG6 2.7 28.1 1.0
C2' B:DG6 3.3 26.3 1.0
O B:HOH357 3.4 38.3 1.0
ND1 A:HIS125 3.5 22.8 1.0
C4' B:DG7 3.9 28.0 1.0
C4' B:DG6 4.0 27.1 1.0
NE A:ARG114 4.2 54.1 1.0
C1' B:DG6 4.3 25.1 1.0
CE1 A:HIS125 4.4 22.6 1.0
C3' B:DG7 4.4 28.5 1.0
CZ A:PHE116 4.4 32.2 1.0
O4' B:DG7 4.5 27.1 1.0
CG A:HIS125 4.5 22.4 1.0
NH2 A:ARG114 4.6 57.1 1.0
CE1 A:PHE116 4.6 33.1 1.0
CB A:HIS125 4.7 22.5 1.0
C2' B:DG7 4.7 27.2 1.0
O4' B:DG6 4.8 25.1 1.0
CZ A:ARG114 4.9 56.8 1.0
C5' B:DG6 4.9 28.1 1.0

Phosphorus binding site 7 out of 20 in 1aay

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Phosphorus binding site 7 out of 20 in the ZIF268 Zinc Finger-Dna Complex


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Stereo pair view

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

b:32.4
occ:1.00
 P B:DG8 0.0 32.4 1.0
OP1 B:DG8 1.5 34.1 1.0
OP2 B:DG8 1.5 32.3 1.0
O5' B:DG8 1.6 32.2 1.0
O3' B:DG7 1.6 28.9 1.0
C5' B:DG8 2.6 31.5 1.0
C3' B:DG7 2.6 28.5 1.0
C2' B:DG7 3.4 27.2 1.0
NH1 A:ARG103 3.4 55.6 1.0
O A:HOH234 3.5 50.7 1.0
NH2 A:ARG103 3.5 55.6 1.0
O B:HOH206 3.7 31.4 1.0
C4' B:DG8 3.8 30.1 1.0
C4' B:DG7 3.9 28.0 1.0
CZ A:ARG103 3.9 55.2 1.0
NH2 A:ARG114 4.0 57.1 1.0
O A:HOH241 4.0 39.0 1.0
C1' B:DG7 4.2 26.2 1.0
C3' B:DG8 4.3 30.1 1.0
O4' B:DG7 4.7 27.1 1.0
CE1 A:PHE116 4.8 33.1 1.0
C2' B:DG8 4.8 27.4 1.0
CD1 A:PHE116 4.8 32.0 1.0
O4' B:DG8 4.9 29.9 1.0
C5' B:DG7 4.9 30.1 1.0

Phosphorus binding site 8 out of 20 in 1aay

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Phosphorus binding site 8 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:33.5
occ:1.00
 P B:DC9 0.0 33.5 1.0
OP1 B:DC9 1.5 35.0 1.0
OP2 B:DC9 1.5 34.3 1.0
O5' B:DC9 1.6 32.1 1.0
O3' B:DG8 1.6 31.0 1.0
C5' B:DC9 2.6 29.7 1.0
C3' B:DG8 2.6 30.1 1.0
C2' B:DG8 3.2 27.4 1.0
O B:HOH247 3.7 51.1 1.0
O B:HOH277 3.9 57.4 1.0
C4' B:DC9 3.9 28.7 1.0
C4' B:DG8 3.9 30.1 1.0
O A:HOH204 4.0 29.2 1.0
C1' B:DG8 4.0 27.2 1.0
O A:HOH384 4.1 67.2 1.0
O4' B:DC9 4.3 26.7 1.0
C3' B:DC9 4.4 29.2 1.0
O4' B:DG8 4.4 29.9 1.0
C2' B:DC9 4.8 27.2 1.0

Phosphorus binding site 9 out of 20 in 1aay

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Phosphorus binding site 9 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:32.0
occ:1.00
 P B:DG10 0.0 32.0 1.0
OP2 B:DG10 1.5 33.1 1.0
OP1 B:DG10 1.5 33.1 1.0
O5' B:DG10 1.6 30.2 1.0
O3' B:DC9 1.6 31.1 1.0
C5' B:DG10 2.6 27.2 1.0
C3' B:DC9 2.7 29.2 1.0
C2' B:DC9 3.7 27.2 1.0
C4' B:DC9 3.8 28.7 1.0
C4' B:DG10 3.9 25.0 1.0
C8 B:DG10 4.2 18.9 1.0
O4' B:DG10 4.2 23.9 1.0
C3' B:DG10 4.3 23.6 1.0
C2' B:DG10 4.4 22.1 1.0
C1' B:DC9 4.5 25.5 1.0
O A:HOH232 4.6 31.0 1.0
C5' B:DC9 4.6 29.7 1.0
C1' B:DG10 4.8 22.6 1.0
O4' B:DC9 4.8 26.7 1.0
N9 B:DG10 4.8 21.4 1.0

Phosphorus binding site 10 out of 20 in 1aay

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Phosphorus binding site 10 out of 20 in the ZIF268 Zinc Finger-Dna Complex


Mono view


Stereo pair view

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

b:26.4
occ:1.00
 P B:DT11 0.0 26.4 1.0
OP2 B:DT11 1.5 26.0 1.0
OP1 B:DT11 1.5 28.3 1.0
O5' B:DT11 1.6 24.3 1.0
O3' B:DG10 1.6 25.1 1.0
C3' B:DG10 2.6 23.6 1.0
C5' B:DT11 2.6 21.9 1.0
C2' B:DG10 3.3 22.1 1.0
C4' B:DG10 3.9 25.0 1.0
C4' B:DT11 3.9 21.5 1.0
C1' B:DG10 4.2 22.6 1.0
O4' B:DT11 4.3 21.1 1.0
C3' B:DT11 4.4 21.4 1.0
O4' B:DG10 4.6 23.9 1.0
C5' B:DG10 4.9 27.2 1.0

Reference:

M.Elrod-Erickson, M.A.Rould, L.Nekludova, C.O.Pabo. ZIF268 Protein-Dna Complex Refined at 1.6 A: A Model System For Understanding Zinc Finger-Dna Interactions. Structure V. 4 1171 1996.
ISSN: ISSN 0969-2126
PubMed: 8939742
DOI: 10.1016/S0969-2126(96)00125-6
Page generated: Fri Sep 25 12:41:53 2020

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