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
Go back to
Phosphorus Binding Sites List in 1aay
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 Sites List in 1aay
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 Sites List in 1aay
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 Sites List in 1aay
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
Go back to
Phosphorus Binding Sites List in 1aay
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
Go back to
Phosphorus Binding Sites List in 1aay
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
Go back to
Phosphorus Binding Sites List in 1aay
Phosphorus binding site 7 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 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
Go back to
Phosphorus Binding Sites List in 1aay
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
Go back to
Phosphorus Binding Sites List in 1aay
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
Go back to
Phosphorus Binding Sites List in 1aay
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
|