Phosphorus in PDB 187d: Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Protein crystallography data
The structure of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition, PDB code: 187d
was solved by
M.Eisenstein,
Z.Shakked,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.25
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.360,
43.360,
24.830,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
(pdb code 187d). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 7 binding sites of Phosphorus where determined in the
Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition, PDB code: 187d:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
Phosphorus binding site 1 out
of 7 in 187d
Go back to
Phosphorus Binding Sites List in 187d
Phosphorus binding site 1 out
of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P2
b:25.4
occ:1.00
|
P
|
A:DC2
|
0.0
|
25.4
|
1.0
|
OP1
|
A:DC2
|
1.5
|
27.5
|
1.0
|
OP2
|
A:DC2
|
1.5
|
24.9
|
1.0
|
O5'
|
A:DC2
|
1.6
|
23.4
|
1.0
|
O3'
|
A:DC1
|
1.6
|
24.8
|
1.0
|
C5'
|
A:DC2
|
2.6
|
23.5
|
1.0
|
C3'
|
A:DC1
|
2.6
|
24.4
|
1.0
|
C2'
|
A:DC1
|
3.6
|
24.3
|
1.0
|
C4'
|
A:DC2
|
3.8
|
25.1
|
1.0
|
C4'
|
A:DC1
|
3.8
|
23.5
|
1.0
|
O
|
A:HOH23
|
3.9
|
18.2
|
1.0
|
O4'
|
A:DC2
|
4.0
|
25.4
|
1.0
|
C6
|
A:DC2
|
4.3
|
24.1
|
1.0
|
C5'
|
A:DC1
|
4.3
|
23.2
|
1.0
|
C3'
|
A:DC2
|
4.4
|
25.3
|
1.0
|
O
|
A:HOH22
|
4.9
|
18.6
|
1.0
|
O
|
A:HOH24
|
4.9
|
67.5
|
1.0
|
O
|
A:HOH29
|
4.9
|
52.9
|
1.0
|
C1'
|
A:DC1
|
4.9
|
23.3
|
1.0
|
O5'
|
A:DC1
|
4.9
|
23.6
|
1.0
|
O4'
|
A:DC1
|
5.0
|
22.8
|
1.0
|
C5
|
A:DC2
|
5.0
|
23.6
|
1.0
|
|
Phosphorus binding site 2 out
of 7 in 187d
Go back to
Phosphorus Binding Sites List in 187d
Phosphorus binding site 2 out
of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P3
b:26.1
occ:1.00
|
P
|
A:DC3
|
0.0
|
26.1
|
1.0
|
OP2
|
A:DC3
|
1.5
|
25.8
|
1.0
|
OP1
|
A:DC3
|
1.5
|
26.8
|
1.0
|
O3'
|
A:DC2
|
1.6
|
26.0
|
1.0
|
O5'
|
A:DC3
|
1.6
|
25.7
|
1.0
|
C5'
|
A:DC3
|
2.6
|
24.9
|
1.0
|
C3'
|
A:DC2
|
2.6
|
25.3
|
1.0
|
C2'
|
A:DC2
|
3.4
|
24.1
|
1.0
|
C4'
|
A:DC3
|
3.8
|
23.4
|
1.0
|
C4'
|
A:DC2
|
4.0
|
25.1
|
1.0
|
O
|
A:HOH30
|
4.0
|
46.7
|
1.0
|
O4'
|
A:DC3
|
4.1
|
23.1
|
1.0
|
C3'
|
A:DC3
|
4.4
|
22.2
|
1.0
|
C6
|
A:DC3
|
4.4
|
17.9
|
1.0
|
C5'
|
A:DC2
|
4.6
|
23.5
|
1.0
|
O5'
|
A:DC2
|
4.7
|
23.4
|
1.0
|
C1'
|
A:DC2
|
4.7
|
24.5
|
1.0
|
O4'
|
A:DC2
|
5.0
|
25.4
|
1.0
|
|
Phosphorus binding site 3 out
of 7 in 187d
Go back to
Phosphorus Binding Sites List in 187d
Phosphorus binding site 3 out
of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P4
b:24.1
occ:1.00
|
P
|
A:DC4
|
0.0
|
24.1
|
1.0
|
OP1
|
A:DC4
|
1.5
|
24.9
|
1.0
|
OP2
|
A:DC4
|
1.5
|
25.6
|
1.0
|
O3'
|
A:DC3
|
1.6
|
23.1
|
1.0
|
O5'
|
A:DC4
|
1.6
|
21.8
|
1.0
|
C5'
|
A:DC4
|
2.6
|
19.2
|
1.0
|
C3'
|
A:DC3
|
2.7
|
22.2
|
1.0
|
C2'
|
A:DC3
|
3.4
|
21.8
|
1.0
|
C4'
|
A:DC3
|
3.9
|
23.4
|
1.0
|
C4'
|
A:DC4
|
4.0
|
17.8
|
1.0
|
O
|
A:HOH45
|
4.0
|
61.1
|
1.0
|
O
|
A:HOH46
|
4.0
|
98.3
|
1.0
|
O
|
A:HOH14
|
4.2
|
41.1
|
1.0
|
O4'
|
A:DC4
|
4.4
|
16.6
|
1.0
|
C3'
|
A:DC4
|
4.6
|
17.9
|
1.0
|
C5'
|
A:DC3
|
4.6
|
24.9
|
1.0
|
C6
|
A:DC4
|
4.7
|
13.6
|
1.0
|
C1'
|
A:DC3
|
4.8
|
20.8
|
1.0
|
O5'
|
A:DC3
|
5.0
|
25.7
|
1.0
|
|
Phosphorus binding site 4 out
of 7 in 187d
Go back to
Phosphorus Binding Sites List in 187d
Phosphorus binding site 4 out
of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P5
b:19.4
occ:1.00
|
P
|
A:DG5
|
0.0
|
19.4
|
1.0
|
OP1
|
A:DG5
|
1.5
|
21.1
|
1.0
|
OP2
|
A:DG5
|
1.5
|
19.2
|
1.0
|
O5'
|
A:DG5
|
1.6
|
19.9
|
1.0
|
O3'
|
A:DC4
|
1.6
|
19.8
|
1.0
|
C3'
|
A:DC4
|
2.5
|
17.9
|
1.0
|
C5'
|
A:DG5
|
2.6
|
20.3
|
1.0
|
C2'
|
A:DC4
|
3.3
|
17.3
|
1.0
|
O
|
A:HOH21
|
3.5
|
44.1
|
1.0
|
O
|
A:HOH32
|
3.8
|
81.0
|
1.0
|
C4'
|
A:DC4
|
3.9
|
17.8
|
1.0
|
C4'
|
A:DG5
|
3.9
|
20.2
|
1.0
|
O4'
|
A:DG5
|
4.3
|
20.6
|
1.0
|
O
|
A:HOH45
|
4.4
|
61.1
|
1.0
|
C5'
|
A:DC4
|
4.4
|
19.2
|
1.0
|
O
|
A:HOH40
|
4.5
|
77.7
|
1.0
|
C1'
|
A:DC4
|
4.7
|
14.8
|
1.0
|
O5'
|
A:DC4
|
4.8
|
21.8
|
1.0
|
O4'
|
A:DC4
|
4.9
|
16.6
|
1.0
|
|
Phosphorus binding site 5 out
of 7 in 187d
Go back to
Phosphorus Binding Sites List in 187d
Phosphorus binding site 5 out
of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P6
b:22.6
occ:1.00
|
P
|
A:DG6
|
0.0
|
22.6
|
1.0
|
OP2
|
A:DG6
|
1.5
|
21.8
|
1.0
|
OP1
|
A:DG6
|
1.5
|
20.9
|
1.0
|
O3'
|
A:DG5
|
1.6
|
21.4
|
1.0
|
O5'
|
A:DG6
|
1.6
|
21.7
|
1.0
|
C5'
|
A:DG6
|
2.7
|
20.0
|
1.0
|
C3'
|
A:DG5
|
2.7
|
19.9
|
1.0
|
C2'
|
A:DG5
|
3.5
|
18.2
|
1.0
|
O
|
A:HOH42
|
3.6
|
68.0
|
1.0
|
C4'
|
A:DG6
|
3.9
|
20.9
|
1.0
|
O
|
A:HOH25
|
3.9
|
61.6
|
1.0
|
C4'
|
A:DG5
|
4.0
|
20.2
|
1.0
|
O
|
A:HOH13
|
4.0
|
71.7
|
1.0
|
O4'
|
A:DG6
|
4.1
|
18.4
|
1.0
|
O
|
A:HOH16
|
4.1
|
51.6
|
1.0
|
C8
|
A:DG6
|
4.2
|
13.5
|
1.0
|
C3'
|
A:DG6
|
4.6
|
23.2
|
1.0
|
O
|
A:HOH15
|
4.6
|
52.6
|
1.0
|
C5'
|
A:DG5
|
4.7
|
20.3
|
1.0
|
C1'
|
A:DG5
|
4.8
|
15.2
|
1.0
|
OP2
|
A:DG7
|
4.9
|
29.7
|
1.0
|
|
Phosphorus binding site 6 out
of 7 in 187d
Go back to
Phosphorus Binding Sites List in 187d
Phosphorus binding site 6 out
of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P7
b:29.1
occ:1.00
|
P
|
A:DG7
|
0.0
|
29.1
|
1.0
|
OP2
|
A:DG7
|
1.5
|
29.7
|
1.0
|
OP1
|
A:DG7
|
1.5
|
31.0
|
1.0
|
O3'
|
A:DG6
|
1.6
|
27.1
|
1.0
|
O5'
|
A:DG7
|
1.6
|
27.0
|
1.0
|
C3'
|
A:DG6
|
2.6
|
23.2
|
1.0
|
C5'
|
A:DG7
|
2.6
|
21.9
|
1.0
|
C2'
|
A:DG6
|
3.5
|
20.4
|
1.0
|
C4'
|
A:DG6
|
3.8
|
20.9
|
1.0
|
C4'
|
A:DG7
|
3.9
|
19.8
|
1.0
|
O4'
|
A:DG7
|
4.0
|
17.2
|
1.0
|
O
|
A:HOH16
|
4.3
|
51.6
|
1.0
|
C5'
|
A:DG6
|
4.3
|
20.0
|
1.0
|
C1'
|
A:DG6
|
4.7
|
17.3
|
1.0
|
C3'
|
A:DG7
|
4.7
|
20.2
|
1.0
|
O5'
|
A:DG6
|
4.8
|
21.7
|
1.0
|
O
|
A:HOH13
|
4.9
|
71.7
|
1.0
|
O4'
|
A:DG6
|
4.9
|
18.4
|
1.0
|
C8
|
A:DG7
|
4.9
|
16.2
|
1.0
|
|
Phosphorus binding site 7 out
of 7 in 187d
Go back to
Phosphorus Binding Sites List in 187d
Phosphorus binding site 7 out
of 7 in the Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P8
b:24.9
occ:1.00
|
P
|
A:DG8
|
0.0
|
24.9
|
1.0
|
OP1
|
A:DG8
|
1.5
|
24.7
|
1.0
|
OP2
|
A:DG8
|
1.5
|
24.3
|
1.0
|
O5'
|
A:DG8
|
1.6
|
25.7
|
1.0
|
O3'
|
A:DG7
|
1.6
|
22.7
|
1.0
|
C3'
|
A:DG7
|
2.6
|
20.2
|
1.0
|
C5'
|
A:DG8
|
2.7
|
27.6
|
1.0
|
C2'
|
A:DG7
|
3.2
|
19.0
|
1.0
|
C4'
|
A:DG8
|
3.9
|
28.7
|
1.0
|
C4'
|
A:DG7
|
3.9
|
19.8
|
1.0
|
O4'
|
A:DG8
|
4.3
|
27.7
|
1.0
|
C3'
|
A:DG8
|
4.3
|
29.4
|
1.0
|
C8
|
A:DG8
|
4.4
|
23.3
|
1.0
|
C1'
|
A:DG7
|
4.6
|
17.0
|
1.0
|
C2'
|
A:DG8
|
4.6
|
27.5
|
1.0
|
C5'
|
A:DG7
|
4.6
|
21.9
|
1.0
|
O4'
|
A:DG7
|
4.9
|
17.2
|
1.0
|
C1'
|
A:DG8
|
5.0
|
26.1
|
1.0
|
|
Reference:
M.Eisenstein,
Z.Shakked.
Hydration Patterns and Intermolecular Interactions in A-Dna Crystal Structures. Implications For Dna Recognition. J.Mol.Biol. V. 248 662 1995.
ISSN: ISSN 0022-2836
PubMed: 7752232
DOI: 10.1006/JMBI.1995.0250
Page generated: Fri Sep 25 11:48:02 2020
|