Phosphorus in PDB 10mh: Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Enzymatic activity of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
All present enzymatic activity of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target:
2.1.1.73;
Protein crystallography data
The structure of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target, PDB code: 10mh
was solved by
G.Sheikhnejad,
A.Brank,
J.K.Christman,
A.Goddard,
E.Alvarez,
H.Ford Junior,
V.E.Marquez,
C.J.Marasco,
J.R.Sufrin,
M.O'gara,
X.Cheng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.30 /
2.55
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.860,
99.860,
325.200,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.5 /
n/a
|
Phosphorus Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Phosphorus atom in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
(pdb code 10mh). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 24 binding sites of Phosphorus where determined in the
Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target, PDB code: 10mh:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Phosphorus binding site 1 out
of 24 in 10mh
Go back to
Phosphorus Binding Sites List in 10mh
Phosphorus binding site 1 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P402
b:57.0
occ:1.00
|
P
|
B:DC402
|
0.0
|
57.0
|
1.0
|
OP2
|
B:DC402
|
1.5
|
55.8
|
1.0
|
OP1
|
B:DC402
|
1.5
|
57.6
|
1.0
|
O5'
|
B:DC402
|
1.7
|
49.8
|
1.0
|
C5'
|
B:DC402
|
2.7
|
40.4
|
1.0
|
O4'
|
B:DC402
|
3.5
|
32.4
|
1.0
|
C4'
|
B:DC402
|
3.7
|
35.3
|
1.0
|
C6
|
B:DC402
|
4.2
|
15.5
|
1.0
|
C3'
|
B:DC402
|
4.6
|
35.8
|
1.0
|
C1'
|
B:DC402
|
4.8
|
25.9
|
1.0
|
C5
|
B:DC402
|
4.9
|
15.1
|
1.0
|
O
|
A:HOH385
|
4.9
|
41.7
|
1.0
|
N1
|
B:DC402
|
5.0
|
14.8
|
1.0
|
|
Phosphorus binding site 2 out
of 24 in 10mh
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Phosphorus Binding Sites List in 10mh
Phosphorus binding site 2 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P403
b:38.6
occ:1.00
|
P
|
B:DC403
|
0.0
|
38.6
|
1.0
|
OP1
|
B:DC403
|
1.5
|
37.6
|
1.0
|
OP2
|
B:DC403
|
1.5
|
36.0
|
1.0
|
O5'
|
B:DC403
|
1.6
|
28.0
|
1.0
|
O3'
|
B:DC402
|
1.6
|
38.1
|
1.0
|
C3'
|
B:DC402
|
2.7
|
35.8
|
1.0
|
C5'
|
B:DC403
|
2.7
|
16.9
|
1.0
|
C2'
|
B:DC402
|
3.6
|
28.1
|
1.0
|
C4'
|
B:DC402
|
3.9
|
35.3
|
1.0
|
C4'
|
B:DC403
|
4.0
|
11.3
|
1.0
|
O4'
|
B:DC403
|
4.0
|
10.7
|
1.0
|
OE1
|
A:GLN297
|
4.1
|
12.7
|
1.0
|
C5'
|
B:DC402
|
4.4
|
40.4
|
1.0
|
CB
|
A:SER296
|
4.4
|
16.2
|
1.0
|
OG
|
A:SER296
|
4.4
|
25.5
|
1.0
|
C3'
|
B:DC403
|
4.6
|
13.0
|
1.0
|
O
|
A:HOH429
|
4.6
|
46.7
|
1.0
|
O
|
A:HOH385
|
4.8
|
41.7
|
1.0
|
OG
|
A:SER294
|
4.8
|
10.0
|
1.0
|
C1'
|
B:DC402
|
4.9
|
25.9
|
1.0
|
O4'
|
B:DC402
|
4.9
|
32.4
|
1.0
|
CD
|
A:GLN297
|
5.0
|
8.1
|
1.0
|
CG
|
A:GLN297
|
5.0
|
2.0
|
1.0
|
|
Phosphorus binding site 3 out
of 24 in 10mh
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Phosphorus Binding Sites List in 10mh
Phosphorus binding site 3 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P404
b:21.6
occ:1.00
|
P
|
B:DA404
|
0.0
|
21.6
|
1.0
|
OP1
|
B:DA404
|
1.5
|
16.8
|
1.0
|
OP2
|
B:DA404
|
1.5
|
23.7
|
1.0
|
O5'
|
B:DA404
|
1.6
|
22.2
|
1.0
|
O3'
|
B:DC403
|
1.7
|
18.2
|
1.0
|
C5'
|
B:DA404
|
2.8
|
18.8
|
1.0
|
C3'
|
B:DC403
|
2.9
|
13.0
|
1.0
|
C2'
|
B:DC403
|
3.4
|
10.5
|
1.0
|
C4'
|
B:DA404
|
4.0
|
15.4
|
1.0
|
C4'
|
B:DC403
|
4.1
|
11.3
|
1.0
|
O4'
|
B:DA404
|
4.1
|
16.9
|
1.0
|
C3'
|
B:DA404
|
4.6
|
12.8
|
1.0
|
C1'
|
B:DC403
|
4.7
|
7.5
|
1.0
|
O4'
|
B:DC403
|
4.9
|
10.7
|
1.0
|
C5'
|
B:DC403
|
5.0
|
16.9
|
1.0
|
|
Phosphorus binding site 4 out
of 24 in 10mh
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Phosphorus Binding Sites List in 10mh
Phosphorus binding site 4 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P405
b:22.4
occ:1.00
|
P
|
B:DT405
|
0.0
|
22.4
|
1.0
|
OP1
|
B:DT405
|
1.5
|
24.7
|
1.0
|
OP2
|
B:DT405
|
1.5
|
21.4
|
1.0
|
O5'
|
B:DT405
|
1.6
|
15.6
|
1.0
|
O3'
|
B:DA404
|
1.6
|
18.0
|
1.0
|
C5'
|
B:DT405
|
2.6
|
13.2
|
1.0
|
C3'
|
B:DA404
|
2.8
|
12.8
|
1.0
|
C2'
|
B:DA404
|
3.5
|
14.4
|
1.0
|
O
|
A:HOH361
|
3.7
|
25.1
|
1.0
|
C4'
|
B:DA404
|
4.0
|
15.4
|
1.0
|
C4'
|
B:DT405
|
4.0
|
13.5
|
1.0
|
O
|
B:HOH415
|
4.2
|
44.1
|
1.0
|
CD1
|
A:ILE258
|
4.2
|
8.7
|
1.0
|
C3'
|
B:DT405
|
4.3
|
12.6
|
1.0
|
C2'
|
B:DT405
|
4.6
|
13.9
|
1.0
|
O4'
|
B:DT405
|
4.7
|
15.2
|
1.0
|
C1'
|
B:DA404
|
4.7
|
10.4
|
1.0
|
O4'
|
B:DA404
|
4.9
|
16.9
|
1.0
|
C5'
|
B:DA404
|
4.9
|
18.8
|
1.0
|
|
Phosphorus binding site 5 out
of 24 in 10mh
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Phosphorus Binding Sites List in 10mh
Phosphorus binding site 5 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P406
b:21.3
occ:1.00
|
P
|
B:DG406
|
0.0
|
21.3
|
1.0
|
OP1
|
B:DG406
|
1.5
|
24.6
|
1.0
|
OP2
|
B:DG406
|
1.5
|
26.9
|
1.0
|
O5'
|
B:DG406
|
1.6
|
18.2
|
1.0
|
O3'
|
B:DT405
|
1.7
|
17.8
|
1.0
|
C5'
|
B:DG406
|
2.8
|
19.4
|
1.0
|
C3'
|
B:DT405
|
2.8
|
12.6
|
1.0
|
C4'
|
B:DT405
|
3.8
|
13.5
|
1.0
|
C2'
|
B:DT405
|
4.0
|
13.9
|
1.0
|
C4'
|
B:DG406
|
4.1
|
19.2
|
1.0
|
O
|
A:HOH364
|
4.1
|
11.9
|
1.0
|
O4'
|
B:DG406
|
4.3
|
17.0
|
1.0
|
NH1
|
A:ARG209
|
4.4
|
31.2
|
1.0
|
C1'
|
B:DT405
|
4.6
|
9.5
|
1.0
|
C2'
|
B:DG406
|
4.6
|
19.4
|
1.0
|
C3'
|
B:DG406
|
4.7
|
19.6
|
1.0
|
O4'
|
B:DT405
|
4.7
|
15.2
|
1.0
|
NH2
|
A:ARG209
|
4.7
|
33.3
|
1.0
|
C5'
|
B:DT405
|
4.8
|
13.2
|
1.0
|
|
Phosphorus binding site 6 out
of 24 in 10mh
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Phosphorus Binding Sites List in 10mh
Phosphorus binding site 6 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P407
b:31.5
occ:1.00
|
P
|
B:5CM407
|
0.0
|
31.5
|
1.0
|
OP2
|
B:5CM407
|
1.5
|
29.1
|
1.0
|
OP1
|
B:5CM407
|
1.5
|
33.3
|
1.0
|
O5'
|
B:5CM407
|
1.6
|
29.4
|
1.0
|
O3'
|
B:DG406
|
1.7
|
26.6
|
1.0
|
C5'
|
B:5CM407
|
2.6
|
28.8
|
1.0
|
C3'
|
B:DG406
|
2.8
|
19.6
|
1.0
|
C2'
|
B:DG406
|
3.7
|
19.4
|
1.0
|
C4'
|
B:5CM407
|
4.1
|
28.6
|
1.0
|
C4'
|
B:DG406
|
4.2
|
19.2
|
1.0
|
O
|
B:HOH419
|
4.3
|
42.5
|
1.0
|
O4'
|
B:5CM407
|
4.3
|
24.6
|
1.0
|
NZ
|
A:LYS234
|
4.4
|
44.9
|
1.0
|
CE
|
A:LYS234
|
4.5
|
45.0
|
1.0
|
C1'
|
B:DG406
|
4.5
|
13.1
|
1.0
|
O
|
A:HOH358
|
4.5
|
19.1
|
1.0
|
CD
|
A:LYS234
|
4.6
|
39.0
|
1.0
|
O4'
|
B:DG406
|
5.0
|
17.0
|
1.0
|
|
Phosphorus binding site 7 out
of 24 in 10mh
Go back to
Phosphorus Binding Sites List in 10mh
Phosphorus binding site 7 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P408
b:44.8
occ:1.00
|
P
|
B:DG408
|
0.0
|
44.8
|
1.0
|
OP1
|
B:DG408
|
1.5
|
44.1
|
1.0
|
OP2
|
B:DG408
|
1.5
|
36.8
|
1.0
|
O5'
|
B:DG408
|
1.6
|
41.6
|
1.0
|
O3'
|
B:5CM407
|
1.6
|
36.6
|
1.0
|
C3'
|
B:5CM407
|
2.6
|
28.0
|
1.0
|
C5'
|
B:DG408
|
2.7
|
41.2
|
1.0
|
C4'
|
B:5CM407
|
3.7
|
28.6
|
1.0
|
C4'
|
B:DG408
|
3.8
|
40.1
|
1.0
|
C2'
|
B:DG408
|
3.8
|
36.6
|
1.0
|
C2'
|
B:5CM407
|
3.9
|
23.2
|
1.0
|
C3'
|
B:DG408
|
4.0
|
41.1
|
1.0
|
C5'
|
B:5CM407
|
4.1
|
28.8
|
1.0
|
O4'
|
B:DG408
|
4.3
|
35.0
|
1.0
|
O4'
|
B:5CM407
|
4.7
|
24.6
|
1.0
|
C1'
|
B:DG408
|
4.7
|
30.8
|
1.0
|
C1'
|
B:5CM407
|
4.9
|
20.2
|
1.0
|
|
Phosphorus binding site 8 out
of 24 in 10mh
Go back to
Phosphorus Binding Sites List in 10mh
Phosphorus binding site 8 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P409
b:49.4
occ:1.00
|
P
|
B:DC409
|
0.0
|
49.4
|
1.0
|
OP2
|
B:DC409
|
1.5
|
48.8
|
1.0
|
OP1
|
B:DC409
|
1.5
|
46.3
|
1.0
|
O3'
|
B:DG408
|
1.6
|
45.2
|
1.0
|
O5'
|
B:DC409
|
1.6
|
44.8
|
1.0
|
C5'
|
B:DC409
|
2.6
|
42.3
|
1.0
|
C3'
|
B:DG408
|
2.7
|
41.1
|
1.0
|
C4'
|
B:DG408
|
3.6
|
40.1
|
1.0
|
C4'
|
B:DC409
|
3.8
|
38.6
|
1.0
|
C2'
|
B:DG408
|
3.9
|
36.6
|
1.0
|
O4'
|
B:DC409
|
4.0
|
34.3
|
1.0
|
C1'
|
B:DG408
|
4.4
|
30.8
|
1.0
|
C3'
|
B:DC409
|
4.5
|
36.9
|
1.0
|
O4'
|
B:DG408
|
4.5
|
35.0
|
1.0
|
C5'
|
B:DG408
|
4.7
|
41.2
|
1.0
|
O5'
|
B:DG408
|
4.9
|
41.6
|
1.0
|
C2'
|
B:DC409
|
5.0
|
33.8
|
1.0
|
|
Phosphorus binding site 9 out
of 24 in 10mh
Go back to
Phosphorus Binding Sites List in 10mh
Phosphorus binding site 9 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 9 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P410
b:40.5
occ:1.00
|
P
|
B:DT410
|
0.0
|
40.5
|
1.0
|
OP2
|
B:DT410
|
1.5
|
35.3
|
1.0
|
OP1
|
B:DT410
|
1.5
|
40.9
|
1.0
|
O5'
|
B:DT410
|
1.6
|
40.0
|
1.0
|
O3'
|
B:DC409
|
1.6
|
38.5
|
1.0
|
C5'
|
B:DT410
|
2.7
|
37.8
|
1.0
|
C3'
|
B:DC409
|
2.7
|
36.9
|
1.0
|
C2'
|
B:DC409
|
3.5
|
33.8
|
1.0
|
C4'
|
B:DC409
|
4.0
|
38.6
|
1.0
|
C4'
|
B:DT410
|
4.1
|
35.5
|
1.0
|
C3'
|
B:DT410
|
4.4
|
34.0
|
1.0
|
C1'
|
B:DC409
|
4.5
|
26.8
|
1.0
|
O4'
|
B:DT410
|
4.5
|
31.6
|
1.0
|
C2'
|
B:DT410
|
4.6
|
33.4
|
1.0
|
C5'
|
B:DC409
|
4.9
|
42.3
|
1.0
|
O4'
|
B:DC409
|
4.9
|
34.3
|
1.0
|
C6
|
B:DT410
|
5.0
|
26.5
|
1.0
|
|
Phosphorus binding site 10 out
of 24 in 10mh
Go back to
Phosphorus Binding Sites List in 10mh
Phosphorus binding site 10 out
of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 10 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P411
b:40.0
occ:1.00
|
P
|
B:DG411
|
0.0
|
40.0
|
1.0
|
OP2
|
B:DG411
|
1.5
|
33.6
|
1.0
|
OP1
|
B:DG411
|
1.5
|
41.0
|
1.0
|
O5'
|
B:DG411
|
1.6
|
39.3
|
1.0
|
O3'
|
B:DT410
|
1.7
|
35.7
|
1.0
|
C5'
|
B:DG411
|
2.8
|
34.9
|
1.0
|
C3'
|
B:DT410
|
2.8
|
34.0
|
1.0
|
C2'
|
B:DT410
|
3.5
|
33.4
|
1.0
|
NE2
|
A:GLN90
|
3.6
|
34.7
|
1.0
|
C4'
|
B:DG411
|
4.1
|
30.4
|
1.0
|
C4'
|
B:DT410
|
4.1
|
35.5
|
1.0
|
C3'
|
B:DG411
|
4.3
|
29.7
|
1.0
|
OE1
|
A:GLN90
|
4.3
|
37.2
|
1.0
|
CD
|
A:GLN90
|
4.4
|
36.9
|
1.0
|
C1'
|
B:DT410
|
4.6
|
30.0
|
1.0
|
O4'
|
B:DG411
|
4.7
|
32.0
|
1.0
|
C2'
|
B:DG411
|
4.8
|
26.2
|
1.0
|
O4'
|
B:DT410
|
4.9
|
31.6
|
1.0
|
|
Reference:
G.Sheikhnejad,
A.Brank,
J.K.Christman,
A.Goddard,
E.Alvarez,
H.Ford Jr.,
V.E.Marquez,
C.J.Marasco,
J.R.Sufrin,
M.O'gara,
X.Cheng.
Mechanism of Inhibition of Dna (Cytosine C5)-Methyltransferases By Oligodeoxyribonucleotides Containing 5,6-Dihydro-5-Azacytosine. J.Mol.Biol. V. 285 2021 1999.
ISSN: ISSN 0022-2836
PubMed: 9925782
DOI: 10.1006/JMBI.1998.2426
Page generated: Fri Sep 25 11:06:55 2020
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