Phosphorus in PDB 1a4i: Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
Enzymatic activity of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
All present enzymatic activity of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase:
1.5.1.5;
3.5.4.9;
Protein crystallography data
The structure of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase, PDB code: 1a4i
was solved by
M.Allaire,
Y.Li,
R.E.Mackenzie,
M.Cygler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.523,
135.843,
61.403,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.9 /
23.5
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
(pdb code 1a4i). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the
Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase, PDB code: 1a4i:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
Phosphorus binding site 1 out
of 6 in 1a4i
Go back to
Phosphorus Binding Sites List in 1a4i
Phosphorus binding site 1 out
of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P302
b:20.5
occ:1.00
|
PA
|
A:NDP302
|
0.0
|
20.5
|
1.0
|
O1A
|
A:NDP302
|
1.4
|
20.0
|
1.0
|
O2A
|
A:NDP302
|
1.5
|
23.9
|
1.0
|
O3
|
A:NDP302
|
1.6
|
19.8
|
1.0
|
O5B
|
A:NDP302
|
1.6
|
19.3
|
1.0
|
C5B
|
A:NDP302
|
2.6
|
18.3
|
1.0
|
PN
|
A:NDP302
|
3.0
|
22.2
|
1.0
|
O1N
|
A:NDP302
|
3.4
|
23.8
|
1.0
|
O2N
|
A:NDP302
|
3.6
|
19.8
|
1.0
|
O
|
A:HOH466
|
3.6
|
36.8
|
1.0
|
O
|
A:HOH435
|
3.7
|
31.4
|
1.0
|
C4B
|
A:NDP302
|
3.9
|
13.4
|
1.0
|
O
|
A:HOH411
|
3.9
|
31.4
|
1.0
|
O5D
|
A:NDP302
|
4.0
|
22.4
|
1.0
|
CB
|
A:SER174
|
4.1
|
15.9
|
1.0
|
C3B
|
A:NDP302
|
4.4
|
15.4
|
1.0
|
C5D
|
A:NDP302
|
4.5
|
23.2
|
1.0
|
O
|
A:HOH365
|
4.7
|
33.9
|
1.0
|
OG
|
A:SER174
|
4.8
|
16.3
|
1.0
|
O4B
|
A:NDP302
|
5.0
|
16.5
|
1.0
|
|
Phosphorus binding site 2 out
of 6 in 1a4i
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Phosphorus Binding Sites List in 1a4i
Phosphorus binding site 2 out
of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P302
b:22.2
occ:1.00
|
PN
|
A:NDP302
|
0.0
|
22.2
|
1.0
|
O1N
|
A:NDP302
|
1.5
|
23.8
|
1.0
|
O2N
|
A:NDP302
|
1.5
|
19.8
|
1.0
|
O3
|
A:NDP302
|
1.6
|
19.8
|
1.0
|
O5D
|
A:NDP302
|
1.6
|
22.4
|
1.0
|
C5D
|
A:NDP302
|
2.7
|
23.2
|
1.0
|
PA
|
A:NDP302
|
3.0
|
20.5
|
1.0
|
O1A
|
A:NDP302
|
3.4
|
20.0
|
1.0
|
OG
|
A:SER174
|
3.6
|
16.3
|
1.0
|
O5B
|
A:NDP302
|
3.7
|
19.3
|
1.0
|
O
|
A:HOH411
|
3.7
|
31.4
|
1.0
|
C4D
|
A:NDP302
|
4.0
|
22.4
|
1.0
|
O2A
|
A:NDP302
|
4.0
|
23.9
|
1.0
|
CB
|
A:SER174
|
4.0
|
15.9
|
1.0
|
O4D
|
A:NDP302
|
4.2
|
23.7
|
1.0
|
O
|
A:HOH314
|
4.2
|
14.4
|
1.0
|
C5B
|
A:NDP302
|
4.2
|
18.3
|
1.0
|
C6N
|
A:NDP302
|
4.3
|
25.5
|
1.0
|
C3D
|
A:NDP302
|
4.4
|
22.4
|
1.0
|
C2D
|
A:NDP302
|
4.4
|
22.4
|
1.0
|
CG2
|
A:VAL177
|
4.5
|
15.2
|
1.0
|
O
|
A:ALA215
|
4.7
|
14.3
|
1.0
|
C1D
|
A:NDP302
|
4.9
|
23.5
|
1.0
|
CB
|
A:VAL177
|
5.0
|
13.3
|
1.0
|
|
Phosphorus binding site 3 out
of 6 in 1a4i
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Phosphorus Binding Sites List in 1a4i
Phosphorus binding site 3 out
of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P302
b:16.0
occ:1.00
|
P2B
|
A:NDP302
|
0.0
|
16.0
|
1.0
|
O1X
|
A:NDP302
|
1.5
|
15.9
|
1.0
|
O2X
|
A:NDP302
|
1.5
|
14.6
|
1.0
|
O3X
|
A:NDP302
|
1.5
|
18.8
|
1.0
|
O2B
|
A:NDP302
|
1.5
|
13.0
|
1.0
|
C2B
|
A:NDP302
|
2.6
|
14.4
|
1.0
|
C3B
|
A:NDP302
|
3.3
|
15.4
|
1.0
|
O3B
|
A:NDP302
|
3.3
|
15.4
|
1.0
|
OG
|
A:SER197
|
3.6
|
19.1
|
1.0
|
O
|
A:HOH365
|
3.8
|
33.9
|
1.0
|
NH2
|
A:ARG173
|
3.8
|
16.3
|
1.0
|
NE
|
A:ARG173
|
3.8
|
13.5
|
1.0
|
O
|
A:HOH404
|
3.8
|
35.9
|
1.0
|
O
|
A:HOH390
|
3.9
|
40.7
|
1.0
|
C1B
|
A:NDP302
|
3.9
|
15.5
|
1.0
|
N
|
A:SER197
|
3.9
|
15.8
|
1.0
|
CB
|
A:SER197
|
4.1
|
18.4
|
1.0
|
CZ
|
A:ARG173
|
4.2
|
14.4
|
1.0
|
CB
|
A:HIS196
|
4.2
|
14.5
|
1.0
|
N9A
|
A:NDP302
|
4.6
|
16.4
|
1.0
|
CA
|
A:SER197
|
4.6
|
18.0
|
1.0
|
C4B
|
A:NDP302
|
4.7
|
13.4
|
1.0
|
CG
|
A:ARG173
|
4.7
|
12.5
|
1.0
|
CD
|
A:ARG173
|
4.9
|
13.6
|
1.0
|
C
|
A:HIS196
|
4.9
|
15.4
|
1.0
|
CA
|
A:HIS196
|
4.9
|
14.1
|
1.0
|
O4B
|
A:NDP302
|
5.0
|
16.5
|
1.0
|
|
Phosphorus binding site 4 out
of 6 in 1a4i
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Phosphorus Binding Sites List in 1a4i
Phosphorus binding site 4 out
of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P302
b:16.2
occ:1.00
|
PA
|
B:NDP302
|
0.0
|
16.2
|
1.0
|
O1A
|
B:NDP302
|
1.5
|
17.1
|
1.0
|
O2A
|
B:NDP302
|
1.5
|
18.8
|
1.0
|
O3
|
B:NDP302
|
1.6
|
16.4
|
1.0
|
O5B
|
B:NDP302
|
1.6
|
15.7
|
1.0
|
C5B
|
B:NDP302
|
2.7
|
14.6
|
1.0
|
PN
|
B:NDP302
|
2.9
|
17.6
|
1.0
|
O2N
|
B:NDP302
|
3.5
|
18.0
|
1.0
|
O1N
|
B:NDP302
|
3.6
|
19.7
|
1.0
|
O
|
B:HOH417
|
3.8
|
26.2
|
1.0
|
O
|
B:HOH371
|
3.8
|
24.7
|
1.0
|
C4B
|
B:NDP302
|
3.9
|
12.8
|
1.0
|
O5D
|
B:NDP302
|
4.0
|
18.5
|
1.0
|
CB
|
B:SER174
|
4.1
|
12.5
|
1.0
|
C5D
|
B:NDP302
|
4.4
|
17.9
|
1.0
|
C3B
|
B:NDP302
|
4.5
|
13.6
|
1.0
|
OG
|
B:SER174
|
4.7
|
12.8
|
1.0
|
O
|
B:HOH374
|
4.9
|
30.8
|
1.0
|
O4B
|
B:NDP302
|
5.0
|
12.7
|
1.0
|
|
Phosphorus binding site 5 out
of 6 in 1a4i
Go back to
Phosphorus Binding Sites List in 1a4i
Phosphorus binding site 5 out
of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P302
b:17.6
occ:1.00
|
PN
|
B:NDP302
|
0.0
|
17.6
|
1.0
|
O1N
|
B:NDP302
|
1.5
|
19.7
|
1.0
|
O2N
|
B:NDP302
|
1.5
|
18.0
|
1.0
|
O3
|
B:NDP302
|
1.6
|
16.4
|
1.0
|
O5D
|
B:NDP302
|
1.6
|
18.5
|
1.0
|
C5D
|
B:NDP302
|
2.6
|
17.9
|
1.0
|
PA
|
B:NDP302
|
2.9
|
16.2
|
1.0
|
O1A
|
B:NDP302
|
3.4
|
17.1
|
1.0
|
O
|
B:HOH417
|
3.5
|
26.2
|
1.0
|
O5B
|
B:NDP302
|
3.6
|
15.7
|
1.0
|
OG
|
B:SER174
|
3.7
|
12.8
|
1.0
|
C4D
|
B:NDP302
|
3.9
|
16.6
|
1.0
|
O2A
|
B:NDP302
|
4.0
|
18.8
|
1.0
|
CB
|
B:SER174
|
4.0
|
12.5
|
1.0
|
C6N
|
B:NDP302
|
4.2
|
19.7
|
1.0
|
O4D
|
B:NDP302
|
4.3
|
16.9
|
1.0
|
O
|
B:HOH309
|
4.3
|
13.2
|
1.0
|
C3D
|
B:NDP302
|
4.4
|
16.9
|
1.0
|
C5B
|
B:NDP302
|
4.4
|
14.6
|
1.0
|
C2D
|
B:NDP302
|
4.4
|
16.4
|
1.0
|
CG2
|
B:VAL177
|
4.5
|
13.2
|
1.0
|
O
|
B:ALA215
|
4.9
|
12.7
|
1.0
|
C1D
|
B:NDP302
|
4.9
|
17.7
|
1.0
|
CB
|
B:VAL177
|
5.0
|
12.6
|
1.0
|
|
Phosphorus binding site 6 out
of 6 in 1a4i
Go back to
Phosphorus Binding Sites List in 1a4i
Phosphorus binding site 6 out
of 6 in the Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of Human Tetrahydrofolate Dehydrogenase / Cyclohydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P302
b:12.1
occ:1.00
|
P2B
|
B:NDP302
|
0.0
|
12.1
|
1.0
|
O1X
|
B:NDP302
|
1.5
|
12.3
|
1.0
|
O2X
|
B:NDP302
|
1.5
|
12.7
|
1.0
|
O3X
|
B:NDP302
|
1.5
|
15.0
|
1.0
|
O2B
|
B:NDP302
|
1.6
|
12.6
|
1.0
|
C2B
|
B:NDP302
|
2.7
|
13.1
|
1.0
|
C3B
|
B:NDP302
|
3.3
|
13.6
|
1.0
|
O3B
|
B:NDP302
|
3.3
|
12.4
|
1.0
|
OG
|
B:SER197
|
3.6
|
15.1
|
1.0
|
O
|
B:HOH364
|
3.7
|
32.1
|
1.0
|
NH2
|
B:ARG173
|
3.7
|
12.7
|
1.0
|
NE
|
B:ARG173
|
3.7
|
10.8
|
1.0
|
O
|
B:HOH374
|
3.8
|
30.8
|
1.0
|
O
|
B:HOH477
|
3.8
|
30.7
|
1.0
|
CB
|
B:SER197
|
3.9
|
14.0
|
1.0
|
C1B
|
B:NDP302
|
4.0
|
13.1
|
1.0
|
N
|
B:SER197
|
4.0
|
12.2
|
1.0
|
CB
|
B:HIS196
|
4.2
|
11.6
|
1.0
|
CZ
|
B:ARG173
|
4.3
|
10.6
|
1.0
|
N9A
|
B:NDP302
|
4.6
|
12.8
|
1.0
|
CG
|
B:ARG173
|
4.6
|
10.4
|
1.0
|
CA
|
B:SER197
|
4.7
|
13.9
|
1.0
|
C4B
|
B:NDP302
|
4.7
|
12.8
|
1.0
|
CD
|
B:ARG173
|
4.8
|
9.9
|
1.0
|
CA
|
B:HIS196
|
4.9
|
10.3
|
1.0
|
O4B
|
B:NDP302
|
5.0
|
12.7
|
1.0
|
C
|
B:HIS196
|
5.0
|
11.7
|
1.0
|
|
Reference:
M.Allaire,
Y.Li,
R.E.Mackenzie,
M.Cygler.
The 3-D Structure of A Folate-Dependent Dehydrogenase/Cyclohydrolase Bifunctional Enzyme at 1.5 A Resolution. Structure V. 6 173 1998.
ISSN: ISSN 0969-2126
PubMed: 9519408
DOI: 10.1016/S0969-2126(98)00019-7
Page generated: Fri Sep 25 12:11:38 2020
|