Phosphorus in PDB 1a7a: Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength
Enzymatic activity of Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength
All present enzymatic activity of Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength:
3.3.1.1;
Protein crystallography data
The structure of Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength, PDB code: 1a7a
was solved by
M.A.Turner,
C.-S.Yuan,
R.T.Borchardt,
M.S.Hershfield,
G.D.Smith,
P.L.Howell,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.80
|
Space group
|
C 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.930,
168.020,
137.770,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.7 /
24.7
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength
(pdb code 1a7a). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 4 binding sites of Phosphorus where determined in the
Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength, PDB code: 1a7a:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
Phosphorus binding site 1 out
of 4 in 1a7a
Go back to
Phosphorus Binding Sites List in 1a7a
Phosphorus binding site 1 out
of 4 in the Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P433
b:14.3
occ:1.00
|
PA
|
A:NAD433
|
0.0
|
14.3
|
1.0
|
O1A
|
A:NAD433
|
1.5
|
13.8
|
1.0
|
O2A
|
A:NAD433
|
1.5
|
13.8
|
1.0
|
O5B
|
A:NAD433
|
1.6
|
15.0
|
1.0
|
O3
|
A:NAD433
|
1.6
|
14.7
|
1.0
|
C5B
|
A:NAD433
|
2.8
|
15.5
|
1.0
|
PN
|
A:NAD433
|
3.1
|
13.5
|
1.0
|
C4B
|
A:NAD433
|
3.3
|
15.3
|
1.0
|
C3B
|
A:NAD433
|
3.4
|
15.9
|
1.0
|
O5D
|
A:NAD433
|
3.6
|
13.6
|
1.0
|
O1N
|
A:NAD433
|
3.6
|
14.4
|
1.0
|
O
|
A:HOH459
|
3.6
|
12.5
|
1.0
|
OH
|
B:TYR430
|
3.7
|
10.4
|
1.0
|
O3B
|
A:NAD433
|
3.8
|
19.7
|
1.0
|
CA
|
A:GLY222
|
3.9
|
14.3
|
1.0
|
C5D
|
A:NAD433
|
4.0
|
15.6
|
1.0
|
O2N
|
A:NAD433
|
4.3
|
15.7
|
1.0
|
CE1
|
B:TYR430
|
4.4
|
8.0
|
1.0
|
CZ
|
B:TYR430
|
4.4
|
8.0
|
1.0
|
CE
|
B:LYS426
|
4.6
|
12.2
|
1.0
|
N
|
A:ASP223
|
4.7
|
14.0
|
1.0
|
O4B
|
A:NAD433
|
4.7
|
16.5
|
1.0
|
N
|
A:GLY222
|
4.8
|
12.8
|
1.0
|
C2B
|
A:NAD433
|
4.8
|
15.8
|
1.0
|
C
|
A:GLY222
|
4.8
|
14.4
|
1.0
|
CG2
|
A:THR158
|
4.9
|
13.1
|
1.0
|
|
Phosphorus binding site 2 out
of 4 in 1a7a
Go back to
Phosphorus Binding Sites List in 1a7a
Phosphorus binding site 2 out
of 4 in the Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P433
b:13.5
occ:1.00
|
PN
|
A:NAD433
|
0.0
|
13.5
|
1.0
|
O1N
|
A:NAD433
|
1.4
|
14.4
|
1.0
|
O2N
|
A:NAD433
|
1.5
|
15.7
|
1.0
|
O5D
|
A:NAD433
|
1.6
|
13.6
|
1.0
|
O3
|
A:NAD433
|
1.7
|
14.7
|
1.0
|
C5D
|
A:NAD433
|
2.8
|
15.6
|
1.0
|
O1A
|
A:NAD433
|
2.9
|
13.8
|
1.0
|
PA
|
A:NAD433
|
3.1
|
14.3
|
1.0
|
O5B
|
A:NAD433
|
3.3
|
15.0
|
1.0
|
O
|
A:HOH459
|
3.5
|
12.5
|
1.0
|
OG1
|
A:THR158
|
3.7
|
13.1
|
1.0
|
O2A
|
A:NAD433
|
3.7
|
13.8
|
1.0
|
CG2
|
A:VAL224
|
3.8
|
7.0
|
1.0
|
C4D
|
A:NAD433
|
3.9
|
16.9
|
1.0
|
O4D
|
A:NAD433
|
4.0
|
16.7
|
1.0
|
N
|
A:VAL224
|
4.1
|
9.0
|
1.0
|
CB
|
A:THR158
|
4.2
|
13.9
|
1.0
|
CG2
|
A:THR158
|
4.2
|
13.1
|
1.0
|
N
|
A:ASP223
|
4.2
|
14.0
|
1.0
|
OD1
|
A:ASN191
|
4.3
|
10.3
|
1.0
|
CB
|
A:VAL224
|
4.3
|
6.8
|
1.0
|
CB
|
A:ASP223
|
4.5
|
16.0
|
1.0
|
OD2
|
A:ASP223
|
4.6
|
19.2
|
1.0
|
C6N
|
A:NAD433
|
4.7
|
15.3
|
1.0
|
C5B
|
A:NAD433
|
4.7
|
15.5
|
1.0
|
C3D
|
A:NAD433
|
4.7
|
18.6
|
1.0
|
C2D
|
A:NAD433
|
4.8
|
18.8
|
1.0
|
CA
|
A:ASP223
|
4.8
|
13.3
|
1.0
|
C
|
A:GLY222
|
4.8
|
14.4
|
1.0
|
CA
|
A:VAL224
|
4.9
|
7.6
|
1.0
|
C1D
|
A:NAD433
|
4.9
|
17.8
|
1.0
|
CA
|
A:GLY222
|
4.9
|
14.3
|
1.0
|
C
|
A:ASP223
|
5.0
|
11.8
|
1.0
|
|
Phosphorus binding site 3 out
of 4 in 1a7a
Go back to
Phosphorus Binding Sites List in 1a7a
Phosphorus binding site 3 out
of 4 in the Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P434
b:17.3
occ:1.00
|
PA
|
B:NAD434
|
0.0
|
17.3
|
1.0
|
O1A
|
B:NAD434
|
1.5
|
17.8
|
1.0
|
O2A
|
B:NAD434
|
1.5
|
16.4
|
1.0
|
O5B
|
B:NAD434
|
1.6
|
15.5
|
1.0
|
O3
|
B:NAD434
|
1.7
|
16.8
|
1.0
|
C5B
|
B:NAD434
|
2.8
|
17.4
|
1.0
|
PN
|
B:NAD434
|
3.1
|
17.1
|
1.0
|
C4B
|
B:NAD434
|
3.2
|
19.2
|
1.0
|
C3B
|
B:NAD434
|
3.3
|
20.0
|
1.0
|
O5D
|
B:NAD434
|
3.5
|
16.9
|
1.0
|
O1N
|
B:NAD434
|
3.6
|
18.6
|
1.0
|
OH
|
A:TYR430
|
3.7
|
12.9
|
1.0
|
O3B
|
B:NAD434
|
3.7
|
22.3
|
1.0
|
CA
|
B:GLY222
|
3.9
|
15.0
|
1.0
|
C5D
|
B:NAD434
|
4.0
|
15.9
|
1.0
|
O2N
|
B:NAD434
|
4.3
|
17.4
|
1.0
|
CE1
|
A:TYR430
|
4.4
|
9.6
|
1.0
|
O
|
B:HOH440
|
4.4
|
12.2
|
1.0
|
CZ
|
A:TYR430
|
4.4
|
9.3
|
1.0
|
CE
|
A:LYS426
|
4.4
|
14.2
|
1.0
|
O4B
|
B:NAD434
|
4.6
|
20.2
|
1.0
|
C2B
|
B:NAD434
|
4.7
|
19.7
|
1.0
|
N
|
B:ASP223
|
4.7
|
14.2
|
1.0
|
N
|
B:GLY222
|
4.7
|
16.7
|
1.0
|
C
|
B:GLY222
|
4.8
|
15.0
|
1.0
|
CG2
|
B:THR158
|
4.9
|
19.6
|
1.0
|
|
Phosphorus binding site 4 out
of 4 in 1a7a
Go back to
Phosphorus Binding Sites List in 1a7a
Phosphorus binding site 4 out
of 4 in the Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Structure of Human Placental S-Adenosylhomocysteine Hydrolase: Determination of A 30 Selenium Atom Substructure From Data at A Single Wavelength within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P434
b:17.1
occ:1.00
|
PN
|
B:NAD434
|
0.0
|
17.1
|
1.0
|
O1N
|
B:NAD434
|
1.4
|
18.6
|
1.0
|
O2N
|
B:NAD434
|
1.5
|
17.4
|
1.0
|
O5D
|
B:NAD434
|
1.7
|
16.9
|
1.0
|
O3
|
B:NAD434
|
1.7
|
16.8
|
1.0
|
C5D
|
B:NAD434
|
2.8
|
15.9
|
1.0
|
O1A
|
B:NAD434
|
2.9
|
17.8
|
1.0
|
PA
|
B:NAD434
|
3.1
|
17.3
|
1.0
|
O5B
|
B:NAD434
|
3.3
|
15.5
|
1.0
|
OG1
|
B:THR158
|
3.6
|
22.0
|
1.0
|
O2A
|
B:NAD434
|
3.7
|
16.4
|
1.0
|
C4D
|
B:NAD434
|
3.9
|
15.9
|
1.0
|
CG2
|
B:VAL224
|
3.9
|
12.3
|
1.0
|
O
|
B:HOH440
|
4.0
|
12.2
|
1.0
|
O4D
|
B:NAD434
|
4.1
|
15.5
|
1.0
|
CG2
|
B:THR158
|
4.1
|
19.6
|
1.0
|
N
|
B:VAL224
|
4.1
|
13.3
|
1.0
|
CB
|
B:THR158
|
4.2
|
20.5
|
1.0
|
N
|
B:ASP223
|
4.2
|
14.2
|
1.0
|
OD1
|
B:ASN191
|
4.3
|
19.6
|
1.0
|
CB
|
B:VAL224
|
4.4
|
13.1
|
1.0
|
CB
|
B:ASP223
|
4.6
|
13.7
|
1.0
|
OD2
|
B:ASP223
|
4.7
|
14.5
|
1.0
|
C6N
|
B:NAD434
|
4.7
|
18.6
|
1.0
|
C5B
|
B:NAD434
|
4.7
|
17.4
|
1.0
|
C3D
|
B:NAD434
|
4.7
|
16.2
|
1.0
|
C2D
|
B:NAD434
|
4.8
|
17.1
|
1.0
|
CA
|
B:ASP223
|
4.8
|
13.9
|
1.0
|
C
|
B:GLY222
|
4.8
|
15.0
|
1.0
|
C1D
|
B:NAD434
|
4.9
|
16.7
|
1.0
|
CA
|
B:VAL224
|
4.9
|
12.1
|
1.0
|
CA
|
B:GLY222
|
4.9
|
15.0
|
1.0
|
|
Reference:
M.A.Turner,
C.S.Yuan,
R.T.Borchardt,
M.S.Hershfield,
G.D.Smith,
P.L.Howell.
Structure Determination of Selenomethionyl S-Adenosylhomocysteine Hydrolase Using Data at A Single Wavelength. Nat.Struct.Biol. V. 5 369 1998.
ISSN: ISSN 1072-8368
PubMed: 9586999
DOI: 10.1038/NSB0598-369
Page generated: Fri Sep 25 12:23:56 2020
|