Magnesium in PDB 3qu2: Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation
Enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation
All present enzymatic activity of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation:
3.6.1.1;
Protein crystallography data
The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation, PDB code: 3qu2
was solved by
Y.Patskovsky,
H.Huang,
R.Toro,
J.A.Gerlt,
S.K.Burley,
D.Dunaway-Mariano,
S.C.Almo,
New York Sgx Research Center For Structural Genomics(Nysgxrc),
Enzyme Function Initiative (Efi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.95
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
137.602,
71.761,
114.525,
90.00,
105.80,
90.00
|
R / Rfree (%)
|
23.2 /
27.5
|
Other elements in 3qu2:
The structure of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation
(pdb code 3qu2). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation, PDB code: 3qu2:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 3qu2
Go back to
Magnesium Binding Sites List in 3qu2
Magnesium binding site 1 out
of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg225
b:12.5
occ:1.00
|
OD2
|
A:ASP11
|
2.0
|
30.7
|
1.0
|
OE2
|
A:GLU47
|
2.1
|
33.9
|
1.0
|
OD1
|
A:ASN172
|
2.3
|
16.4
|
1.0
|
O
|
A:ASP13
|
2.4
|
16.7
|
1.0
|
O
|
A:HOH549
|
2.7
|
26.6
|
1.0
|
CD
|
A:GLU47
|
3.2
|
21.0
|
1.0
|
CG
|
A:ASP11
|
3.2
|
19.0
|
1.0
|
CG
|
A:ASN172
|
3.3
|
12.1
|
1.0
|
C
|
A:ASP13
|
3.5
|
24.5
|
1.0
|
ND2
|
A:ASN172
|
3.6
|
13.2
|
1.0
|
CG
|
A:GLU47
|
3.7
|
22.2
|
1.0
|
OE1
|
A:GLU171
|
3.9
|
23.7
|
1.0
|
CB
|
A:ASP11
|
4.0
|
21.5
|
1.0
|
OD1
|
A:ASP11
|
4.1
|
24.6
|
1.0
|
OE1
|
A:GLU47
|
4.1
|
28.7
|
1.0
|
CB
|
A:ALA173
|
4.2
|
11.9
|
1.0
|
CB
|
A:ASP13
|
4.3
|
16.2
|
1.0
|
CA
|
A:ASP13
|
4.3
|
14.6
|
1.0
|
N
|
A:ASP13
|
4.4
|
17.4
|
1.0
|
O
|
A:HOH228
|
4.4
|
11.9
|
1.0
|
N
|
A:GLY14
|
4.5
|
17.2
|
1.0
|
O4
|
A:CIT227
|
4.5
|
30.9
|
1.0
|
CB
|
A:ASN172
|
4.6
|
13.6
|
1.0
|
CA
|
A:GLY14
|
4.6
|
18.7
|
1.0
|
CG2
|
A:VAL15
|
4.7
|
20.4
|
1.0
|
N
|
A:ALA173
|
4.7
|
13.4
|
1.0
|
N
|
A:ASN172
|
4.7
|
21.7
|
1.0
|
O
|
A:HOH298
|
4.8
|
14.2
|
1.0
|
CD
|
A:GLU171
|
4.9
|
24.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 3qu2
Go back to
Magnesium Binding Sites List in 3qu2
Magnesium binding site 2 out
of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg225
b:13.3
occ:1.00
|
OE2
|
B:GLU47
|
2.1
|
25.2
|
1.0
|
O
|
B:ASP13
|
2.3
|
14.6
|
1.0
|
OD1
|
B:ASN172
|
2.3
|
17.8
|
1.0
|
O
|
B:HOH263
|
2.5
|
10.3
|
1.0
|
OD2
|
B:ASP11
|
2.5
|
19.8
|
1.0
|
O
|
B:HOH276
|
2.9
|
32.8
|
1.0
|
CD
|
B:GLU47
|
3.1
|
21.1
|
1.0
|
CG
|
B:ASN172
|
3.3
|
8.3
|
1.0
|
CG
|
B:ASP11
|
3.3
|
28.5
|
1.0
|
C
|
B:ASP13
|
3.4
|
24.9
|
1.0
|
ND2
|
B:ASN172
|
3.6
|
14.0
|
1.0
|
CG
|
B:GLU47
|
3.6
|
19.1
|
1.0
|
OD1
|
B:ASP11
|
3.9
|
28.9
|
1.0
|
OE1
|
B:GLU171
|
4.0
|
26.9
|
1.0
|
OE1
|
B:GLU47
|
4.1
|
32.9
|
1.0
|
CB
|
B:ASP13
|
4.2
|
27.5
|
1.0
|
CB
|
B:ALA173
|
4.2
|
11.6
|
1.0
|
CA
|
B:ASP13
|
4.3
|
18.9
|
1.0
|
CB
|
B:ASP11
|
4.3
|
16.3
|
1.0
|
N
|
B:GLY14
|
4.3
|
18.4
|
1.0
|
CA
|
B:GLY14
|
4.5
|
14.3
|
1.0
|
N
|
B:ASP13
|
4.6
|
16.0
|
1.0
|
CB
|
B:ASN172
|
4.7
|
15.2
|
1.0
|
O1
|
B:GOL226
|
4.8
|
22.1
|
1.0
|
N
|
B:ALA173
|
4.8
|
17.4
|
1.0
|
N
|
B:ASN172
|
4.9
|
18.0
|
1.0
|
C
|
B:GLY14
|
4.9
|
19.2
|
1.0
|
CD
|
B:GLU171
|
5.0
|
21.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 3qu2
Go back to
Magnesium Binding Sites List in 3qu2
Magnesium binding site 3 out
of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg225
b:16.9
occ:1.00
|
OD2
|
C:ASP11
|
2.1
|
23.7
|
1.0
|
OD1
|
C:ASN172
|
2.1
|
16.3
|
1.0
|
OE2
|
C:GLU47
|
2.4
|
21.4
|
1.0
|
O
|
C:ASP13
|
2.4
|
30.0
|
1.0
|
O
|
C:HOH569
|
2.8
|
30.8
|
1.0
|
O
|
C:HOH568
|
2.9
|
53.0
|
1.0
|
CG
|
C:ASN172
|
3.2
|
11.1
|
1.0
|
CG
|
C:ASP11
|
3.3
|
19.8
|
1.0
|
CD
|
C:GLU47
|
3.4
|
22.6
|
1.0
|
ND2
|
C:ASN172
|
3.6
|
16.8
|
1.0
|
C
|
C:ASP13
|
3.6
|
11.7
|
1.0
|
OE1
|
C:GLU171
|
3.7
|
22.8
|
1.0
|
CG
|
C:GLU47
|
3.9
|
27.0
|
1.0
|
CB
|
C:ASP11
|
4.0
|
22.1
|
1.0
|
CB
|
C:ALA173
|
4.2
|
26.6
|
1.0
|
OD1
|
C:ASP11
|
4.3
|
16.5
|
1.0
|
CB
|
C:ASP13
|
4.4
|
11.9
|
1.0
|
CA
|
C:ASP13
|
4.4
|
19.0
|
1.0
|
OE1
|
C:GLU47
|
4.4
|
25.5
|
1.0
|
O
|
C:HOH228
|
4.4
|
7.7
|
1.0
|
CB
|
C:ASN172
|
4.5
|
16.8
|
1.0
|
N
|
C:ASN172
|
4.5
|
20.8
|
1.0
|
N
|
C:ASP13
|
4.6
|
13.9
|
1.0
|
N
|
C:GLY14
|
4.6
|
17.2
|
1.0
|
N
|
C:ALA173
|
4.6
|
15.0
|
1.0
|
O
|
C:HOH271
|
4.6
|
17.2
|
1.0
|
CA
|
C:GLY14
|
4.7
|
11.3
|
1.0
|
CG2
|
C:VAL15
|
4.8
|
17.2
|
1.0
|
CD
|
C:GLU171
|
4.8
|
21.3
|
1.0
|
CA
|
C:ASN172
|
4.9
|
18.6
|
1.0
|
C
|
C:ASN172
|
5.0
|
16.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 3qu2
Go back to
Magnesium Binding Sites List in 3qu2
Magnesium binding site 4 out
of 4 in the Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Pyrophosphatase From Bacteroides Thetaiotaomicron, A Closed Cap Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg225
b:13.0
occ:1.00
|
OE2
|
D:GLU47
|
2.2
|
15.7
|
1.0
|
O
|
D:ASP13
|
2.2
|
16.6
|
1.0
|
OD1
|
D:ASN172
|
2.3
|
13.6
|
1.0
|
OD2
|
D:ASP11
|
2.4
|
19.8
|
1.0
|
O
|
D:HOH272
|
2.7
|
16.8
|
1.0
|
CG
|
D:ASN172
|
3.2
|
20.8
|
1.0
|
CG
|
D:ASP11
|
3.2
|
17.4
|
1.0
|
CD
|
D:GLU47
|
3.3
|
16.2
|
1.0
|
C
|
D:ASP13
|
3.4
|
19.1
|
1.0
|
ND2
|
D:ASN172
|
3.5
|
13.2
|
1.0
|
O
|
D:HOH741
|
3.5
|
40.3
|
1.0
|
CG
|
D:GLU47
|
3.7
|
14.4
|
1.0
|
OD1
|
D:ASP11
|
3.9
|
16.2
|
1.0
|
OE1
|
D:GLU171
|
4.0
|
21.9
|
1.0
|
CB
|
D:ASP11
|
4.1
|
15.8
|
1.0
|
CB
|
D:ASP13
|
4.2
|
21.0
|
1.0
|
CB
|
D:ALA173
|
4.2
|
21.6
|
1.0
|
CA
|
D:ASP13
|
4.2
|
15.9
|
1.0
|
N
|
D:GLY14
|
4.3
|
14.8
|
1.0
|
OE1
|
D:GLU47
|
4.3
|
13.8
|
1.0
|
CA
|
D:GLY14
|
4.4
|
9.8
|
1.0
|
N
|
D:ASP13
|
4.6
|
14.1
|
1.0
|
CB
|
D:ASN172
|
4.6
|
12.2
|
1.0
|
N
|
D:ALA173
|
4.8
|
18.5
|
1.0
|
C
|
D:GLY14
|
4.8
|
12.7
|
1.0
|
O3
|
D:GOL226
|
4.8
|
17.1
|
1.0
|
N
|
D:ASN172
|
4.9
|
15.0
|
1.0
|
CG2
|
D:VAL15
|
4.9
|
8.3
|
1.0
|
N
|
D:VAL15
|
5.0
|
12.9
|
1.0
|
|
Reference:
H.Huang,
Y.Patskovsky,
R.Toro,
J.D.Farelli,
C.Pandya,
S.C.Almo,
K.N.Allen,
D.Dunaway-Mariano.
Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides Thetaiotaomicron BT2127 Is An Inorganic Pyrophosphatase. Biochemistry V. 50 8937 2011.
ISSN: ISSN 0006-2960
PubMed: 21894910
DOI: 10.1021/BI201181Q
Page generated: Thu Aug 15 10:10:21 2024
|