Magnesium in PDB 4wf7: Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis
Enzymatic activity of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis
All present enzymatic activity of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis:
5.4.99.16;
Protein crystallography data
The structure of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis, PDB code: 4wf7
was solved by
Y.L.Wang,
S.Y.Chow,
Y.T.Lin,
Y.C.Hsieh,
G.C.Lee,
S.H.Liaw,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.21
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
96.250,
133.705,
196.614,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16 /
20
|
Other elements in 4wf7:
The structure of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis
(pdb code 4wf7). 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 Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis, PDB code: 4wf7:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 4wf7
Go back to
Magnesium Binding Sites List in 4wf7
Magnesium binding site 1 out
of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:20.0
occ:1.00
|
OD1
|
A:ASN26
|
2.0
|
36.1
|
1.0
|
O
|
A:HOH833
|
2.2
|
34.4
|
1.0
|
OD1
|
A:ASP24
|
2.2
|
22.8
|
1.0
|
O
|
A:LYS30
|
2.2
|
28.7
|
1.0
|
OD2
|
A:ASP32
|
2.2
|
25.2
|
1.0
|
OD1
|
A:ASP28
|
2.4
|
29.1
|
1.0
|
CG
|
A:ASP24
|
3.2
|
23.0
|
1.0
|
CG
|
A:ASN26
|
3.2
|
35.0
|
1.0
|
CG
|
A:ASP32
|
3.4
|
25.5
|
1.0
|
CG
|
A:ASP28
|
3.4
|
28.4
|
1.0
|
C
|
A:LYS30
|
3.4
|
26.3
|
1.0
|
OD2
|
A:ASP28
|
3.7
|
29.3
|
1.0
|
N
|
A:ASN26
|
3.9
|
30.4
|
1.0
|
CB
|
A:ASP32
|
3.9
|
26.2
|
1.0
|
OD2
|
A:ASP24
|
4.0
|
21.1
|
1.0
|
ND2
|
A:ASN26
|
4.0
|
36.8
|
1.0
|
CB
|
A:ASP24
|
4.1
|
24.7
|
1.0
|
CA
|
A:ASP24
|
4.1
|
24.4
|
1.0
|
N
|
A:LYS30
|
4.1
|
25.0
|
1.0
|
N
|
A:GLY25
|
4.1
|
28.1
|
1.0
|
CA
|
A:LYS30
|
4.1
|
27.3
|
1.0
|
CB
|
A:LYS30
|
4.2
|
29.8
|
1.0
|
CB
|
A:ASN26
|
4.3
|
31.8
|
1.0
|
N
|
A:ASP28
|
4.3
|
25.7
|
1.0
|
OD1
|
A:ASP32
|
4.4
|
26.4
|
1.0
|
C
|
A:GLY31
|
4.4
|
26.1
|
1.0
|
CA
|
A:ASN26
|
4.4
|
31.1
|
1.0
|
N
|
A:GLY31
|
4.4
|
26.6
|
1.0
|
C
|
A:ASP24
|
4.4
|
26.7
|
1.0
|
O
|
A:ASP77
|
4.5
|
31.3
|
1.0
|
O
|
A:GLY31
|
4.5
|
27.0
|
1.0
|
CB
|
A:ASP28
|
4.6
|
26.9
|
1.0
|
N
|
A:ASP32
|
4.7
|
23.4
|
1.0
|
C
|
A:ASN26
|
4.7
|
29.3
|
1.0
|
CA
|
A:GLY31
|
4.7
|
25.2
|
1.0
|
N
|
A:GLY27
|
4.7
|
29.4
|
1.0
|
C
|
A:GLY25
|
4.8
|
30.1
|
1.0
|
CA
|
A:ASP28
|
4.8
|
26.7
|
1.0
|
N
|
A:GLY29
|
4.9
|
25.9
|
1.0
|
CA
|
A:ASP32
|
4.9
|
24.4
|
1.0
|
CA
|
A:GLY25
|
5.0
|
29.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 4wf7
Go back to
Magnesium Binding Sites List in 4wf7
Magnesium binding site 2 out
of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:21.8
occ:1.00
|
OD2
|
B:ASP32
|
2.1
|
25.6
|
1.0
|
O
|
B:HOH747
|
2.2
|
25.7
|
1.0
|
OD1
|
B:ASN26
|
2.2
|
30.9
|
1.0
|
OD1
|
B:ASP24
|
2.3
|
23.1
|
1.0
|
O
|
B:LYS30
|
2.3
|
26.9
|
1.0
|
OD1
|
B:ASP28
|
2.3
|
27.1
|
1.0
|
CG
|
B:ASP28
|
3.1
|
28.5
|
1.0
|
CG
|
B:ASN26
|
3.2
|
31.9
|
1.0
|
CG
|
B:ASP24
|
3.3
|
24.6
|
1.0
|
CG
|
B:ASP32
|
3.3
|
26.3
|
1.0
|
OD2
|
B:ASP28
|
3.4
|
26.4
|
1.0
|
C
|
B:LYS30
|
3.4
|
26.9
|
1.0
|
ND2
|
B:ASN26
|
3.8
|
34.6
|
1.0
|
N
|
B:ASN26
|
3.9
|
26.8
|
1.0
|
CB
|
B:ASP32
|
4.0
|
25.2
|
1.0
|
N
|
B:LYS30
|
4.0
|
27.4
|
1.0
|
OD2
|
B:ASP24
|
4.0
|
23.9
|
1.0
|
N
|
B:GLY25
|
4.1
|
30.8
|
1.0
|
CA
|
B:ASP24
|
4.1
|
25.8
|
1.0
|
CA
|
B:LYS30
|
4.1
|
27.9
|
1.0
|
CB
|
B:ASP24
|
4.2
|
25.1
|
1.0
|
CB
|
B:LYS30
|
4.3
|
27.1
|
1.0
|
CB
|
B:ASN26
|
4.3
|
28.3
|
1.0
|
OD1
|
B:ASP32
|
4.3
|
29.1
|
1.0
|
N
|
B:ASP28
|
4.3
|
27.2
|
1.0
|
CB
|
B:ASP28
|
4.4
|
26.3
|
1.0
|
CA
|
B:ASN26
|
4.4
|
27.2
|
1.0
|
O
|
B:HOH823
|
4.4
|
53.6
|
1.0
|
N
|
B:GLY31
|
4.5
|
25.4
|
1.0
|
C
|
B:ASP24
|
4.5
|
28.5
|
1.0
|
O
|
B:ASP77
|
4.5
|
29.8
|
1.0
|
C
|
B:GLY31
|
4.5
|
24.8
|
1.0
|
C
|
B:ASN26
|
4.6
|
27.3
|
1.0
|
N
|
B:ASP32
|
4.6
|
23.3
|
1.0
|
N
|
B:GLY27
|
4.7
|
27.3
|
1.0
|
CA
|
B:GLY31
|
4.8
|
24.7
|
1.0
|
CA
|
B:ASP28
|
4.8
|
26.8
|
1.0
|
O
|
B:GLY31
|
4.8
|
25.9
|
1.0
|
N
|
B:GLY29
|
4.8
|
29.6
|
1.0
|
C
|
B:GLY25
|
4.9
|
30.1
|
1.0
|
CA
|
B:ASP32
|
5.0
|
24.0
|
1.0
|
C
|
B:ASP28
|
5.0
|
28.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 4wf7
Go back to
Magnesium Binding Sites List in 4wf7
Magnesium binding site 3 out
of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:23.2
occ:1.00
|
OD1
|
C:ASN26
|
2.2
|
37.0
|
1.0
|
O
|
C:HOH832
|
2.2
|
23.1
|
1.0
|
O
|
C:LYS30
|
2.3
|
25.1
|
1.0
|
OD2
|
C:ASP32
|
2.3
|
27.2
|
1.0
|
OD1
|
C:ASP28
|
2.3
|
32.4
|
1.0
|
OD1
|
C:ASP24
|
2.4
|
24.8
|
1.0
|
CG
|
C:ASP28
|
3.1
|
32.6
|
1.0
|
CG
|
C:ASP24
|
3.3
|
25.9
|
1.0
|
OD2
|
C:ASP28
|
3.3
|
32.9
|
1.0
|
CG
|
C:ASN26
|
3.3
|
33.1
|
1.0
|
C
|
C:LYS30
|
3.4
|
25.4
|
1.0
|
CG
|
C:ASP32
|
3.4
|
27.6
|
1.0
|
CB
|
C:ASP32
|
3.9
|
27.0
|
1.0
|
ND2
|
C:ASN26
|
4.0
|
35.2
|
1.0
|
OD2
|
C:ASP24
|
4.0
|
22.9
|
1.0
|
N
|
C:LYS30
|
4.0
|
25.0
|
1.0
|
N
|
C:ASN26
|
4.0
|
31.2
|
1.0
|
N
|
C:GLY25
|
4.1
|
26.0
|
1.0
|
CA
|
C:LYS30
|
4.1
|
25.5
|
1.0
|
CA
|
C:ASP24
|
4.1
|
24.9
|
1.0
|
CB
|
C:ASP24
|
4.2
|
25.1
|
1.0
|
N
|
C:ASP28
|
4.3
|
28.6
|
1.0
|
CB
|
C:LYS30
|
4.3
|
29.9
|
1.0
|
O
|
C:ASP77
|
4.4
|
27.6
|
1.0
|
CB
|
C:ASP28
|
4.4
|
30.0
|
1.0
|
C
|
C:GLY31
|
4.4
|
25.0
|
1.0
|
N
|
C:GLY31
|
4.4
|
25.1
|
1.0
|
CB
|
C:ASN26
|
4.5
|
31.6
|
1.0
|
OD1
|
C:ASP32
|
4.5
|
30.0
|
1.0
|
C
|
C:ASP24
|
4.5
|
25.1
|
1.0
|
N
|
C:GLY27
|
4.6
|
32.7
|
1.0
|
N
|
C:ASP32
|
4.6
|
24.8
|
1.0
|
CA
|
C:GLY31
|
4.6
|
24.8
|
1.0
|
O
|
C:GLY31
|
4.6
|
24.6
|
1.0
|
CA
|
C:ASN26
|
4.7
|
33.3
|
1.0
|
CA
|
C:ASP28
|
4.8
|
28.6
|
1.0
|
N
|
C:GLY29
|
4.8
|
28.2
|
1.0
|
CA
|
C:ASP32
|
4.9
|
26.1
|
1.0
|
C
|
C:ASN26
|
4.9
|
33.6
|
1.0
|
C
|
C:ASP28
|
5.0
|
29.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 4wf7
Go back to
Magnesium Binding Sites List in 4wf7
Magnesium binding site 4 out
of 4 in the Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in the Intramolecular Isomerization Catalysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:26.7
occ:1.00
|
O
|
D:LYS30
|
2.2
|
26.8
|
1.0
|
OD2
|
D:ASP32
|
2.2
|
31.5
|
1.0
|
OD1
|
D:ASN26
|
2.2
|
32.9
|
1.0
|
O
|
D:HOH825
|
2.4
|
32.1
|
1.0
|
OD1
|
D:ASP28
|
2.4
|
28.2
|
1.0
|
OD1
|
D:ASP24
|
2.5
|
26.6
|
1.0
|
CG
|
D:ASP28
|
3.2
|
31.8
|
1.0
|
CG
|
D:ASP24
|
3.3
|
26.1
|
1.0
|
CG
|
D:ASN26
|
3.4
|
33.4
|
1.0
|
C
|
D:LYS30
|
3.4
|
28.0
|
1.0
|
CG
|
D:ASP32
|
3.4
|
30.3
|
1.0
|
OD2
|
D:ASP28
|
3.4
|
32.2
|
1.0
|
CB
|
D:ASP32
|
3.9
|
27.6
|
1.0
|
ND2
|
D:ASN26
|
4.0
|
35.2
|
1.0
|
OD2
|
D:ASP24
|
4.0
|
27.2
|
1.0
|
N
|
D:LYS30
|
4.0
|
28.0
|
1.0
|
CA
|
D:LYS30
|
4.1
|
28.8
|
1.0
|
N
|
D:ASN26
|
4.1
|
31.2
|
1.0
|
CB
|
D:ASP24
|
4.1
|
25.2
|
1.0
|
CA
|
D:ASP24
|
4.2
|
25.5
|
1.0
|
N
|
D:GLY25
|
4.2
|
29.2
|
1.0
|
CB
|
D:LYS30
|
4.2
|
31.6
|
1.0
|
N
|
D:ASP28
|
4.3
|
29.0
|
1.0
|
N
|
D:GLY31
|
4.4
|
27.5
|
1.0
|
O
|
D:ASP77
|
4.4
|
34.1
|
1.0
|
OD1
|
D:ASP32
|
4.4
|
28.9
|
1.0
|
N
|
D:GLY27
|
4.5
|
32.0
|
1.0
|
C
|
D:GLY31
|
4.5
|
28.6
|
1.0
|
CB
|
D:ASP28
|
4.5
|
29.8
|
1.0
|
C
|
D:ASP24
|
4.5
|
27.7
|
1.0
|
CB
|
D:ASN26
|
4.5
|
32.4
|
1.0
|
N
|
D:ASP32
|
4.7
|
25.8
|
1.0
|
CA
|
D:GLY31
|
4.7
|
28.9
|
1.0
|
CA
|
D:ASN26
|
4.7
|
33.0
|
1.0
|
O
|
D:GLY31
|
4.8
|
28.1
|
1.0
|
CA
|
D:ASP28
|
4.8
|
29.0
|
1.0
|
C
|
D:ASN26
|
4.9
|
33.9
|
1.0
|
N
|
D:GLY29
|
4.9
|
29.4
|
1.0
|
CA
|
D:ASP32
|
4.9
|
26.3
|
1.0
|
|
Reference:
Y.L.Wang,
S.Y.Chow,
Y.T.Lin,
Y.C.Hsieh,
G.C.Lee,
S.H.Liaw.
Structures of Trehalose Synthase From Deinococcus Radiodurans Reveal That A Closed Conformation Is Involved in Catalysis of the Intramolecular Isomerization. Acta Crystallogr.,Sect.D V. 70 3144 2014.
ISSN: ESSN 1399-0047
PubMed: 25478833
DOI: 10.1107/S1399004714022500
Page generated: Tue Aug 20 13:12:33 2024
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