Magnesium in PDB 2yid: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate
Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate
All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate:
4.1.1.71;
Protein crystallography data
The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate, PDB code: 2yid
was solved by
T.Wagner,
M.Bellinzoni,
A.M.Wehenkel,
H.M.O'hare,
P.M.Alzari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.94 /
2.25
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.843,
82.287,
163.478,
99.23,
99.03,
100.63
|
R / Rfree (%)
|
19.2 /
22.34
|
Other elements in 2yid:
The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate
(pdb code 2yid). 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 the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate, PDB code: 2yid:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 2yid
Go back to
Magnesium Binding Sites List in 2yid
Magnesium binding site 1 out
of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate
![](/pictures/MG/pdb/yi/2yid-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/yi/2yid-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2002
b:12.0
occ:1.00
|
O2A
|
A:TD72001
|
2.0
|
15.9
|
1.0
|
OD1
|
A:ASN678
|
2.0
|
26.5
|
1.0
|
O3B
|
A:TD72001
|
2.0
|
11.3
|
1.0
|
O
|
A:ILE680
|
2.1
|
23.6
|
1.0
|
OD1
|
A:ASP645
|
2.1
|
19.6
|
1.0
|
O
|
A:HOH3047
|
2.2
|
14.9
|
1.0
|
CG
|
A:ASN678
|
3.0
|
30.3
|
1.0
|
PB
|
A:TD72001
|
3.0
|
17.7
|
1.0
|
PA
|
A:TD72001
|
3.1
|
18.1
|
1.0
|
O3A
|
A:TD72001
|
3.2
|
18.7
|
1.0
|
CG
|
A:ASP645
|
3.3
|
21.6
|
1.0
|
C
|
A:ILE680
|
3.3
|
23.6
|
1.0
|
ND2
|
A:ASN678
|
3.3
|
19.5
|
1.0
|
O2B
|
A:TD72001
|
3.6
|
21.3
|
1.0
|
OD2
|
A:ASP645
|
3.8
|
22.9
|
1.0
|
N
|
A:ASP645
|
4.0
|
13.9
|
1.0
|
O7
|
A:TD72001
|
4.1
|
20.7
|
1.0
|
N
|
A:GLY681
|
4.2
|
20.2
|
1.0
|
N
|
A:ILE680
|
4.2
|
20.3
|
1.0
|
CA
|
A:GLY681
|
4.2
|
19.4
|
1.0
|
O1A
|
A:TD72001
|
4.2
|
16.8
|
1.0
|
O
|
A:VAL676
|
4.3
|
27.3
|
1.0
|
O
|
A:HOH3024
|
4.3
|
24.1
|
1.0
|
CA
|
A:ILE680
|
4.3
|
19.6
|
1.0
|
CB
|
A:ASN678
|
4.4
|
12.5
|
1.0
|
O1B
|
A:TD72001
|
4.4
|
19.2
|
1.0
|
N
|
A:ASN678
|
4.4
|
13.4
|
1.0
|
N
|
A:ALA646
|
4.5
|
13.1
|
1.0
|
CB
|
A:ASP645
|
4.5
|
15.8
|
1.0
|
CG2
|
A:ILE680
|
4.5
|
20.7
|
1.0
|
CA
|
A:ASP645
|
4.7
|
13.8
|
1.0
|
CA
|
A:GLY644
|
4.7
|
17.1
|
1.0
|
C
|
A:GLY644
|
4.7
|
17.9
|
1.0
|
CA
|
A:ASN678
|
4.8
|
13.0
|
1.0
|
C
|
A:ASN678
|
4.9
|
19.0
|
1.0
|
N
|
A:GLN679
|
4.9
|
19.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 2yid
Go back to
Magnesium Binding Sites List in 2yid
Magnesium binding site 2 out
of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate
![](/pictures/MG/pdb/yi/2yid-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/yi/2yid-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2002
b:12.2
occ:1.00
|
O2A
|
B:TD72001
|
1.9
|
11.2
|
1.0
|
OD1
|
B:ASN678
|
2.0
|
20.6
|
1.0
|
OD1
|
B:ASP645
|
2.1
|
21.5
|
1.0
|
O
|
B:ILE680
|
2.1
|
17.9
|
1.0
|
O
|
B:HOH3050
|
2.2
|
11.2
|
1.0
|
O3B
|
B:TD72001
|
2.2
|
9.8
|
1.0
|
CG
|
B:ASN678
|
3.0
|
25.9
|
1.0
|
PA
|
B:TD72001
|
3.1
|
14.2
|
1.0
|
PB
|
B:TD72001
|
3.1
|
15.9
|
1.0
|
O3A
|
B:TD72001
|
3.2
|
18.2
|
1.0
|
CG
|
B:ASP645
|
3.2
|
23.9
|
1.0
|
C
|
B:ILE680
|
3.3
|
18.0
|
1.0
|
ND2
|
B:ASN678
|
3.3
|
16.8
|
1.0
|
O2B
|
B:TD72001
|
3.6
|
14.3
|
1.0
|
OD2
|
B:ASP645
|
3.8
|
24.7
|
1.0
|
N
|
B:ASP645
|
3.9
|
15.9
|
1.0
|
O7
|
B:TD72001
|
4.0
|
13.3
|
1.0
|
N
|
B:ILE680
|
4.2
|
17.1
|
1.0
|
N
|
B:GLY681
|
4.2
|
14.1
|
1.0
|
O1A
|
B:TD72001
|
4.2
|
11.4
|
1.0
|
O
|
B:VAL676
|
4.2
|
28.0
|
1.0
|
CA
|
B:GLY681
|
4.2
|
14.6
|
1.0
|
CA
|
B:ILE680
|
4.3
|
16.5
|
1.0
|
CB
|
B:ASN678
|
4.4
|
18.2
|
1.0
|
N
|
B:ASN678
|
4.4
|
16.1
|
1.0
|
CB
|
B:ASP645
|
4.4
|
18.0
|
1.0
|
N
|
B:ALA646
|
4.4
|
12.6
|
1.0
|
O
|
B:HOH3065
|
4.5
|
15.8
|
1.0
|
O1B
|
B:TD72001
|
4.5
|
15.0
|
1.0
|
CG2
|
B:ILE680
|
4.5
|
17.9
|
1.0
|
CA
|
B:ASP645
|
4.6
|
15.8
|
1.0
|
CA
|
B:GLY644
|
4.7
|
13.8
|
1.0
|
C
|
B:GLY644
|
4.7
|
18.6
|
1.0
|
CA
|
B:ASN678
|
4.7
|
16.3
|
1.0
|
C
|
B:ASN678
|
4.8
|
21.0
|
1.0
|
N
|
B:GLN679
|
4.9
|
16.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 2yid
Go back to
Magnesium Binding Sites List in 2yid
Magnesium binding site 3 out
of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate
![](/pictures/MG/pdb/yi/2yid-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/yi/2yid-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg2002
b:8.2
occ:1.00
|
OD1
|
C:ASN678
|
1.9
|
18.2
|
1.0
|
OD1
|
C:ASP645
|
2.0
|
19.7
|
1.0
|
O
|
C:ILE680
|
2.1
|
20.3
|
1.0
|
O3B
|
C:TD72001
|
2.1
|
13.3
|
1.0
|
O2A
|
C:TD72001
|
2.1
|
20.2
|
1.0
|
O
|
C:HOH3062
|
2.3
|
10.2
|
1.0
|
CG
|
C:ASN678
|
2.9
|
20.6
|
1.0
|
PB
|
C:TD72001
|
3.1
|
15.2
|
1.0
|
CG
|
C:ASP645
|
3.2
|
24.3
|
1.0
|
PA
|
C:TD72001
|
3.2
|
18.7
|
1.0
|
O3A
|
C:TD72001
|
3.3
|
18.8
|
1.0
|
C
|
C:ILE680
|
3.3
|
20.8
|
1.0
|
ND2
|
C:ASN678
|
3.3
|
19.2
|
1.0
|
O2B
|
C:TD72001
|
3.7
|
17.5
|
1.0
|
OD2
|
C:ASP645
|
3.7
|
26.1
|
1.0
|
N
|
C:ASP645
|
4.0
|
15.5
|
1.0
|
N
|
C:ILE680
|
4.1
|
17.6
|
1.0
|
N
|
C:GLY681
|
4.2
|
17.2
|
1.0
|
O7
|
C:TD72001
|
4.2
|
18.2
|
1.0
|
O
|
C:VAL676
|
4.2
|
20.1
|
1.0
|
CA
|
C:GLY681
|
4.2
|
17.8
|
1.0
|
CA
|
C:ILE680
|
4.3
|
17.3
|
1.0
|
CB
|
C:ASN678
|
4.3
|
9.0
|
1.0
|
N
|
C:ASN678
|
4.3
|
10.7
|
1.0
|
O1A
|
C:TD72001
|
4.4
|
17.5
|
1.0
|
CB
|
C:ASP645
|
4.4
|
15.3
|
1.0
|
O
|
C:HOH3034
|
4.4
|
18.2
|
1.0
|
CG2
|
C:ILE680
|
4.4
|
18.1
|
1.0
|
O1B
|
C:TD72001
|
4.5
|
18.7
|
1.0
|
N
|
C:ALA646
|
4.5
|
11.2
|
1.0
|
CA
|
C:ASN678
|
4.7
|
10.6
|
1.0
|
CA
|
C:ASP645
|
4.7
|
14.4
|
1.0
|
C
|
C:ASN678
|
4.7
|
18.6
|
1.0
|
N
|
C:GLN679
|
4.8
|
19.1
|
1.0
|
C
|
C:GLY644
|
4.8
|
16.4
|
1.0
|
CA
|
C:GLY644
|
4.8
|
13.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 2yid
Go back to
Magnesium Binding Sites List in 2yid
Magnesium binding site 4 out
of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate
![](/pictures/MG/pdb/yi/2yid-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/yi/2yid-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg2002
b:8.9
occ:1.00
|
O3B
|
D:TD72001
|
1.9
|
12.6
|
1.0
|
OD1
|
D:ASN678
|
2.0
|
20.5
|
1.0
|
O
|
D:ILE680
|
2.0
|
20.7
|
1.0
|
O2A
|
D:TD72001
|
2.1
|
11.8
|
1.0
|
OD1
|
D:ASP645
|
2.2
|
22.9
|
1.0
|
O
|
D:HOH3038
|
2.2
|
7.4
|
1.0
|
CG
|
D:ASN678
|
3.0
|
23.1
|
1.0
|
PB
|
D:TD72001
|
3.0
|
13.7
|
1.0
|
PA
|
D:TD72001
|
3.2
|
15.9
|
1.0
|
O3A
|
D:TD72001
|
3.2
|
14.5
|
1.0
|
C
|
D:ILE680
|
3.2
|
20.4
|
1.0
|
CG
|
D:ASP645
|
3.3
|
22.6
|
1.0
|
ND2
|
D:ASN678
|
3.3
|
18.6
|
1.0
|
O2B
|
D:TD72001
|
3.6
|
15.2
|
1.0
|
OD2
|
D:ASP645
|
3.8
|
20.9
|
1.0
|
O7
|
D:TD72001
|
4.1
|
18.5
|
1.0
|
N
|
D:ASP645
|
4.1
|
14.5
|
1.0
|
N
|
D:GLY681
|
4.1
|
16.9
|
1.0
|
N
|
D:ILE680
|
4.1
|
16.1
|
1.0
|
CA
|
D:GLY681
|
4.2
|
17.2
|
1.0
|
CA
|
D:ILE680
|
4.2
|
16.4
|
1.0
|
CB
|
D:ASN678
|
4.3
|
12.0
|
1.0
|
O1A
|
D:TD72001
|
4.4
|
9.8
|
1.0
|
O
|
D:HOH3021
|
4.4
|
17.8
|
1.0
|
O1B
|
D:TD72001
|
4.4
|
12.3
|
1.0
|
O
|
D:VAL676
|
4.4
|
25.1
|
1.0
|
CG2
|
D:ILE680
|
4.4
|
16.0
|
1.0
|
N
|
D:ASN678
|
4.4
|
10.9
|
1.0
|
N
|
D:ALA646
|
4.5
|
13.4
|
1.0
|
CB
|
D:ASP645
|
4.5
|
17.2
|
1.0
|
CA
|
D:ASN678
|
4.8
|
9.9
|
1.0
|
CA
|
D:ASP645
|
4.8
|
14.6
|
1.0
|
C
|
D:ASN678
|
4.8
|
17.0
|
1.0
|
CA
|
D:GLY644
|
4.8
|
14.4
|
1.0
|
C
|
D:GLY644
|
4.8
|
18.9
|
1.0
|
N
|
D:GLN679
|
4.9
|
16.1
|
1.0
|
CB
|
D:ILE680
|
5.0
|
18.9
|
1.0
|
|
Reference:
T.Wagner,
M.Bellinzoni,
A.M.Wehenkel,
H.M.O'hare,
P.M.Alzari.
Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism. Chem.Biol. V. 18 1011 2011.
ISSN: ISSN 1074-5521
PubMed: 21867916
DOI: 10.1016/J.CHEMBIOL.2011.06.004
Page generated: Wed Aug 14 07:32:22 2024
|