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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:

Calcium (Ca) 4 atoms

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


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 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


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 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


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 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


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 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

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