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Magnesium in PDB 2xta: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form):
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 Acetyl-Coa (Triclinic Form), PDB code: 2xta 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) 78.11 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.550, 83.580, 160.070, 99.59, 98.94, 100.68
R / Rfree (%) 18.8 / 21.36

Other elements in 2xta:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form) 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 Acetyl-Coa (Triclinic Form) (pdb code 2xta). 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 Acetyl-Coa (Triclinic Form), PDB code: 2xta:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2xta

Go back to Magnesium Binding Sites List in 2xta
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)


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 Acetyl-Coa (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:18.8
occ:1.00
 O2A A:TPP2001 2.0 22.6 1.0
O A:ILE680 2.0 28.7 1.0
O2B A:TPP2001 2.1 26.0 1.0
OD1 A:ASN678 2.1 29.6 1.0
O A:HOH3046 2.2 20.0 1.0
OD1 A:ASP645 2.2 25.3 1.0
CG A:ASN678 3.2 34.3 1.0
PA A:TPP2001 3.2 23.1 1.0
PB A:TPP2001 3.2 26.4 1.0
C A:ILE680 3.3 28.5 1.0
O3A A:TPP2001 3.3 33.5 1.0
CG A:ASP645 3.3 27.3 1.0
ND2 A:ASN678 3.6 21.6 1.0
O3B A:TPP2001 3.8 24.0 1.0
OD2 A:ASP645 3.9 25.0 1.0
O7 A:TPP2001 4.1 30.0 1.0
N A:ILE680 4.1 26.9 1.0
N A:ASP645 4.1 24.4 1.0
N A:GLY681 4.1 23.2 1.0
O A:HOH3189 4.2 35.8 1.0
CA A:GLY681 4.2 23.0 1.0
CA A:ILE680 4.3 26.0 1.0
O1A A:TPP2001 4.3 22.9 1.0
N A:ASN678 4.4 27.1 1.0
CB A:ASN678 4.5 23.8 1.0
N A:ALA646 4.5 22.4 1.0
O A:VAL676 4.5 32.2 1.0
CB A:ASP645 4.5 24.0 1.0
O1B A:TPP2001 4.5 35.5 1.0
CG2 A:ILE680 4.6 27.7 1.0
N A:GLN679 4.7 26.4 1.0
CA A:ASN678 4.8 26.0 1.0
CA A:ASP645 4.8 23.2 1.0
C A:ASN678 4.8 29.6 1.0
CA A:GLY644 4.9 24.6 1.0
C A:GLY644 4.9 28.1 1.0

Magnesium binding site 2 out of 4 in 2xta

Go back to Magnesium Binding Sites List in 2xta
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)


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 Acetyl-Coa (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:23.3
occ:1.00
 O B:ILE680 2.0 28.2 1.0
OD1 B:ASN678 2.0 28.3 1.0
O2A B:TPP2001 2.1 33.6 1.0
O2B B:TPP2001 2.1 18.1 1.0
OD1 B:ASP645 2.1 28.0 1.0
O B:HOH3047 2.1 19.4 1.0
CG B:ASN678 3.1 31.4 1.0
C B:ILE680 3.2 30.4 1.0
PA B:TPP2001 3.2 27.5 1.0
PB B:TPP2001 3.2 30.1 1.0
CG B:ASP645 3.3 32.4 1.0
O3A B:TPP2001 3.4 47.4 1.0
ND2 B:ASN678 3.5 24.5 1.0
OD2 B:ASP645 3.8 34.3 1.0
O3B B:TPP2001 3.9 27.1 1.0
N B:ASP645 4.0 24.3 1.0
N B:ILE680 4.0 25.8 1.0
O7 B:TPP2001 4.1 27.8 1.0
N B:GLY681 4.1 28.5 1.0
CA B:ILE680 4.2 25.2 1.0
CA B:GLY681 4.2 27.6 1.0
N B:ASN678 4.3 23.8 1.0
O B:HOH3184 4.3 29.6 1.0
CG2 B:ILE680 4.4 26.6 1.0
O1A B:TPP2001 4.4 34.9 1.0
CB B:ASN678 4.4 21.0 1.0
O B:VAL676 4.4 30.2 1.0
CB B:ASP645 4.5 27.9 1.0
N B:ALA646 4.5 25.6 1.0
O1B B:TPP2001 4.6 36.1 1.0
N B:GLN679 4.7 24.4 1.0
CA B:ASN678 4.7 24.7 1.0
CA B:ASP645 4.7 24.7 1.0
C B:ASN678 4.8 30.3 1.0
CA B:GLY644 4.8 24.6 1.0
C B:GLY644 4.8 27.3 1.0
CB B:ILE680 4.9 26.9 1.0

Magnesium binding site 3 out of 4 in 2xta

Go back to Magnesium Binding Sites List in 2xta
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)


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 Acetyl-Coa (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:18.4
occ:1.00
 OD1 C:ASN678 2.0 24.4 1.0
O C:ILE680 2.0 31.5 1.0
O2A C:TPP2001 2.0 25.4 1.0
OD1 C:ASP645 2.1 25.6 1.0
O C:HOH3049 2.2 19.1 1.0
O2B C:TPP2001 2.2 18.5 1.0
CG C:ASN678 3.1 33.0 1.0
CG C:ASP645 3.2 33.1 1.0
PA C:TPP2001 3.3 30.7 1.0
C C:ILE680 3.3 32.4 1.0
PB C:TPP2001 3.3 34.3 1.0
O3A C:TPP2001 3.4 41.6 1.0
ND2 C:ASN678 3.6 20.8 1.0
OD2 C:ASP645 3.8 32.8 1.0
O3B C:TPP2001 3.8 30.6 1.0
N C:ASP645 4.0 28.8 1.0
N C:ILE680 4.0 29.4 1.0
O7 C:TPP2001 4.1 33.0 1.0
N C:GLY681 4.2 29.4 1.0
CA C:ILE680 4.2 28.9 1.0
N C:ASN678 4.3 30.0 1.0
CA C:GLY681 4.3 27.7 1.0
O C:HOH3055 4.3 32.8 1.0
O1A C:TPP2001 4.4 38.0 1.0
CB C:ASP645 4.4 30.5 1.0
N C:ALA646 4.4 26.4 1.0
O C:VAL676 4.4 31.7 1.0
CB C:ASN678 4.4 23.8 1.0
CG2 C:ILE680 4.5 30.7 1.0
O1B C:TPP2001 4.6 35.4 1.0
CA C:ASP645 4.7 28.5 1.0
N C:GLN679 4.7 30.6 1.0
CA C:ASN678 4.7 29.0 1.0
C C:ASN678 4.8 34.4 1.0
CA C:GLY644 4.8 27.3 1.0
C C:GLY644 4.8 31.6 1.0

Magnesium binding site 4 out of 4 in 2xta

Go back to Magnesium Binding Sites List in 2xta
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)


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 Acetyl-Coa (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:23.1
occ:1.00
 O D:HOH3050 2.0 30.4 1.0
O2A D:TPP2001 2.1 22.0 1.0
OD1 D:ASN678 2.1 26.5 1.0
O2B D:TPP2001 2.1 22.7 1.0
OD1 D:ASP645 2.1 25.4 1.0
O D:ILE680 2.2 25.2 1.0
CG D:ASN678 3.1 34.1 1.0
PB D:TPP2001 3.2 27.8 1.0
PA D:TPP2001 3.2 29.8 1.0
CG D:ASP645 3.3 26.6 1.0
O3A D:TPP2001 3.3 40.8 1.0
C D:ILE680 3.4 24.9 1.0
ND2 D:ASN678 3.5 21.2 1.0
O3B D:TPP2001 3.7 30.6 1.0
OD2 D:ASP645 3.9 29.3 1.0
N D:ASP645 4.0 23.9 1.0
O7 D:TPP2001 4.1 24.1 1.0
N D:ILE680 4.1 23.9 1.0
O D:VAL676 4.3 26.0 1.0
N D:ASN678 4.3 24.4 1.0
O D:HOH3183 4.3 28.3 1.0
O1A D:TPP2001 4.3 27.8 1.0
N D:GLY681 4.3 19.6 1.0
CA D:ILE680 4.4 23.5 1.0
CA D:GLY681 4.4 19.6 1.0
CB D:ASN678 4.4 21.1 1.0
CB D:ASP645 4.4 23.4 1.0
N D:ALA646 4.5 19.2 1.0
O1B D:TPP2001 4.5 47.8 1.0
CG2 D:ILE680 4.6 24.4 1.0
CA D:ASP645 4.7 23.0 1.0
CA D:ASN678 4.7 24.8 1.0
CA D:GLY644 4.8 21.3 1.0
C D:GLY644 4.8 25.9 1.0
C D:ASN678 4.8 30.1 1.0
N D:GLN679 4.8 24.0 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 07:17:49 2024

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