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Magnesium in PDB 2xt6: Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form)

Enzymatic activity of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form)

All present enzymatic activity of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form):
4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form), PDB code: 2xt6 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) 40.12 / 2.74
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 151.990, 247.720, 79.980, 90.00, 90.00, 90.00
R / Rfree (%) 18.54 / 22.36

Other elements in 2xt6:

The structure of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) (pdb code 2xt6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form), PDB code: 2xt6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2xt6

Go back to Magnesium Binding Sites List in 2xt6
Magnesium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic 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 Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:41.3
occ:1.00
 O A:HOH3017 2.0 46.2 1.0
O2A A:TPP2001 2.0 57.0 1.0
OD1 A:ASP645 2.1 39.8 1.0
OD1 A:ASN678 2.1 47.6 1.0
O A:ILE680 2.2 48.6 1.0
O2B A:TPP2001 2.3 57.9 1.0
CG A:ASN678 3.2 59.9 1.0
PB A:TPP2001 3.2 61.6 1.0
PA A:TPP2001 3.2 50.4 1.0
CG A:ASP645 3.2 46.3 1.0
O3A A:TPP2001 3.3 66.7 1.0
C A:ILE680 3.4 51.0 1.0
O3B A:TPP2001 3.6 60.1 1.0
ND2 A:ASN678 3.6 56.4 1.0
N A:ASP645 3.9 45.6 1.0
OD2 A:ASP645 4.0 57.3 1.0
O7 A:TPP2001 4.2 74.4 1.0
N A:ILE680 4.3 48.2 1.0
CB A:ASP645 4.3 45.0 1.0
N A:ASN678 4.3 49.1 1.0
O1A A:TPP2001 4.3 54.6 1.0
O A:VAL676 4.3 52.5 1.0
N A:GLY681 4.3 47.0 1.0
CA A:GLY681 4.4 46.8 1.0
N A:ALA646 4.4 35.6 1.0
CA A:ILE680 4.4 48.7 1.0
CB A:ASN678 4.5 44.1 1.0
CA A:ASP645 4.5 43.0 1.0
O A:HOH3054 4.6 38.0 1.0
CG2 A:ILE680 4.7 52.7 1.0
C A:GLY644 4.7 49.6 1.0
O1B A:TPP2001 4.7 49.7 1.0
CA A:GLY644 4.7 46.5 1.0
CA A:ASN678 4.8 47.2 1.0
C A:ASN678 4.9 51.0 1.0
N A:GLN679 4.9 47.0 1.0

Magnesium binding site 2 out of 2 in 2xt6

Go back to Magnesium Binding Sites List in 2xt6
Magnesium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic 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 Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:32.1
occ:1.00
 O2A B:TPP2001 2.0 35.1 1.0
O B:ILE680 2.0 43.2 1.0
OD1 B:ASN678 2.1 47.7 1.0
OD1 B:ASP645 2.2 47.5 1.0
O B:HOH3062 2.3 40.8 1.0
O2B B:TPP2001 2.4 34.5 1.0
CG B:ASP645 2.9 49.3 1.0
OD2 B:ASP645 3.1 48.5 1.0
CG B:ASN678 3.2 60.6 1.0
C B:ILE680 3.3 45.2 1.0
PA B:TPP2001 3.3 44.5 1.0
PB B:TPP2001 3.3 45.2 1.0
O3A B:TPP2001 3.4 33.3 1.0
ND2 B:ASN678 3.7 51.8 1.0
O3B B:TPP2001 3.9 36.8 1.0
N B:ASP645 4.0 41.2 1.0
N B:ILE680 4.1 41.9 1.0
N B:GLY681 4.1 42.2 1.0
CA B:GLY681 4.2 42.2 1.0
O7 B:TPP2001 4.2 43.1 1.0
CB B:ASP645 4.3 42.4 1.0
CA B:ILE680 4.3 41.9 1.0
N B:ASN678 4.3 42.9 1.0
N B:ALA646 4.4 38.4 1.0
O1A B:TPP2001 4.4 32.9 1.0
O B:HOH3021 4.5 41.6 1.0
CB B:ASN678 4.5 42.0 1.0
O B:VAL676 4.5 46.2 1.0
CG2 B:ILE680 4.6 47.1 1.0
CA B:ASP645 4.6 40.1 1.0
N B:GLN679 4.7 39.9 1.0
CA B:ASN678 4.7 42.3 1.0
O1B B:TPP2001 4.8 41.0 1.0
C B:ASN678 4.8 45.4 1.0
C B:GLY644 4.8 44.1 1.0
CA B:GLY644 4.9 38.3 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 07:17:27 2024

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