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Magnesium in PDB 2y0p: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate and Acetyl-Coa

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate and Acetyl-Coa

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate and Acetyl-Coa:
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 and Acetyl-Coa, PDB code: 2y0p 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) 35.14 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 81.062, 81.953, 161.876, 99.26, 97.09, 100.58
R / Rfree (%) 19.68 / 22.02

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 and Acetyl-Coa (pdb code 2y0p). 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 and Acetyl-Coa, PDB code: 2y0p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2y0p

Go back to Magnesium Binding Sites List in 2y0p
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 and Acetyl-Coa


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

b:17.2
occ:1.00
 O A:ILE680 1.9 27.3 1.0
OD1 A:ASN678 2.0 27.5 1.0
OD1 A:ASP645 2.0 34.8 1.0
O2A A:TD72001 2.1 19.6 1.0
O3B A:TD72001 2.2 23.5 1.0
O A:HOH2036 2.4 18.7 1.0
CG A:ASN678 3.1 36.8 1.0
CG A:ASP645 3.1 35.4 1.0
C A:ILE680 3.2 29.0 1.0
PB A:TD72001 3.2 32.4 1.0
PA A:TD72001 3.3 25.9 1.0
O3A A:TD72001 3.4 32.4 1.0
ND2 A:ASN678 3.6 23.1 1.0
OD2 A:ASP645 3.6 41.3 1.0
N A:ILE680 3.9 27.8 1.0
O2B A:TD72001 4.0 37.7 1.0
N A:ASP645 4.1 25.9 1.0
N A:GLY681 4.1 27.4 1.0
CA A:ILE680 4.1 27.8 1.0
CA A:GLY681 4.3 27.4 1.0
O7 A:TD72001 4.3 24.9 1.0
CG2 A:ILE680 4.3 30.8 1.0
N A:ASN678 4.3 27.8 1.0
O A:HOH2041 4.4 33.0 1.0
CB A:ASP645 4.4 27.2 1.0
CB A:ASN678 4.4 30.1 1.0
O1A A:TD72001 4.4 16.3 1.0
O A:VAL676 4.5 34.0 1.0
N A:ALA646 4.5 25.8 1.0
O1B A:TD72001 4.5 23.6 1.0
CA A:ASN678 4.7 27.9 1.0
CA A:ASP645 4.7 25.2 1.0
C A:ASN678 4.7 30.4 1.0
N A:GLN679 4.7 25.5 1.0
CB A:ILE680 4.8 31.9 1.0
C A:GLY644 4.9 27.3 1.0
CA A:GLY644 4.9 22.9 1.0

Magnesium binding site 2 out of 4 in 2y0p

Go back to Magnesium Binding Sites List in 2y0p
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 and Acetyl-Coa


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

b:14.9
occ:1.00
 OD1 B:ASN678 2.0 30.8 1.0
OD1 B:ASP645 2.0 35.1 1.0
O B:ILE680 2.0 22.9 1.0
O3B B:TD72001 2.2 27.4 1.0
O2A B:TD72001 2.2 26.3 1.0
O B:HOH2044 2.3 13.5 1.0
CG B:ASN678 3.1 37.6 1.0
CG B:ASP645 3.1 33.0 1.0
PB B:TD72001 3.2 26.4 1.0
C B:ILE680 3.3 24.9 1.0
PA B:TD72001 3.3 24.0 1.0
O3A B:TD72001 3.4 29.9 1.0
ND2 B:ASN678 3.6 31.1 1.0
OD2 B:ASP645 3.7 32.4 1.0
O2B B:TD72001 3.9 20.0 1.0
N B:ILE680 4.0 23.3 1.0
N B:ASP645 4.0 23.5 1.0
CA B:ILE680 4.2 23.1 1.0
N B:GLY681 4.2 23.6 1.0
N B:ASN678 4.2 23.9 1.0
O B:VAL676 4.3 29.7 1.0
CB B:ASN678 4.3 25.1 1.0
CG2 B:ILE680 4.4 25.6 1.0
CB B:ASP645 4.4 24.8 1.0
O7 B:TD72001 4.4 19.9 1.0
O1A B:TD72001 4.4 21.6 1.0
CA B:GLY681 4.4 23.3 1.0
O B:HOH2050 4.4 21.8 1.0
N B:ALA646 4.5 23.5 1.0
O1B B:TD72001 4.6 18.5 1.0
CA B:ASN678 4.6 23.5 1.0
C B:ASN678 4.7 27.0 1.0
CA B:ASP645 4.7 23.1 1.0
N B:GLN679 4.7 20.9 1.0
CA B:GLY644 4.9 21.2 1.0
C B:GLY644 4.9 26.0 1.0
CB B:ILE680 4.9 26.4 1.0

Magnesium binding site 3 out of 4 in 2y0p

Go back to Magnesium Binding Sites List in 2y0p
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 and Acetyl-Coa


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

b:16.0
occ:1.00
 OD1 C:ASP645 1.9 30.2 1.0
OD1 C:ASN678 2.0 28.8 1.0
O3B C:TD72001 2.2 25.9 1.0
O2A C:TD72001 2.2 20.4 1.0
O C:ILE680 2.3 29.6 1.0
O C:HOH2033 2.6 22.0 1.0
CG C:ASN678 3.0 37.4 1.0
CG C:ASP645 3.1 31.9 1.0
PB C:TD72001 3.2 41.3 1.0
O3A C:TD72001 3.3 49.0 1.0
PA C:TD72001 3.3 29.2 1.0
ND2 C:ASN678 3.5 31.2 1.0
C C:ILE680 3.5 30.9 1.0
OD2 C:ASP645 3.7 32.5 1.0
O2B C:TD72001 3.8 23.1 1.0
N C:ASP645 3.9 27.2 1.0
O C:VAL676 4.1 30.2 1.0
N C:ASN678 4.2 29.0 1.0
N C:ILE680 4.2 27.1 1.0
CB C:ASP645 4.3 27.6 1.0
CB C:ASN678 4.3 29.6 1.0
O1A C:TD72001 4.3 21.9 1.0
CA C:ILE680 4.4 27.0 1.0
O7 C:TD72001 4.4 30.9 1.0
N C:GLY681 4.5 29.6 1.0
N C:ALA646 4.5 27.6 1.0
O1B C:TD72001 4.5 23.1 1.0
CG2 C:ILE680 4.6 29.4 1.0
CA C:ASP645 4.6 26.4 1.0
O C:HOH2037 4.6 16.2 1.0
CA C:ASN678 4.6 29.0 1.0
CA C:GLY681 4.6 30.4 1.0
CA C:GLY644 4.7 28.0 1.0
C C:GLY644 4.7 31.4 1.0
C C:ASN678 4.7 32.9 1.0
N C:GLN679 4.8 28.6 1.0

Magnesium binding site 4 out of 4 in 2y0p

Go back to Magnesium Binding Sites List in 2y0p
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 and Acetyl-Coa


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

b:20.3
occ:1.00
 OD1 D:ASP645 1.9 34.9 1.0
OD1 D:ASN678 2.0 31.1 1.0
O2A D:TD72001 2.2 31.2 1.0
O D:ILE680 2.2 26.2 1.0
O3B D:TD72001 2.2 21.3 1.0
O D:HOH2036 2.6 22.6 1.0
CG D:ASN678 3.0 40.1 1.0
CG D:ASP645 3.1 34.6 1.0
PB D:TD72001 3.2 30.5 1.0
PA D:TD72001 3.4 35.2 1.0
O3A D:TD72001 3.4 33.4 1.0
C D:ILE680 3.4 27.5 1.0
ND2 D:ASN678 3.5 32.3 1.0
OD2 D:ASP645 3.7 37.0 1.0
O2B D:TD72001 3.9 33.9 1.0
N D:ASP645 3.9 28.1 1.0
N D:ILE680 4.1 24.2 1.0
N D:ASN678 4.1 25.5 1.0
O D:VAL676 4.2 32.9 1.0
CB D:ASP645 4.3 30.1 1.0
CB D:ASN678 4.3 27.0 1.0
CA D:ILE680 4.3 24.0 1.0
O1A D:TD72001 4.4 25.2 1.0
N D:GLY681 4.4 24.9 1.0
O7 D:TD72001 4.4 23.1 1.0
CG2 D:ILE680 4.5 25.9 1.0
N D:ALA646 4.5 28.0 1.0
CA D:ASP645 4.6 27.9 1.0
O D:HOH2051 4.6 33.0 1.0
CA D:ASN678 4.6 25.2 1.0
CA D:GLY681 4.6 25.1 1.0
O1B D:TD72001 4.6 22.4 1.0
C D:ASN678 4.7 27.8 1.0
N D:GLN679 4.7 23.9 1.0
CA D:GLY644 4.7 27.7 1.0
C D:GLY644 4.7 30.8 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: Sun Aug 10 16:35:45 2025

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