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Magnesium in PDB 2yic: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form):
4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form), PDB code: 2yic 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) 39.20 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.539, 83.244, 158.610, 99.48, 99.06, 101.25
R / Rfree (%) 18.84 / 21.08

Other elements in 2yic:

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

Magnesium binding site 1 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (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 (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:10.3
occ:1.00
 O2A A:TPP2001 2.0 13.6 1.0
O A:HOH3083 2.1 17.8 1.0
OD1 A:ASP645 2.1 25.6 1.0
OD1 A:ASN678 2.1 22.0 1.0
O A:ILE680 2.2 19.2 1.0
O2B A:TPP2001 2.2 15.5 1.0
CG A:ASP645 3.1 24.4 1.0
CG A:ASN678 3.2 25.4 1.0
PA A:TPP2001 3.2 16.1 1.0
PB A:TPP2001 3.3 17.3 1.0
O3A A:TPP2001 3.4 16.1 1.0
C A:ILE680 3.4 18.8 1.0
OD2 A:ASP645 3.5 31.2 1.0
ND2 A:ASN678 3.7 16.0 1.0
O3B A:TPP2001 3.9 14.5 1.0
N A:ASP645 3.9 13.1 1.0
O7 A:TPP2001 4.0 17.0 1.0
N A:ILE680 4.1 17.2 1.0
N A:ASN678 4.2 17.3 1.0
N A:GLY681 4.3 12.2 1.0
O A:VAL676 4.3 18.6 1.0
CA A:GLY681 4.4 11.2 1.0
CB A:ASP645 4.4 12.4 1.0
N A:ALA646 4.4 11.4 1.0
CA A:ILE680 4.4 17.1 1.0
O1A A:TPP2001 4.4 16.5 1.0
O A:HOH3048 4.4 17.8 1.0
CB A:ASN678 4.5 8.8 1.0
O1B A:TPP2001 4.6 20.2 1.0
CA A:ASP645 4.6 11.6 1.0
N A:GLN679 4.6 17.9 1.0
CG2 A:ILE680 4.7 20.8 1.0
CA A:ASN678 4.7 15.7 1.0
C A:GLY644 4.7 19.0 1.0
CA A:GLY644 4.7 17.6 1.0
C A:ASN678 4.8 21.5 1.0

Magnesium binding site 2 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (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 (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:11.8
occ:1.00
 O2A B:TPP2001 2.1 10.4 1.0
OD1 B:ASP645 2.1 22.5 1.0
OD1 B:ASN678 2.1 21.6 1.0
O2B B:TPP2001 2.2 15.3 1.0
O B:HOH3084 2.2 10.7 1.0
O B:ILE680 2.2 21.3 1.0
CG B:ASP645 3.1 22.5 1.0
PA B:TPP2001 3.2 12.3 1.0
CG B:ASN678 3.2 26.3 1.0
PB B:TPP2001 3.3 16.2 1.0
O3A B:TPP2001 3.3 15.6 1.0
C B:ILE680 3.4 21.2 1.0
OD2 B:ASP645 3.6 23.2 1.0
ND2 B:ASN678 3.6 11.9 1.0
N B:ASP645 3.9 13.8 1.0
O3B B:TPP2001 3.9 16.4 1.0
O7 B:TPP2001 4.0 15.8 1.0
N B:ILE680 4.1 17.9 1.0
N B:ASN678 4.2 15.3 1.0
N B:GLY681 4.3 18.3 1.0
CA B:GLY681 4.3 17.9 1.0
CB B:ASP645 4.3 13.5 1.0
O B:VAL676 4.4 17.1 1.0
N B:ALA646 4.4 14.3 1.0
O1A B:TPP2001 4.4 10.9 1.0
CA B:ILE680 4.4 16.5 1.0
O B:HOH3104 4.4 15.7 1.0
CB B:ASN678 4.5 16.1 1.0
O1B B:TPP2001 4.6 14.1 1.0
CA B:ASP645 4.6 13.1 1.0
N B:GLN679 4.6 19.8 1.0
CG2 B:ILE680 4.7 17.1 1.0
C B:GLY644 4.7 15.6 1.0
CA B:ASN678 4.7 16.3 1.0
CA B:GLY644 4.7 16.1 1.0
C B:ASN678 4.8 22.9 1.0

Magnesium binding site 3 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (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 (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:10.4
occ:1.00
 OD1 C:ASN678 2.1 17.6 1.0
O C:ILE680 2.1 20.6 1.0
O2A C:TPP2001 2.1 13.4 1.0
OD1 C:ASP645 2.2 20.3 1.0
O2B C:TPP2001 2.2 20.5 1.0
O C:HOH3073 2.2 17.8 1.0
CG C:ASN678 3.1 24.7 1.0
CG C:ASP645 3.1 24.7 1.0
PA C:TPP2001 3.3 15.3 1.0
PB C:TPP2001 3.3 17.6 1.0
C C:ILE680 3.3 20.2 1.0
O3A C:TPP2001 3.4 17.3 1.0
OD2 C:ASP645 3.6 29.2 1.0
ND2 C:ASN678 3.6 15.9 1.0
O3B C:TPP2001 3.9 18.6 1.0
N C:ASP645 4.0 12.7 1.0
O7 C:TPP2001 4.1 18.2 1.0
N C:ILE680 4.1 15.6 1.0
N C:ASN678 4.2 17.8 1.0
N C:GLY681 4.2 16.4 1.0
CA C:GLY681 4.3 15.9 1.0
CA C:ILE680 4.3 15.5 1.0
O C:HOH3100 4.3 24.9 1.0
O C:VAL676 4.4 22.8 1.0
CB C:ASP645 4.4 12.8 1.0
N C:ALA646 4.4 12.7 1.0
CB C:ASN678 4.4 14.9 1.0
O1A C:TPP2001 4.5 14.8 1.0
CG2 C:ILE680 4.6 16.4 1.0
O1B C:TPP2001 4.6 19.9 1.0
N C:GLN679 4.6 16.0 1.0
CA C:ASN678 4.7 17.2 1.0
CA C:ASP645 4.7 11.6 1.0
C C:ASN678 4.7 19.9 1.0
C C:GLY644 4.8 16.0 1.0
CA C:GLY644 4.8 14.4 1.0

Magnesium binding site 4 out of 4 in 2yic

Go back to Magnesium Binding Sites List in 2yic
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (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 (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:12.5
occ:1.00
 O2A D:TPP2001 2.1 15.2 1.0
O2B D:TPP2001 2.1 15.7 1.0
O D:ILE680 2.1 18.1 1.0
OD1 D:ASN678 2.1 17.8 1.0
OD1 D:ASP645 2.2 21.7 1.0
O D:HOH3067 2.3 19.2 1.0
CG D:ASP645 3.2 22.5 1.0
PA D:TPP2001 3.2 15.2 1.0
CG D:ASN678 3.2 24.1 1.0
PB D:TPP2001 3.2 16.0 1.0
O3A D:TPP2001 3.3 19.7 1.0
C D:ILE680 3.3 19.1 1.0
OD2 D:ASP645 3.6 21.4 1.0
ND2 D:ASN678 3.6 16.4 1.0
O3B D:TPP2001 3.9 16.6 1.0
O7 D:TPP2001 4.0 16.7 1.0
N D:ASP645 4.0 14.0 1.0
N D:ILE680 4.1 14.2 1.0
O D:HOH3084 4.2 20.0 1.0
N D:GLY681 4.2 17.4 1.0
CA D:GLY681 4.2 17.4 1.0
N D:ASN678 4.3 15.6 1.0
CA D:ILE680 4.3 13.6 1.0
N D:ALA646 4.4 12.7 1.0
O1A D:TPP2001 4.4 12.4 1.0
O D:VAL676 4.4 22.8 1.0
CB D:ASP645 4.4 15.5 1.0
CB D:ASN678 4.5 20.1 1.0
O1B D:TPP2001 4.5 17.0 1.0
CG2 D:ILE680 4.6 14.4 1.0
N D:GLN679 4.7 15.2 1.0
CA D:ASP645 4.7 14.2 1.0
CA D:ASN678 4.7 15.6 1.0
C D:GLY644 4.8 16.9 1.0
CA D:GLY644 4.8 15.5 1.0
C D:ASN678 4.8 18.4 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 07:32:19 2024

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