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Magnesium in PDB 6i2r: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara:
1.2.4.2; 2.2.1.5; 2.3.1.61; 4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara, PDB code: 6i2r was solved by T.Wagner, M.Bellinzoni, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.15 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.745, 143.145, 167.106, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.9

Other elements in 6i2r:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara (pdb code 6i2r). 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 the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara, PDB code: 6i2r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6i2r

Go back to Magnesium Binding Sites List in 6i2r
Magnesium binding site 1 out of 2 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara


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 Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:14.7
occ:1.00
O A:ILE680 2.0 22.9 1.0
O2A A:TPP2001 2.0 19.8 1.0
O2B A:TPP2001 2.0 22.6 1.0
OD1 A:ASP645 2.1 29.4 1.0
OD1 A:ASN678 2.1 18.1 1.0
O A:HOH2202 2.2 17.2 1.0
CG A:ASP645 3.1 29.1 1.0
PB A:TPP2001 3.2 22.6 1.0
CG A:ASN678 3.2 26.3 1.0
PA A:TPP2001 3.2 21.5 1.0
C A:ILE680 3.3 25.4 1.0
O3A A:TPP2001 3.3 25.3 1.0
OD2 A:ASP645 3.6 32.2 1.0
ND2 A:ASN678 3.6 20.4 1.0
O1B A:TPP2001 3.9 19.5 1.0
O7 A:TPP2001 4.0 21.9 1.0
N A:ILE680 4.1 23.1 1.0
N A:ASP645 4.1 22.2 1.0
N A:GLY681 4.1 22.1 1.0
CA A:GLY681 4.1 21.1 1.0
O A:HOH2237 4.2 26.7 1.0
CA A:ILE680 4.3 21.8 1.0
CB A:ASP645 4.4 22.9 1.0
N A:ASN678 4.4 20.5 1.0
O1A A:TPP2001 4.4 27.5 1.0
N A:ALA646 4.4 20.7 1.0
O A:VAL676 4.4 26.8 1.0
O3B A:TPP2001 4.5 25.4 1.0
CB A:ASN678 4.5 19.6 1.0
CG2 A:ILE680 4.6 26.1 1.0
CA A:ASP645 4.7 21.5 1.0
N A:GLN679 4.7 20.1 1.0
CA A:ASN678 4.8 19.5 1.0
C A:ASN678 4.8 22.9 1.0
C A:GLY644 4.9 25.6 1.0
CA A:GLY644 4.9 23.7 1.0

Magnesium binding site 2 out of 2 in 6i2r

Go back to Magnesium Binding Sites List in 6i2r
Magnesium binding site 2 out of 2 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara


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 Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:17.8
occ:1.00
OD1 C:ASP645 2.0 25.2 1.0
O C:ILE680 2.0 19.1 1.0
OD1 C:ASN678 2.1 27.8 1.0
O1A C:TPP2001 2.1 20.2 1.0
O3B C:TPP2001 2.1 18.9 1.0
O C:HOH2147 2.1 22.3 1.0
CG C:ASP645 3.1 27.0 1.0
CG C:ASN678 3.1 22.7 1.0
PB C:TPP2001 3.2 23.3 1.0
PA C:TPP2001 3.3 20.6 1.0
C C:ILE680 3.3 20.5 1.0
O3A C:TPP2001 3.4 23.8 1.0
ND2 C:ASN678 3.5 14.2 1.0
OD2 C:ASP645 3.5 33.4 1.0
O2B C:TPP2001 3.9 25.3 1.0
N C:ILE680 4.0 18.8 1.0
N C:ASP645 4.1 20.3 1.0
O7 C:TPP2001 4.1 24.3 1.0
N C:GLY681 4.2 17.1 1.0
CA C:GLY681 4.2 17.2 1.0
N C:ASN678 4.2 21.9 1.0
CA C:ILE680 4.3 18.1 1.0
O C:HOH2241 4.3 23.2 1.0
CB C:ASP645 4.3 18.4 1.0
O C:VAL676 4.4 24.2 1.0
CB C:ASN678 4.4 21.7 1.0
O2A C:TPP2001 4.4 25.4 1.0
N C:ALA646 4.5 17.4 1.0
O1B C:TPP2001 4.5 22.4 1.0
CG2 C:ILE680 4.6 23.4 1.0
N C:GLN679 4.6 23.2 1.0
CA C:ASN678 4.7 22.1 1.0
CA C:ASP645 4.7 18.7 1.0
C C:ASN678 4.7 27.2 1.0
CA C:GLY644 4.9 21.5 1.0
C C:GLY644 4.9 23.1 1.0

Reference:

T.Wagner, G.Andre-Leroux, V.Hindie, N.Barilone, M.N.Lisa, S.Hoos, B.Raynal, B.Vulliez-Le Normand, H.M.O'hare, M.Bellinzoni, P.M.Alzari. Structural Insights Into the Functional Versatility of An Fha Domain Protein in Mycobacterial Signaling. Sci.Signal. V. 12 2019.
ISSN: ESSN 1937-9145
PubMed: 31064884
DOI: 10.1126/SCISIGNAL.AAV9504
Page generated: Tue Oct 1 02:56:48 2024

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