Atomistry » Magnesium » PDB 2xni-2xzs » 2xta
Atomistry »
  Magnesium »
    PDB 2xni-2xzs »
      2xta »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy