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Magnesium in PDB 3zht: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate:
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, First Post-Decarboxylation Intermediate From 2-Oxoadipate, PDB code: 3zht was solved by T.Wagner, N.Barilone, M.Bellinzoni, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.11 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.366, 83.800, 159.513, 99.76, 99.06, 100.61
R / Rfree (%) 22.3 / 24.57

Other elements in 3zht:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate 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 Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate (pdb code 3zht). 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 Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate, PDB code: 3zht:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3zht

Go back to Magnesium Binding Sites List in 3zht
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate


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, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:25.3
occ:1.00
O A:ILE680 2.0 32.7 1.0
O1B A:TD92001 2.1 27.7 1.0
OD1 A:ASP645 2.1 29.6 1.0
O2A A:TD92001 2.2 28.1 1.0
O A:HOH3074 2.2 22.6 1.0
OD1 A:ASN678 2.2 30.6 1.0
O3A A:TD92001 3.1 32.6 1.0
CG A:ASP645 3.2 30.3 1.0
CG A:ASN678 3.2 34.3 1.0
C A:ILE680 3.3 32.3 1.0
PA A:TD92001 3.3 29.5 1.0
PB A:TD92001 3.3 32.2 1.0
ND2 A:ASN678 3.7 25.0 1.0
OD2 A:ASP645 3.7 25.4 1.0
O2B A:TD92001 3.9 29.7 1.0
N A:ASP645 4.0 24.1 1.0
O5G A:TD92001 4.0 28.4 1.0
N A:ILE680 4.0 29.4 1.0
N A:GLY681 4.1 28.2 1.0
CA A:ILE680 4.2 29.2 1.0
CA A:GLY681 4.2 27.9 1.0
N A:ALA646 4.4 21.6 1.0
O A:HOH3041 4.4 32.2 1.0
N A:ASN678 4.4 29.1 1.0
CB A:ASP645 4.4 24.0 1.0
O1A A:TD92001 4.4 33.3 1.0
O A:VAL676 4.5 31.8 1.0
O3B A:TD92001 4.5 30.9 1.0
CB A:ASN678 4.5 30.0 1.0
CG2 A:ILE680 4.6 30.8 1.0
CA A:ASP645 4.7 22.4 1.0
N A:GLN679 4.8 31.6 1.0
C A:ASN678 4.8 33.9 1.0
CA A:ASN678 4.8 28.5 1.0
C A:GLY644 4.8 27.6 1.0
CA A:GLY644 4.9 25.9 1.0

Magnesium binding site 2 out of 4 in 3zht

Go back to Magnesium Binding Sites List in 3zht
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate


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, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:28.4
occ:1.00
O B:HOH3067 2.1 33.7 1.0
O B:ILE680 2.1 30.2 1.0
O2A B:TD92001 2.1 26.9 1.0
OD1 B:ASN678 2.1 29.2 1.0
O1B B:TD92001 2.2 20.4 1.0
OD1 B:ASP645 2.2 31.6 1.0
CG B:ASN678 3.1 32.6 1.0
O3A B:TD92001 3.2 32.9 1.0
CG B:ASP645 3.3 31.0 1.0
PB B:TD92001 3.3 29.0 1.0
C B:ILE680 3.3 30.9 1.0
PA B:TD92001 3.3 32.7 1.0
ND2 B:ASN678 3.6 20.3 1.0
O2B B:TD92001 3.8 27.8 1.0
OD2 B:ASP645 3.8 36.5 1.0
N B:ASP645 3.9 27.1 1.0
O5G B:TD92001 4.1 29.3 1.0
N B:ILE680 4.1 28.2 1.0
N B:GLY681 4.2 27.1 1.0
O B:HOH3083 4.3 34.0 1.0
O B:VAL676 4.3 34.0 1.0
CA B:ILE680 4.3 27.6 1.0
N B:ASN678 4.3 27.7 1.0
CA B:GLY681 4.3 26.1 1.0
N B:ALA646 4.4 27.2 1.0
CB B:ASP645 4.4 29.7 1.0
CB B:ASN678 4.4 25.2 1.0
O1A B:TD92001 4.5 31.9 1.0
O3B B:TD92001 4.5 35.9 1.0
CG2 B:ILE680 4.6 28.7 1.0
CA B:ASP645 4.6 27.2 1.0
CA B:ASN678 4.7 27.8 1.0
C B:GLY644 4.7 29.0 1.0
CA B:GLY644 4.8 27.3 1.0
N B:GLN679 4.8 26.0 1.0
C B:ASN678 4.8 31.8 1.0

Magnesium binding site 3 out of 4 in 3zht

Go back to Magnesium Binding Sites List in 3zht
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate


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 Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:22.8
occ:1.00
OD1 C:ASP645 2.1 35.8 1.0
O C:HOH3066 2.1 19.8 1.0
O C:ILE680 2.1 31.7 1.0
O2A C:TD92001 2.1 26.8 1.0
O1B C:TD92001 2.2 24.7 1.0
OD1 C:ASN678 2.2 34.6 1.0
O3A C:TD92001 3.0 33.5 1.0
CG C:ASP645 3.1 38.1 1.0
PA C:TD92001 3.2 32.6 1.0
CG C:ASN678 3.2 35.7 1.0
PB C:TD92001 3.3 33.1 1.0
C C:ILE680 3.4 32.4 1.0
ND2 C:ASN678 3.7 24.5 1.0
OD2 C:ASP645 3.7 35.6 1.0
O2B C:TD92001 3.8 30.7 1.0
N C:ASP645 3.9 26.2 1.0
O5G C:TD92001 4.1 29.6 1.0
N C:ILE680 4.1 28.7 1.0
N C:GLY681 4.2 29.5 1.0
N C:ALA646 4.3 22.5 1.0
CB C:ASP645 4.3 29.3 1.0
CA C:ILE680 4.3 28.5 1.0
CA C:GLY681 4.3 28.3 1.0
O C:VAL676 4.4 29.5 1.0
N C:ASN678 4.4 31.9 1.0
O C:HOH3039 4.4 34.6 1.0
O1A C:TD92001 4.4 39.0 1.0
CB C:ASN678 4.5 32.3 1.0
CA C:ASP645 4.5 26.9 1.0
O3B C:TD92001 4.5 33.5 1.0
CG2 C:ILE680 4.7 29.5 1.0
C C:GLY644 4.7 29.4 1.0
CA C:GLY644 4.7 26.7 1.0
CA C:ASN678 4.8 32.2 1.0
N C:GLN679 4.8 33.5 1.0
C C:ASN678 4.8 37.8 1.0
C C:ASP645 4.9 29.0 1.0

Magnesium binding site 4 out of 4 in 3zht

Go back to Magnesium Binding Sites List in 3zht
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate


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 Kgd, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:24.2
occ:1.00
O1B D:TD92001 2.0 18.9 1.0
O D:ILE680 2.1 28.0 1.0
O2A D:TD92001 2.1 24.2 1.0
O D:HOH3060 2.1 33.4 1.0
OD1 D:ASP645 2.1 30.4 1.0
OD1 D:ASN678 2.2 30.6 1.0
O3A D:TD92001 3.1 24.4 1.0
CG D:ASN678 3.2 28.6 1.0
CG D:ASP645 3.2 31.5 1.0
PB D:TD92001 3.3 25.8 1.0
PA D:TD92001 3.3 28.4 1.0
C D:ILE680 3.3 28.6 1.0
ND2 D:ASN678 3.6 20.6 1.0
OD2 D:ASP645 3.8 32.8 1.0
O2B D:TD92001 3.8 27.6 1.0
N D:ASP645 4.0 26.5 1.0
O5G D:TD92001 4.0 23.3 1.0
N D:ILE680 4.1 25.3 1.0
N D:GLY681 4.1 25.3 1.0
CA D:GLY681 4.2 24.9 1.0
CA D:ILE680 4.3 25.6 1.0
N D:ALA646 4.3 25.2 1.0
N D:ASN678 4.4 30.3 1.0
O D:VAL676 4.4 33.1 1.0
CB D:ASP645 4.4 26.7 1.0
O1A D:TD92001 4.4 29.1 1.0
O D:HOH3032 4.5 27.6 1.0
O3B D:TD92001 4.5 25.8 1.0
CB D:ASN678 4.5 27.7 1.0
CG2 D:ILE680 4.6 30.9 1.0
CA D:ASP645 4.6 25.8 1.0
CA D:ASN678 4.8 30.6 1.0
C D:GLY644 4.8 29.4 1.0
N D:GLN679 4.8 25.8 1.0
C D:ASN678 4.8 31.8 1.0
CA D:GLY644 4.8 27.2 1.0
C D:ASP645 5.0 29.9 1.0

Reference:

T.Wagner, N.Barilone, P.M.Alzari, M.Bellinzoni. A Dual Conformation of the Post-Decarboxylation Intermediate Is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd). Biochem.J. V. 457 425 2014.
ISSN: ISSN 0264-6021
PubMed: 24171907
DOI: 10.1042/BJ20131142
Page generated: Mon Dec 14 09:03:25 2020

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