Magnesium in PDB 3zhv: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp):
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, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp), PDB code: 3zhv 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) 41.06 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.464, 83.702, 160.333, 99.68, 98.87, 100.63
R / Rfree (%) 20.34 / 23.54

Other elements in 3zhv:

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

Magnesium binding site 1 out of 4 in 3zhv

Go back to Magnesium Binding Sites List in 3zhv
Magnesium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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

b:27.3
occ:1.00
 O A:ILE680 2.0 35.5 1.0
O3B A:TDW2001 2.1 36.0 1.0
O A:HOH3065 2.1 23.5 1.0
O2A A:TDW2001 2.2 31.4 1.0
OD1 A:ASN678 2.2 34.5 1.0
OD1 A:ASP645 2.2 32.9 1.0
O3A A:TDW2001 3.1 38.4 1.0
PB A:TDW2001 3.1 38.1 1.0
CG A:ASN678 3.2 41.6 1.0
C A:ILE680 3.2 34.4 1.0
CG A:ASP645 3.3 34.4 1.0
PA A:TDW2001 3.3 32.7 1.0
ND2 A:ASN678 3.6 29.1 1.0
O1B A:TDW2001 3.8 36.9 1.0
OD2 A:ASP645 3.8 31.2 1.0
O7 A:TDW2001 4.0 27.9 1.0
N A:ILE680 4.0 32.7 1.0
N A:GLY681 4.1 28.2 1.0
N A:ASP645 4.1 31.6 1.0
CA A:GLY681 4.2 26.8 1.0
O A:HOH3090 4.2 31.5 1.0
CA A:ILE680 4.2 32.5 1.0
O2B A:TDW2001 4.4 34.1 1.0
N A:ASN678 4.4 34.1 1.0
N A:ALA646 4.5 29.6 1.0
O1A A:TDW2001 4.5 38.5 1.0
CB A:ASN678 4.5 31.4 1.0
O A:VAL676 4.5 34.5 1.0
CB A:ASP645 4.5 31.8 1.0
CG2 A:ILE680 4.6 35.3 1.0
N A:GLN679 4.8 33.9 1.0
CA A:ASP645 4.8 30.4 1.0
CA A:ASN678 4.8 33.3 1.0
C A:ASN678 4.8 37.2 1.0
CA A:GLY644 4.9 34.5 1.0
C A:GLY644 4.9 35.8 1.0

Magnesium binding site 2 out of 4 in 3zhv

Go back to Magnesium Binding Sites List in 3zhv
Magnesium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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

b:34.3
occ:1.00
 O2A B:TDW2001 2.1 32.1 1.0
O B:ILE680 2.1 36.3 1.0
O B:HOH3062 2.1 29.1 1.0
O3B B:TDW2001 2.2 28.1 1.0
OD1 B:ASN678 2.3 44.6 1.0
OD1 B:ASP645 2.3 40.5 1.0
O3A B:TDW2001 3.0 43.5 1.0
PB B:TDW2001 3.1 35.3 1.0
PA B:TDW2001 3.2 38.3 1.0
CG B:ASN678 3.3 41.7 1.0
C B:ILE680 3.3 37.9 1.0
CG B:ASP645 3.4 38.6 1.0
ND2 B:ASN678 3.6 29.9 1.0
O1B B:TDW2001 3.8 37.1 1.0
O7 B:TDW2001 3.9 34.4 1.0
OD2 B:ASP645 3.9 41.7 1.0
N B:ASP645 4.0 30.4 1.0
N B:GLY681 4.1 36.0 1.0
CA B:GLY681 4.1 34.9 1.0
N B:ILE680 4.2 35.1 1.0
O B:HOH3033 4.2 31.5 1.0
CA B:ILE680 4.4 33.7 1.0
N B:ALA646 4.4 32.3 1.0
O1A B:TDW2001 4.4 42.2 1.0
O B:VAL676 4.4 40.6 1.0
O2B B:TDW2001 4.4 36.3 1.0
N B:ASN678 4.5 31.5 1.0
CB B:ASP645 4.5 33.6 1.0
CB B:ASN678 4.6 28.2 1.0
CG2 B:ILE680 4.7 34.0 1.0
CA B:ASP645 4.7 30.8 1.0
CA B:GLY644 4.7 29.6 1.0
C B:GLY644 4.8 32.1 1.0
CA B:ASN678 4.9 32.4 1.0
C B:ASN678 5.0 37.3 1.0
N B:GLN679 5.0 32.8 1.0

Magnesium binding site 3 out of 4 in 3zhv

Go back to Magnesium Binding Sites List in 3zhv
Magnesium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:25.0
occ:1.00
 O C:ILE680 2.0 36.8 1.0
O2A C:TDW2001 2.0 38.3 1.0
O C:HOH3064 2.1 30.0 1.0
OD1 C:ASN678 2.2 39.9 1.0
OD1 C:ASP645 2.2 34.4 1.0
O3B C:TDW2001 2.3 37.2 1.0
O3A C:TDW2001 3.0 42.3 1.0
CG C:ASN678 3.2 42.0 1.0
PB C:TDW2001 3.2 37.5 1.0
PA C:TDW2001 3.2 38.6 1.0
C C:ILE680 3.2 37.4 1.0
CG C:ASP645 3.2 39.0 1.0
ND2 C:ASN678 3.6 23.8 1.0
OD2 C:ASP645 3.8 42.3 1.0
O1B C:TDW2001 3.9 38.0 1.0
N C:ASP645 4.0 34.8 1.0
N C:ILE680 4.1 33.9 1.0
O7 C:TDW2001 4.1 33.5 1.0
N C:GLY681 4.1 34.0 1.0
CA C:GLY681 4.2 32.8 1.0
CA C:ILE680 4.3 34.2 1.0
O1A C:TDW2001 4.3 47.9 1.0
N C:ASN678 4.4 32.9 1.0
N C:ALA646 4.4 31.0 1.0
O C:VAL676 4.4 33.1 1.0
CB C:ASP645 4.5 36.4 1.0
O2B C:TDW2001 4.5 33.1 1.0
CB C:ASN678 4.5 27.7 1.0
O C:HOH3089 4.5 40.4 1.0
CG2 C:ILE680 4.6 39.0 1.0
CA C:ASP645 4.7 34.3 1.0
N C:GLN679 4.7 34.4 1.0
CA C:ASN678 4.8 32.7 1.0
C C:ASN678 4.8 37.2 1.0
CA C:GLY644 4.8 35.6 1.0
C C:GLY644 4.8 39.0 1.0

Magnesium binding site 4 out of 4 in 3zhv

Go back to Magnesium Binding Sites List in 3zhv
Magnesium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:27.5
occ:1.00
 O3B D:TDW2001 2.0 30.6 1.0
O D:ILE680 2.1 35.5 1.0
O D:HOH3060 2.1 36.5 1.0
O2A D:TDW2001 2.2 34.1 1.0
OD1 D:ASN678 2.2 41.8 1.0
OD1 D:ASP645 2.2 39.9 1.0
O3A D:TDW2001 2.9 36.9 1.0
PB D:TDW2001 3.0 34.8 1.0
CG D:ASN678 3.2 41.3 1.0
PA D:TDW2001 3.2 36.0 1.0
CG D:ASP645 3.3 39.3 1.0
C D:ILE680 3.4 36.1 1.0
ND2 D:ASN678 3.5 29.9 1.0
O1B D:TDW2001 3.5 38.4 1.0
OD2 D:ASP645 3.9 42.3 1.0
N D:ASP645 4.0 31.2 1.0
O7 D:TDW2001 4.0 30.6 1.0
N D:GLY681 4.2 34.2 1.0
N D:ILE680 4.2 33.4 1.0
CA D:GLY681 4.2 33.7 1.0
O D:HOH3075 4.3 26.6 1.0
O D:VAL676 4.3 37.9 1.0
O2B D:TDW2001 4.3 32.6 1.0
O1A D:TDW2001 4.4 40.7 1.0
N D:ASN678 4.4 33.0 1.0
CA D:ILE680 4.4 32.2 1.0
N D:ALA646 4.4 33.4 1.0
CB D:ASP645 4.5 32.8 1.0
CB D:ASN678 4.5 33.1 1.0
CA D:ASP645 4.7 30.9 1.0
CG2 D:ILE680 4.7 35.0 1.0
CA D:GLY644 4.7 30.9 1.0
C D:GLY644 4.8 34.9 1.0
CA D:ASN678 4.8 33.6 1.0
C D:ASN678 4.9 36.2 1.0
N D:GLN679 4.9 31.1 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 09:03:37 2020

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