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Magnesium in PDB 5t8g: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid, PDB code: 5t8g was solved by H.-L.Huang, J.C.Sacchetiini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.01 / 2.04
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.850, 78.850, 224.934, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid (pdb code 5t8g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid, PDB code: 5t8g:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5t8g

Go back to Magnesium Binding Sites List in 5t8g
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid


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 Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:21.3
occ:1.00
 O08 A:4Z0804 2.0 24.2 1.0
OD2 A:ASP462 2.0 23.9 1.0
O A:HOH1045 2.1 22.6 1.0
O10 A:4Z0804 2.1 27.0 1.0
O A:HOH996 2.1 18.8 1.0
OE2 A:GLU434 2.1 22.5 1.0
C06 A:4Z0804 2.7 26.9 1.0
C07 A:4Z0804 2.7 23.6 1.0
CG A:ASP462 3.0 24.1 1.0
CD A:GLU434 3.1 21.9 1.0
OE1 A:GLU434 3.5 19.2 1.0
CB A:ASP462 3.5 19.5 1.0
NZ A:LYS399 3.9 21.4 1.0
NH1 A:ARG339 4.0 21.8 1.0
O09 A:4Z0804 4.0 23.3 1.0
OD1 A:ASP462 4.1 22.3 1.0
OD2 A:ASP274 4.2 26.9 1.0
C05 A:4Z0804 4.2 26.2 1.0
OD2 A:ASP633 4.2 29.1 1.0
CB A:ALA635 4.4 19.8 1.0
CG A:GLU434 4.4 19.9 1.0
N A:ASP462 4.4 18.3 1.0
OD1 A:ASP633 4.5 27.7 1.0
CA A:ASP462 4.5 21.1 1.0
OE1 A:GLU273 4.5 21.7 1.0
CB A:GLU434 4.7 22.6 1.0
CG A:ASP633 4.8 27.0 1.0
CZ A:ARG339 4.9 24.6 1.0
CG A:ASP274 4.9 25.1 1.0
C04 A:4Z0804 4.9 26.5 1.0
NH2 A:ARG339 5.0 22.9 1.0

Magnesium binding site 2 out of 3 in 5t8g

Go back to Magnesium Binding Sites List in 5t8g
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid


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 Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:40.2
occ:1.00
 O A:HOH1054 1.9 41.8 1.0
O A:HOH1048 2.0 37.1 1.0
O A:HOH1365 2.2 40.7 1.0
O A:HOH1457 2.3 50.4 1.0
O A:HOH961 2.3 41.2 1.0
NE2 A:HIS235 2.4 33.5 1.0
CE1 A:HIS235 3.1 32.1 1.0
CD2 A:HIS235 3.5 30.7 1.0
O A:HOH1287 4.0 46.0 1.0
ND1 A:HIS235 4.3 29.9 1.0
OD1 A:ASN234 4.4 28.9 1.0
CG A:HIS235 4.5 31.2 1.0
OD2 A:ASP559 4.6 34.1 1.0
CB A:ASP559 4.7 31.0 1.0
O A:HIS556 5.0 28.3 1.0
O A:HOH1458 5.0 58.6 1.0

Magnesium binding site 3 out of 3 in 5t8g

Go back to Magnesium Binding Sites List in 5t8g
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid


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 Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:24.5
occ:1.00
 OG1 A:THR482 3.1 27.8 1.0
NE A:ARG479 3.2 32.9 1.0
NE1 A:TRP589 3.2 33.7 1.0
N A:ARG479 3.3 22.6 1.0
CB A:VAL478 3.6 22.8 1.0
CG A:ARG479 3.7 28.8 1.0
CB A:THR482 3.8 26.8 1.0
CB A:ARG479 3.9 21.6 1.0
CA A:VAL478 4.0 21.8 1.0
CG2 A:THR482 4.0 25.7 1.0
NH2 A:ARG479 4.0 35.3 1.0
CZ A:ARG479 4.1 39.5 1.0
CD A:ARG479 4.1 29.5 1.0
CG1 A:VAL478 4.1 23.5 1.0
C A:VAL478 4.1 26.3 1.0
CE2 A:TRP589 4.2 33.2 1.0
CA A:ARG479 4.2 26.2 1.0
CD1 A:TRP589 4.2 37.3 1.0
CZ2 A:TRP589 4.4 33.8 1.0
CG2 A:VAL478 4.8 23.8 1.0
O A:HOH1182 4.8 34.0 1.0
O A:ARG479 5.0 26.8 1.0

Reference:

H.L.Huang, I.V.Krieger, M.K.Parai, V.B.Gawandi, J.C.Sacchettini. Mycobacterium Tuberculosis Malate Synthase Structures with Fragments Reveal A Portal For Substrate/Product Exchange. J. Biol. Chem. V. 291 27421 2016.
ISSN: ESSN 1083-351X
PubMed: 27738104
DOI: 10.1074/JBC.M116.750877
Page generated: Mon Sep 30 04:46:10 2024

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