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Magnesium in PDB 5c9x: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic Acid:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic Acid, PDB code: 5c9x was solved by H.-L.Huang, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.14 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.359, 79.359, 225.310, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 23.7

Other elements in 5c9x:

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic Acid also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic Acid (pdb code 5c9x). 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 2,4-Dichloro-5-Fluorobenzoic Acid, PDB code: 5c9x:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5c9x

Go back to Magnesium Binding Sites List in 5c9x
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic 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 2,4-Dichloro-5-Fluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:31.4
occ:1.00
 OD2 A:ASP462 2.1 30.3 1.0
OE2 A:GLU434 2.1 28.8 1.0
O A:HOH956 2.1 27.9 1.0
O A:HOH964 2.1 27.6 1.0
O A:HOH1023 2.2 31.1 1.0
O A:HOH1299 2.2 34.1 1.0
CD A:GLU434 3.1 32.1 1.0
CG A:ASP462 3.1 32.9 1.0
OE1 A:GLU434 3.4 27.4 1.0
CB A:ASP462 3.5 28.2 1.0
O01 A:4Z4804 4.1 39.5 1.0
OD2 A:ASP274 4.2 36.3 1.0
NZ A:LYS399 4.2 26.6 1.0
NH1 A:ARG339 4.2 28.0 1.0
O A:HOH1014 4.2 32.0 1.0
OD1 A:ASP462 4.2 29.0 1.0
CG A:GLU434 4.4 27.1 1.0
OD2 A:ASP633 4.5 41.8 1.0
OE1 A:GLU273 4.5 28.6 1.0
CB A:ALA635 4.6 29.1 1.0
CB A:GLU434 4.6 29.3 1.0
N A:ASP462 4.7 32.9 1.0
CA A:ASP462 4.7 31.5 1.0
CE A:MET432 4.8 30.7 1.0
CG A:ASP274 4.9 33.4 1.0
O A:GLY459 4.9 32.5 1.0
C02 A:4Z4804 4.9 39.3 1.0
CA A:GLY459 4.9 36.7 1.0
O03 A:4Z4804 4.9 34.3 1.0

Magnesium binding site 2 out of 3 in 5c9x

Go back to Magnesium Binding Sites List in 5c9x
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic 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 2,4-Dichloro-5-Fluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.3
occ:1.00
 O A:LYS377 2.6 41.0 1.0
O A:LEU385 2.7 46.1 1.0
O A:HIS374 2.7 33.2 1.0
O A:ASN382 2.7 45.8 1.0
O A:ASN295 3.0 33.9 1.0
O A:GLY383 3.0 49.4 1.0
O A:LYS296 3.1 42.5 1.0
CA A:LYS296 3.5 38.0 1.0
C A:LYS296 3.6 42.1 1.0
C A:LEU385 3.6 45.8 1.0
C A:GLY383 3.6 49.8 1.0
C A:ASN382 3.7 48.1 1.0
C A:HIS374 3.7 35.7 1.0
N A:LEU385 3.7 44.5 1.0
C A:LYS377 3.8 46.5 1.0
C A:ASN295 4.0 32.0 1.0
CA A:GLY383 4.2 42.9 1.0
CA A:LEU385 4.2 46.8 1.0
N A:LYS296 4.3 30.7 1.0
N A:GLY383 4.3 45.3 1.0
CA A:ALA378 4.4 42.4 1.0
C A:PRO384 4.4 49.5 1.0
CB A:ASN382 4.4 44.8 1.0
CA A:GLY375 4.4 33.1 1.0
N A:PRO384 4.4 52.2 1.0
N A:GLY375 4.5 29.7 1.0
N A:ALA378 4.5 46.9 1.0
CA A:HIS374 4.7 35.8 1.0
CA A:ASN382 4.7 43.7 1.0
CB A:LYS296 4.7 32.1 1.0
N A:GLY297 4.7 34.2 1.0
N A:ILE386 4.7 43.8 1.0
CB A:HIS374 4.7 31.2 1.0
N A:LYS377 4.8 36.6 1.0
CA A:LYS377 4.8 37.8 1.0
CA A:PRO384 4.9 49.0 1.0
C A:GLY375 4.9 37.5 1.0

Magnesium binding site 3 out of 3 in 5c9x

Go back to Magnesium Binding Sites List in 5c9x
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,4-Dichloro-5-Fluorobenzoic 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 2,4-Dichloro-5-Fluorobenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:36.7
occ:1.00
 O A:HOH1202 1.9 46.7 1.0
O A:HOH1157 1.9 49.2 1.0
O A:HOH1339 1.9 43.5 1.0
O A:HOH1342 1.9 42.6 1.0
NE2 A:HIS235 2.2 42.8 1.0
O A:HOH1469 2.4 52.4 1.0
CE1 A:HIS235 3.0 38.5 1.0
CD2 A:HIS235 3.3 37.1 1.0
ND1 A:HIS235 4.1 37.4 1.0
OD1 A:ASN234 4.3 41.2 1.0
CG A:HIS235 4.3 37.8 1.0
O A:HOH1107 4.3 30.0 1.0
O A:HOH1460 4.4 56.8 1.0
OD2 A:ASP559 4.7 44.2 1.0
CB A:ASP559 4.7 42.4 1.0
CG A:ASP559 5.0 40.2 1.0
O A:HIS556 5.0 38.8 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: Sun Sep 29 02:00:22 2024

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