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Magnesium in PDB 6dko: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid, PDB code: 6dko was solved by I.V.Krieger, J.C.Sacchettini, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.29 / 1.56
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.016, 79.016, 225.961, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.3

Other elements in 6dko:

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid (pdb code 6dko). 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 2,6-F-Phenyldiketoacid, PDB code: 6dko:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6dko

Go back to Magnesium Binding Sites List in 6dko
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid


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 2,6-F-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:22.9
occ:1.00
 OD1 A:ASP462 2.0 22.6 1.0
OE2 A:GLU434 2.0 22.6 1.0
O A:HOH958 2.1 23.0 1.0
O03 A:GXG804 2.1 23.3 1.0
O A:HOH933 2.2 25.0 1.0
O05 A:GXG804 2.3 24.4 1.0
C04 A:GXG804 2.9 24.6 1.0
C02 A:GXG804 2.9 23.8 1.0
CD A:GLU434 3.0 20.6 1.0
CG A:ASP462 3.0 24.9 1.0
OE1 A:GLU434 3.4 23.5 1.0
CB A:ASP462 3.5 22.2 1.0
NH1 A:ARG339 4.0 23.6 1.0
OD2 A:ASP462 4.1 23.6 1.0
O01 A:GXG804 4.1 22.4 1.0
NZ A:LYS399 4.2 24.8 1.0
CG A:GLU434 4.2 20.0 1.0
OD1 A:ASP274 4.3 25.2 1.0
C06 A:GXG804 4.3 24.3 1.0
O08 A:GXG804 4.3 24.2 1.0
CB A:ALA635 4.4 22.9 1.0
CB A:GLU434 4.5 24.1 1.0
N A:ASP462 4.5 24.5 1.0
OE1 A:GLU273 4.6 24.2 1.0
CA A:ASP462 4.6 25.3 1.0
C07 A:GXG804 4.7 23.7 1.0
CE A:MET432 4.8 23.6 1.0
CG A:ASP274 5.0 25.8 1.0
CA A:GLY459 5.0 21.9 1.0
CZ A:ARG339 5.0 24.6 1.0

Magnesium binding site 2 out of 3 in 6dko

Go back to Magnesium Binding Sites List in 6dko
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid


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 2,6-F-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:47.6
occ:1.00
 O A:HOH911 2.0 39.5 1.0
O A:HOH1057 2.0 33.3 1.0
O A:HOH1387 2.1 44.4 1.0
O A:HOH1274 2.3 47.4 1.0
O A:HOH1145 3.7 44.5 1.0
O A:HOH1167 3.8 31.6 1.0
O A:HOH1181 4.1 45.7 1.0
O A:ALA703 4.2 28.0 1.0
OD1 A:ASP65 4.3 36.4 1.0
NE2 A:HIS469 4.4 29.2 1.0
O A:HOH1111 4.7 47.2 1.0
O A:GLN704 4.7 34.9 1.0
CG A:GLN61 4.7 30.5 1.0
O A:HOH1206 4.8 29.7 1.0
O A:HOH1046 4.8 30.9 1.0
O A:GLN705 4.8 28.4 1.0
NE2 A:GLN704 4.9 43.0 1.0
CA A:GLN704 4.9 31.8 1.0
C A:GLN704 4.9 34.0 1.0

Magnesium binding site 3 out of 3 in 6dko

Go back to Magnesium Binding Sites List in 6dko
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-F-Phenyldiketoacid


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 2,6-F-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:38.6
occ:1.00
 O A:HOH1210 1.9 42.8 1.0
O A:HOH1286 2.0 42.4 1.0
O A:HOH1236 2.0 41.7 1.0
O A:HOH1394 2.1 36.3 1.0
O A:HOH1097 2.1 40.0 1.0
NE2 A:HIS235 2.2 31.5 1.0
CE1 A:HIS235 3.1 32.4 1.0
CD2 A:HIS235 3.2 32.6 1.0
O A:HOH1212 4.2 44.0 1.0
ND1 A:HIS235 4.2 29.2 1.0
CG A:HIS235 4.3 29.2 1.0
OD1 A:ASN234 4.4 30.7 1.0
OD2 A:ASP559 4.5 38.1 1.0
CB A:ASP559 4.8 31.4 1.0
CG A:ASP559 5.0 32.0 1.0

Reference:

J.F.Ellenbarger, I.V.Krieger, H.L.Huang, S.Gomez-Coca, T.R.Ioerger, J.C.Sacchettini, S.E.Wheeler, K.R.Dunbar. Anion-Pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase By Phenyl-Diketo Acids. J Chem Inf Model V. 58 2085 2018.
ISSN: ESSN 1549-960X
PubMed: 30137983
DOI: 10.1021/ACS.JCIM.8B00417
Page generated: Mon Sep 30 23:10:19 2024

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