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Magnesium in PDB 6dl9: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-Cl-Phenyldiketoacid

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

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

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-Cl-Phenyldiketoacid, PDB code: 6dl9 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) 49.47 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.045, 78.045, 223.286, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.6

Other elements in 6dl9:

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

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 2,6-Cl-Phenyldiketoacid (pdb code 6dl9). 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-Cl-Phenyldiketoacid, PDB code: 6dl9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6dl9

Go back to Magnesium Binding Sites List in 6dl9
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-Cl-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-Cl-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:22.2
occ:1.00
 OE2 A:GLU434 2.0 20.6 1.0
OD1 A:ASP462 2.1 21.7 1.0
O A:HOH1068 2.1 21.3 1.0
O05 A:GXD804 2.2 26.2 1.0
O01 A:GXD804 2.2 20.4 1.0
O A:HOH951 2.3 23.5 1.0
C04 A:GXD804 2.9 27.6 1.0
C02 A:GXD804 2.9 22.1 1.0
CD A:GLU434 3.0 17.5 1.0
CG A:ASP462 3.0 20.6 1.0
CB A:ASP462 3.4 18.7 1.0
OE1 A:GLU434 3.4 19.9 1.0
NH1 A:ARG339 4.0 21.1 1.0
NZ A:LYS399 4.1 21.2 1.0
O03 A:GXD804 4.1 18.6 1.0
OD2 A:ASP462 4.2 20.4 1.0
C06 A:GXD804 4.2 26.5 1.0
OD1 A:ASP274 4.2 24.1 1.0
O08 A:GXD804 4.2 29.4 1.0
CB A:ALA635 4.3 20.4 1.0
CG A:GLU434 4.3 19.9 1.0
N A:ASP462 4.5 17.3 1.0
CA A:ASP462 4.5 20.3 1.0
OE1 A:GLU273 4.6 21.6 1.0
CB A:GLU434 4.6 20.0 1.0
C07 A:GXD804 4.7 30.2 1.0
CE A:MET432 4.7 22.2 1.0
CA A:GLY459 4.9 20.5 1.0
CZ A:ARG339 5.0 21.6 1.0
CG A:ASP274 5.0 23.7 1.0

Magnesium binding site 2 out of 3 in 6dl9

Go back to Magnesium Binding Sites List in 6dl9
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-Cl-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-Cl-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:38.2
occ:1.00
 O A:HOH1293 2.0 34.8 1.0
O A:HOH1211 2.1 36.2 1.0
O A:HOH940 2.1 32.0 1.0
O A:HOH1245 2.2 29.2 1.0
O A:HOH1301 2.3 31.0 1.0
OD1 A:ASP65 4.0 30.4 1.0
O A:HOH1324 4.1 34.1 1.0
O A:HOH1048 4.2 33.5 1.0
NH1 A:ARG69 4.2 34.7 1.0
NE2 A:GLN704 4.3 35.6 1.0
O A:HOH1134 4.3 27.9 1.0
OE1 A:GLN704 4.5 40.9 1.0
NH2 A:ARG69 4.8 32.6 1.0
CD A:GLN704 4.9 35.0 1.0
CZ A:ARG69 4.9 33.8 1.0
CG A:ASP65 5.0 30.8 1.0

Magnesium binding site 3 out of 3 in 6dl9

Go back to Magnesium Binding Sites List in 6dl9
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2,6-Cl-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-Cl-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:45.1
occ:1.00
 O A:HOH1075 2.0 44.6 1.0
O A:HOH1284 2.3 46.8 1.0
NE2 A:HIS235 2.4 29.7 1.0
O A:HOH1105 2.5 40.9 1.0
O A:HOH1296 2.5 36.9 1.0
CE1 A:HIS235 3.3 27.9 1.0
CD2 A:HIS235 3.5 27.9 1.0
OD1 A:ASN234 4.2 24.9 1.0
ND1 A:HIS235 4.4 24.2 1.0
CG A:HIS235 4.5 23.8 1.0
O A:HOH1297 4.7 52.3 1.0
OD2 A:ASP559 4.7 29.5 1.0
CB A:ASP559 4.9 24.6 1.0
O A:HOH1152 4.9 47.2 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 23:10:18 2024

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