Atomistry » Magnesium » PDB 6d9m-6dlu » 6dl9
Atomistry »
  Magnesium »
    PDB 6d9m-6dlu »
      6dl9 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy