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Magnesium in PDB 6dnp: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid, PDB code: 6dnp was solved by I.V.Krieger, J.C.Sacchettini, Tb Structural Genomics Consortium(Tbsgc), Mycobacterium Tuberculosis Structural Proteomics Project(Xmtb), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.62 / 1.71
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.737, 79.737, 227.288, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.1

Other elements in 6dnp:

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-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-F-3-Methyl-6-F-Phenyldiketoacid (pdb code 6dnp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-3-Methyl-6-F-Phenyldiketoacid, PDB code: 6dnp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dnp

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

b:27.0
occ:1.00
 OD2 A:ASP462 2.1 26.3 1.0
O A:HOH945 2.1 28.3 1.0
O A:HOH925 2.1 26.3 1.0
O12 A:GZV803 2.1 25.3 1.0
O14 A:GZV803 2.2 27.8 1.0
OE2 A:GLU434 2.2 26.1 1.0
C11 A:GZV803 2.9 29.6 1.0
C13 A:GZV803 2.9 26.5 1.0
CG A:ASP462 3.1 28.6 1.0
CD A:GLU434 3.1 29.7 1.0
OE1 A:GLU434 3.4 25.2 1.0
CB A:ASP462 3.5 24.0 1.0
NH1 A:ARG339 4.0 29.3 1.0
C10 A:GZV803 4.1 27.7 1.0
O09 A:GZV803 4.1 30.3 1.0
O15 A:GZV803 4.1 26.1 1.0
NZ A:LYS399 4.1 28.0 1.0
OD1 A:ASP462 4.2 24.2 1.0
OD2 A:ASP274 4.2 28.2 1.0
CB A:ALA635 4.4 27.5 1.0
CG A:GLU434 4.4 22.2 1.0
N A:ASP462 4.6 24.9 1.0
OE1 A:GLU273 4.6 25.1 1.0
C08 A:GZV803 4.6 29.2 1.0
CA A:ASP462 4.6 24.8 1.0
CB A:GLU434 4.7 23.1 1.0
CE A:MET432 4.8 24.6 1.0
CG A:ASP274 5.0 28.1 1.0
CZ A:ARG339 5.0 29.1 1.0

Magnesium binding site 2 out of 2 in 6dnp

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

b:41.0
occ:1.00
 O A:HOH1124 1.8 44.1 1.0
O A:HOH1095 1.9 42.7 1.0
O A:HOH1132 2.0 43.1 1.0
O A:HOH1099 2.1 43.2 1.0
O A:HOH1220 2.1 42.0 1.0
NE2 A:HIS235 2.2 38.1 1.0
CE1 A:HIS235 3.1 37.0 1.0
CD2 A:HIS235 3.2 38.2 1.0
O A:HOH1093 4.2 49.6 1.0
ND1 A:HIS235 4.3 32.8 1.0
CG A:HIS235 4.3 30.8 1.0
OD1 A:ASN234 4.4 39.3 1.0
OD2 A:ASP559 4.6 43.9 1.0
CB A:ASP559 4.7 35.2 1.0
CG A:ASP559 4.9 38.5 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 23:14:26 2024

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