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Magnesium in PDB 6bu1: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid

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

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid, PDB code: 6bu1 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) 45.08 / 1.58
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.538, 79.538, 226.160, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.8

Other elements in 6bu1:

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid also contains other interesting chemical elements:

Bromine (Br) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid (pdb code 6bu1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid, PDB code: 6bu1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6bu1

Go back to Magnesium Binding Sites List in 6bu1
Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-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-Br-3-Oh-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:24.2
occ:1.00
 O A:HOH966 2.0 25.3 1.0
OD1 A:ASP462 2.0 23.9 1.0
O A:HOH1019 2.1 22.0 1.0
O05 A:E9S805 2.1 25.8 1.0
OE2 A:GLU434 2.1 23.3 1.0
O03 A:E9S805 2.2 23.5 1.0
C04 A:E9S805 2.9 29.3 1.0
C02 A:E9S805 2.9 27.5 1.0
CD A:GLU434 3.1 25.5 1.0
CG A:ASP462 3.1 22.6 1.0
OE1 A:GLU434 3.4 21.5 1.0
CB A:ASP462 3.5 23.2 1.0
NH1 A:ARG339 3.9 22.0 1.0
C06 A:E9S805 4.1 25.2 1.0
NZ A:LYS399 4.1 25.9 1.0
OD1 A:ASP274 4.1 29.0 1.0
O01 A:E9S805 4.1 24.8 1.0
OD2 A:ASP462 4.2 22.1 1.0
O08 A:E9S805 4.2 31.4 1.0
CG A:GLU434 4.3 22.9 1.0
CB A:ALA635 4.3 24.3 1.0
OE1 A:GLU273 4.5 26.6 1.0
C07 A:E9S805 4.5 29.6 1.0
N A:ASP462 4.6 22.0 1.0
CB A:GLU434 4.6 22.2 1.0
CA A:ASP462 4.6 22.6 1.0
CE A:MET432 4.8 23.0 1.0
CZ A:ARG339 4.9 24.0 1.0
CG A:ASP274 4.9 27.9 1.0
CA A:GLY459 4.9 20.6 1.0

Magnesium binding site 2 out of 4 in 6bu1

Go back to Magnesium Binding Sites List in 6bu1
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-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-Br-3-Oh-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.4
occ:1.00
 NE1 A:TRP589 3.2 35.4 1.0
OG1 A:THR482 3.3 37.7 1.0
N A:ARG479 3.3 27.6 1.0
CG A:ARG479 3.7 30.9 1.0
CB A:VAL478 3.7 29.2 1.0
CB A:ARG479 3.8 27.7 1.0
CA A:VAL478 3.9 25.4 1.0
CE2 A:TRP589 3.9 36.1 1.0
CZ2 A:TRP589 4.0 35.7 1.0
CB A:THR482 4.0 27.8 1.0
C A:VAL478 4.2 30.2 1.0
CD A:ARG479 4.2 32.3 1.0
CG2 A:THR482 4.2 37.7 1.0
CA A:ARG479 4.2 30.3 1.0
CG1 A:VAL478 4.3 26.2 1.0
CD1 A:TRP589 4.3 41.0 1.0
O A:HOH1101 4.9 42.2 1.0
CG2 A:VAL478 5.0 28.0 1.0
O A:ARG479 5.0 27.0 1.0

Magnesium binding site 3 out of 4 in 6bu1

Go back to Magnesium Binding Sites List in 6bu1
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-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-Br-3-Oh-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:36.9
occ:1.00
 O A:HOH1168 2.0 46.1 1.0
O A:HOH1340 2.0 41.7 1.0
O A:HOH1358 2.1 46.5 1.0
O A:HOH1526 2.1 39.5 1.0
O A:HOH1136 2.2 42.1 1.0
NE2 A:HIS235 2.2 34.7 1.0
CE1 A:HIS235 3.1 37.5 1.0
CD2 A:HIS235 3.3 33.9 1.0
ND1 A:HIS235 4.3 27.5 1.0
OD1 A:ASN234 4.3 32.2 1.0
OD2 A:ASP559 4.4 40.0 1.0
CG A:HIS235 4.4 29.4 1.0
O A:HOH1125 4.5 46.0 1.0
CB A:ASP559 4.6 33.8 1.0
CG A:ASP559 4.8 37.0 1.0

Magnesium binding site 4 out of 4 in 6bu1

Go back to Magnesium Binding Sites List in 6bu1
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Br-3-Oh-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:40.9
occ:1.00
 O A:HOH1402 2.1 41.2 1.0
O A:HOH1408 2.2 41.6 1.0
O A:HOH1234 2.3 34.4 1.0
O A:HOH1132 2.3 37.5 1.0
O A:HOH1399 2.4 39.0 1.0
O A:HOH1456 4.0 37.2 1.0
OE1 A:GLN704 4.3 38.0 1.0
O A:HOH1123 4.3 42.8 1.0
OD1 A:ASP65 4.3 35.3 1.0
NH1 A:ARG69 4.3 33.8 1.0
O A:HOH1199 4.4 35.3 1.0
NE2 A:GLN704 4.5 40.1 1.0
O A:HOH1067 4.5 33.5 1.0
CD A:GLN704 4.8 32.9 1.0
NH2 A:ARG69 5.0 34.1 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 20:01:00 2024

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