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Magnesium in PDB 6c8p: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-Phenyldiketoacid

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

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

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-Phenyldiketoacid, PDB code: 6c8p 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) 44.70 / 1.64
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.772, 78.772, 224.698, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.7

Other elements in 6c8p:

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

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-F-Phenyldiketoacid (pdb code 6c8p). 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-F-Phenyldiketoacid, PDB code: 6c8p:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6c8p

Go back to Magnesium Binding Sites List in 6c8p
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-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-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:26.1
occ:1.00
 OD1 A:ASP462 2.0 24.8 1.0
OE2 A:GLU434 2.0 22.3 1.0
O A:HOH957 2.1 24.0 1.0
O A:HOH974 2.1 27.6 1.0
O01 A:EQA804 2.2 26.3 1.0
O05 A:EQA804 2.2 32.3 1.0
C04 A:EQA804 2.8 31.2 1.0
C02 A:EQA804 2.9 26.2 1.0
CD A:GLU434 3.0 21.9 1.0
CG A:ASP462 3.0 24.5 1.0
OE1 A:GLU434 3.4 22.7 1.0
CB A:ASP462 3.5 20.7 1.0
NH1 A:ARG339 4.0 26.3 1.0
NZ A:LYS399 4.1 25.6 1.0
OD1 A:ASP274 4.1 29.9 1.0
O08 A:EQA804 4.1 35.8 1.0
OD2 A:ASP462 4.1 25.0 1.0
C06 A:EQA804 4.2 33.0 1.0
O03 A:EQA804 4.2 24.1 1.0
CG A:GLU434 4.3 22.4 1.0
CB A:ALA635 4.4 28.5 1.0
OE1 A:GLU273 4.5 26.6 1.0
N A:ASP462 4.5 24.8 1.0
CB A:GLU434 4.6 22.9 1.0
CA A:ASP462 4.6 23.5 1.0
C07 A:EQA804 4.6 40.9 1.0
CE A:MET432 4.9 27.6 1.0
CG A:ASP274 4.9 29.4 1.0

Magnesium binding site 2 out of 3 in 6c8p

Go back to Magnesium Binding Sites List in 6c8p
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-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-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:37.5
occ:1.00
 O A:HOH1192 1.9 42.0 1.0
O A:HOH1301 2.0 41.4 1.0
O A:HOH1197 2.1 42.5 1.0
O A:HOH1404 2.2 38.5 1.0
NE2 A:HIS235 2.2 28.0 1.0
O A:HOH976 2.2 43.1 1.0
CE1 A:HIS235 3.1 32.4 1.0
CD2 A:HIS235 3.2 32.9 1.0
ND1 A:HIS235 4.2 27.9 1.0
CG A:HIS235 4.3 26.6 1.0
OD1 A:ASN234 4.3 29.4 1.0
OD2 A:ASP559 4.4 37.8 1.0
CB A:ASP559 4.8 30.5 1.0
CG A:ASP559 4.9 34.2 1.0

Magnesium binding site 3 out of 3 in 6c8p

Go back to Magnesium Binding Sites List in 6c8p
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-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-F-Phenyldiketoacid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:37.4
occ:1.00
 O A:HOH1073 2.0 30.0 1.0
O A:HOH987 2.1 38.7 1.0
O A:HOH1389 2.1 37.1 1.0
O A:HOH1399 2.1 39.1 1.0
O A:HOH1095 2.2 40.2 1.0
O A:HOH1138 3.8 29.6 1.0
O A:HOH1084 4.0 37.8 1.0
O A:HOH1130 4.1 42.0 1.0
O A:ALA703 4.1 29.7 1.0
NE2 A:HIS469 4.4 27.0 1.0
OD1 A:ASP65 4.4 33.6 1.0
O A:GLN704 4.5 30.1 1.0
O A:HOH958 4.5 46.6 1.0
O A:GLN705 4.7 24.2 1.0
C A:GLN704 4.7 31.2 1.0
O A:HOH1037 4.7 34.5 1.0
CA A:GLN704 4.7 31.2 1.0
O A:HOH1239 4.8 30.0 1.0
CG A:GLN61 4.9 26.0 1.0
CE1 A:HIS469 4.9 25.5 1.0
OE1 A:GLN704 5.0 47.7 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 20:22:52 2024

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