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Magnesium in PDB 5c9w: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide, PDB code: 5c9w was solved by H.-L.Huang, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.43 / 2.09
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.206, 78.206, 223.815, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.5

Other elements in 5c9w:

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide 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 (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide (pdb code 5c9w). 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 (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide, PDB code: 5c9w:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5c9w

Go back to Magnesium Binding Sites List in 5c9w
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide


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 (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:20.7
occ:1.00
 O01 A:4Z3804 2.0 24.9 1.0
OD2 A:ASP462 2.0 23.2 1.0
OE2 A:GLU434 2.1 19.1 1.0
O A:HOH975 2.2 22.9 1.0
O A:HOH1230 2.2 23.9 1.0
O A:HOH1084 2.2 21.8 1.0
N02 A:4Z3804 2.9 32.5 1.0
CG A:ASP462 3.0 21.7 1.0
CD A:GLU434 3.1 19.3 1.0
OE1 A:GLU434 3.4 15.7 1.0
CB A:ASP462 3.5 18.1 1.0
C03 A:4Z3804 3.7 34.1 1.0
NZ A:LYS399 4.0 20.6 1.0
NH1 A:ARG339 4.0 23.2 1.0
OD2 A:ASP274 4.1 25.9 1.0
OD1 A:ASP462 4.1 21.4 1.0
O A:HOH963 4.1 32.1 1.0
CG A:GLU434 4.4 16.4 1.0
CB A:ALA635 4.5 23.1 1.0
O A:HOH1189 4.5 26.8 1.0
N A:ASP462 4.6 20.6 1.0
CA A:ASP462 4.6 20.4 1.0
OE1 A:GLU273 4.6 21.2 1.0
OD2 A:ASP633 4.7 34.4 1.0
CB A:GLU434 4.7 19.2 1.0
CG A:ASP274 4.8 26.9 1.0
CZ A:ARG339 4.9 19.8 1.0
CE A:MET432 4.9 20.1 1.0
NH2 A:ARG339 5.0 25.8 1.0
CA A:GLY459 5.0 19.3 1.0

Magnesium binding site 2 out of 3 in 5c9w

Go back to Magnesium Binding Sites List in 5c9w
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide


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 (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:19.1
occ:1.00
 OG1 A:THR482 3.1 23.7 1.0
N A:ARG479 3.3 19.9 1.0
NE1 A:TRP589 3.3 31.8 1.0
NE A:ARG479 3.3 30.2 1.0
CB A:VAL478 3.6 22.9 1.0
CG A:ARG479 3.7 26.3 1.0
CB A:THR482 3.8 24.7 1.0
CB A:ARG479 3.8 22.8 1.0
CA A:VAL478 3.9 22.3 1.0
CG2 A:THR482 3.9 23.1 1.0
NH2 A:ARG479 4.0 33.9 1.0
C A:VAL478 4.1 24.0 1.0
CG1 A:VAL478 4.1 23.1 1.0
CZ A:ARG479 4.1 35.8 1.0
CD A:ARG479 4.1 28.4 1.0
CE2 A:TRP589 4.1 30.9 1.0
CA A:ARG479 4.2 22.3 1.0
CZ2 A:TRP589 4.3 29.3 1.0
CD1 A:TRP589 4.3 31.3 1.0
O A:HOH1171 4.8 29.8 1.0
CG2 A:VAL478 4.8 19.9 1.0
O A:ARG479 5.0 23.3 1.0

Magnesium binding site 3 out of 3 in 5c9w

Go back to Magnesium Binding Sites List in 5c9w
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide


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 (Z)-N-(2-Bromophenyl)-2-(Hydroxyimino)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:37.2
occ:1.00
 O A:HOH918 1.9 34.9 1.0
O A:HOH1098 2.1 36.6 1.0
O A:HOH1470 2.3 43.8 1.0
NE2 A:HIS235 2.3 29.1 1.0
CD2 A:HIS235 3.3 25.5 1.0
CE1 A:HIS235 3.3 28.5 1.0
OD2 A:ASP559 4.2 33.9 1.0
O A:HOH1310 4.3 36.2 1.0
OD1 A:ASN234 4.4 26.8 1.0
ND1 A:HIS235 4.4 24.8 1.0
CG A:HIS235 4.4 25.1 1.0
CB A:ASP559 4.6 27.4 1.0
CG A:ASP559 4.7 31.3 1.0

Reference:

H.L.Huang, I.V.Krieger, M.K.Parai, V.B.Gawandi, J.C.Sacchettini. Mycobacterium Tuberculosis Malate Synthase Structures with Fragments Reveal A Portal For Substrate/Product Exchange. J. Biol. Chem. V. 291 27421 2016.
ISSN: ESSN 1083-351X
PubMed: 27738104
DOI: 10.1074/JBC.M116.750877
Page generated: Sun Sep 29 02:00:16 2024

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