Magnesium in PDB 5jy4: A High Magnesium Structure of the Isochorismate Synthase, Entc

All present enzymatic activity of A High Magnesium Structure of the Isochorismate Synthase, Entc:
5.4.4.2;

The structure of A High Magnesium Structure of the Isochorismate Synthase, Entc, PDB code: 5jy4 was solved by K.M.Meneely, J.A.Sundlov, A.M.Gulick, A.L.Lamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 2.11
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.907, 80.907, 265.231, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.8

The binding sites of Magnesium atom in the A High Magnesium Structure of the Isochorismate Synthase, Entc (pdb code 5jy4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A High Magnesium Structure of the Isochorismate Synthase, Entc, PDB code: 5jy4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the A High Magnesium Structure of the Isochorismate Synthase, Entc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A High Magnesium Structure of the Isochorismate Synthase, Entc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:38.5 occ:1.00 O2 A:ISC402 2.0 42.6 1.0 O A:HOH522 2.0 38.4 1.0 OE2 A:GLU241 2.1 35.9 1.0 OE2 A:GLU376 2.1 41.9 1.0 O1 A:ISC402 2.2 41.3 1.0 O A:HOH515 2.2 42.2 1.0 C A:ISC402 2.4 36.8 1.0 CD A:GLU241 3.0 42.9 1.0 CD A:GLU376 3.1 39.9 1.0 H A:GLY363 3.2 42.1 1.0 H A:GLY214 3.2 43.2 1.0 HG A:SER215 3.3 54.5 1.0 OE1 A:GLU241 3.3 36.7 1.0 OE1 A:GLU376 3.4 39.6 1.0 HZ3 A:LYS237 3.5 53.0 1.0 HZ1 A:LYS380 3.6 60.6 1.0 HB1 A:ALA362 3.8 42.9 1.0 HA2 A:GLY214 3.8 38.5 1.0 OG A:SER215 3.9 45.4 1.0 HB2 A:SER215 3.9 55.0 1.0 N A:GLY363 3.9 35.1 1.0 C1 A:ISC402 3.9 40.3 1.0 HA A:ALA362 3.9 44.1 1.0 N A:GLY214 4.0 36.0 1.0 HZ1 A:LYS237 4.0 53.0 1.0 HZ2 A:LYS380 4.1 60.6 1.0 NZ A:LYS237 4.1 44.1 1.0 HZ2 A:LYS237 4.3 53.0 1.0 NZ A:LYS380 4.3 50.5 1.0 O A:GLY363 4.3 33.8 1.0 CA A:GLY214 4.3 32.1 1.0 CB A:SER215 4.4 45.8 1.0 H A:SER215 4.4 35.8 1.0 CG A:GLU241 4.4 42.5 1.0 CG A:GLU376 4.5 38.8 1.0 HA3 A:GLY363 4.5 47.8 1.0 N A:SER215 4.5 29.8 1.0 CB A:ALA362 4.5 35.8 1.0 OE1 A:GLU373 4.5 34.4 1.0 HG2 A:GLU376 4.5 46.5 1.0 CA A:ALA362 4.5 36.8 1.0 HG2 A:GLU241 4.6 51.1 1.0 C A:GLY214 4.7 34.3 1.0 CA A:GLY363 4.7 39.9 1.0 H2 A:ISC402 4.7 51.0 1.0 C A:ALA362 4.7 37.6 1.0 HG3 A:GLU241 4.7 51.1 1.0 HE3 A:LYS380 4.7 54.8 1.0 OD1 A:ASP238 4.8 37.4 1.0 H6 A:ISC402 4.8 45.5 1.0 HO3 A:ISC402 4.8 61.7 1.0 HB2 A:ALA362 4.8 42.9 1.0 C2 A:ISC402 4.8 42.5 1.0 C6 A:ISC402 4.9 38.0 1.0 O A:HOH513 4.9 45.7 1.0 HA A:ALA213 4.9 42.8 1.0 HZ3 A:LYS380 4.9 60.6 1.0 HG3 A:GLU376 4.9 46.5 1.0 C A:GLY363 5.0 32.0 1.0

Magnesium binding site 2 out of 2 in the A High Magnesium Structure of the Isochorismate Synthase, Entc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A High Magnesium Structure of the Isochorismate Synthase, Entc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:35.0 occ:1.00 O B:HOH504 1.9 31.1 1.0 OE2 B:GLU241 2.0 46.0 1.0 O B:HOH507 2.0 31.2 1.0 OE2 B:GLU376 2.2 37.4 1.0 O1 B:ISC402 2.2 35.7 1.0 O2 B:ISC402 2.3 37.1 1.0 C B:ISC402 2.6 46.1 1.0 CD B:GLU241 2.8 44.2 1.0 OE1 B:GLU241 2.9 41.3 1.0 CD B:GLU376 3.0 36.1 1.0 HZ3 B:LYS237 3.2 67.2 1.0 H B:GLY363 3.2 44.8 1.0 OE1 B:GLU376 3.2 49.0 1.0 H B:GLY214 3.6 55.9 1.0 HB1 B:ALA362 3.7 43.2 1.0 NZ B:LYS237 3.8 56.0 1.0 HZ2 B:LYS237 3.8 67.2 1.0 HZ1 B:LYS237 3.8 67.2 1.0 HG B:SER215 3.8 51.8 1.0 HA2 B:GLY214 3.8 56.5 1.0 N B:GLY363 4.0 37.3 1.0 HZ1 B:LYS380 4.0 61.8 1.0 O B:GLY363 4.1 36.0 1.0 C1 B:ISC402 4.2 44.4 1.0 HA B:ALA362 4.2 43.7 1.0 H B:SER215 4.3 44.3 1.0 CG B:GLU241 4.3 48.9 1.0 N B:GLY214 4.3 46.6 1.0 OE1 B:GLU373 4.3 39.7 1.0 HA3 B:GLY363 4.4 49.7 1.0 CA B:GLY214 4.5 47.1 1.0 CG B:GLU376 4.5 33.0 1.0 HB2 B:SER215 4.5 53.7 1.0 OG B:SER215 4.5 43.1 1.0 HG2 B:GLU241 4.5 58.6 1.0 HG2 B:GLU376 4.5 39.6 1.0 CB B:ALA362 4.6 36.0 1.0 HZ2 B:LYS380 4.6 61.8 1.0 HG3 B:GLU241 4.6 58.6 1.0 OD1 B:ASP238 4.6 43.0 1.0 N B:SER215 4.6 36.9 1.0 CA B:GLY363 4.6 41.4 1.0 NZ B:LYS380 4.7 51.5 1.0 HE3 B:LYS380 4.7 56.2 1.0 CA B:ALA362 4.7 36.4 1.0 C B:ALA362 4.8 34.6 1.0 HB2 B:ALA362 4.8 43.2 1.0 C B:GLY363 4.9 37.5 1.0 H2 B:ISC402 4.9 68.8 1.0 C B:GLY214 4.9 43.6 1.0 HG3 B:GLU376 4.9 39.6 1.0 CB B:SER215 5.0 44.8 1.0

K.M.Meneely, J.A.Sundlov, A.M.Gulick, G.R.Moran, A.L.Lamb. An Open and Shut Case: the Interaction of Magnesium with Mst Enzymes. J.Am.Chem.Soc. V. 138 9277 2016.
ISSN: ESSN 1520-5126
PubMed: 27373320
DOI: 10.1021/JACS.6B05134