Magnesium in PDB 5jzd: A Re-Refinement of the Isochorismate Synthase Entc

All present enzymatic activity of A Re-Refinement of the Isochorismate Synthase Entc:
5.4.4.2;

The structure of A Re-Refinement of the Isochorismate Synthase Entc, PDB code: 5jzd was solved by K.M.Meneely, A.L.Lamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.95 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.469, 104.795, 140.014, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.6

The binding sites of Magnesium atom in the A Re-Refinement of the Isochorismate Synthase Entc (pdb code 5jzd). 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 Re-Refinement of the Isochorismate Synthase Entc, PDB code: 5jzd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the A Re-Refinement 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 Re-Refinement of the Isochorismate Synthase Entc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:71.6 occ:1.00 O A:HOH510 2.0 47.9 1.0 OE2 A:GLU376 2.3 66.3 1.0 O1 A:ISC401 2.4 62.1 1.0 OE2 A:GLU241 2.4 72.9 1.0 O2 A:ISC401 2.5 66.4 1.0 C A:ISC401 2.8 59.7 1.0 OE1 A:GLU241 2.9 60.5 1.0 CD A:GLU241 3.0 69.8 1.0 HA3 A:GLY363 3.0 79.2 1.0 CD A:GLU376 3.2 70.3 1.0 OE1 A:GLU376 3.4 79.1 1.0 HG A:SER215 3.4 66.1 1.0 HA2 A:GLY214 3.6 68.6 1.0 H A:GLY214 3.6 59.7 1.0 HB1 A:ALA362 3.6 68.0 1.0 CA A:GLY363 3.8 66.0 1.0 HA2 A:GLY363 3.9 79.2 1.0 HZ1 A:LYS380 4.0 75.5 1.0 O A:GLY363 4.0 74.1 1.0 OG A:SER215 4.1 55.1 1.0 N A:GLY214 4.2 49.7 1.0 CA A:GLY214 4.3 57.2 1.0 C1 A:ISC401 4.3 59.8 1.0 HA A:ALA362 4.4 78.2 1.0 OE1 A:GLU373 4.4 81.6 1.0 HB2 A:SER215 4.4 72.6 1.0 CB A:ALA362 4.4 56.7 1.0 C A:GLY363 4.4 73.9 1.0 HB2 A:ALA362 4.4 68.0 1.0 H A:SER215 4.4 78.0 1.0 CG A:GLU241 4.5 71.7 1.0 OD1 A:ASP238 4.5 67.3 1.0 N A:SER215 4.6 65.0 1.0 CG A:GLU376 4.6 55.6 1.0 HZ2 A:LYS380 4.7 75.5 1.0 NZ A:LYS380 4.7 62.9 1.0 HG2 A:GLU241 4.7 86.1 1.0 HG2 A:GLU376 4.8 66.7 1.0 CB A:SER215 4.8 60.5 1.0 C A:GLY214 4.8 58.2 1.0 HG3 A:GLU241 4.8 86.1 1.0 CA A:ALA362 4.9 65.2 1.0 HO3 A:ISC401 5.0 91.1 1.0 OE2 A:GLU373 5.0 87.1 1.0

Magnesium binding site 2 out of 2 in the A Re-Refinement 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 Re-Refinement of the Isochorismate Synthase Entc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:35.5 occ:1.00 O B:HOH514 2.1 30.7 1.0 O1 B:ISC401 2.1 37.5 1.0 OE2 B:GLU376 2.2 40.1 1.0 O2 B:ISC401 2.2 33.7 1.0 OE2 B:GLU241 2.2 39.8 1.0 O B:HOH503 2.3 32.5 1.0 C B:ISC401 2.5 34.0 1.0 CD B:GLU241 3.0 38.6 1.0 CD B:GLU376 3.1 45.1 1.0 OE1 B:GLU241 3.2 32.3 1.0 OE1 B:GLU376 3.3 38.0 1.0 H B:GLY363 3.4 41.0 1.0 H B:GLY214 3.4 38.7 1.0 HA2 B:GLY214 3.5 33.8 1.0 HG B:SER215 3.6 45.4 1.0 HZ1 B:LYS380 3.8 53.2 1.0 HZ3 B:LYS237 3.8 43.4 1.0 HB2 B:SER215 3.9 43.3 1.0 C1 B:ISC401 4.0 35.2 1.0 N B:GLY214 4.1 32.3 1.0 HA B:ALA362 4.1 42.9 1.0 HB1 B:ALA362 4.1 51.2 1.0 N B:GLY363 4.1 34.2 1.0 CA B:GLY214 4.2 28.2 1.0 HZ2 B:LYS237 4.2 43.4 1.0 OG B:SER215 4.2 37.9 1.0 H B:SER215 4.3 34.4 1.0 HZ1 B:LYS237 4.3 43.4 1.0 NZ B:LYS237 4.3 36.2 1.0 O B:GLY363 4.4 36.5 1.0 N B:SER215 4.4 28.7 1.0 CG B:GLU241 4.5 44.6 1.0 HO3 B:ISC401 4.5 63.7 1.0 CB B:SER215 4.5 36.1 1.0 CG B:GLU376 4.5 31.9 1.0 HA3 B:GLY363 4.6 35.1 1.0 OE1 B:GLU373 4.6 37.0 1.0 NZ B:LYS380 4.6 44.3 1.0 C B:GLY214 4.6 29.4 1.0 HG2 B:GLU376 4.6 38.3 1.0 HZ2 B:LYS380 4.7 53.2 1.0 HE3 B:LYS380 4.7 43.7 1.0 H2 B:ISC401 4.7 45.0 1.0 HG2 B:GLU241 4.7 53.5 1.0 OD1 B:ASP238 4.7 33.9 1.0 HG3 B:GLU241 4.7 53.5 1.0 H6 B:ISC401 4.8 37.6 1.0 CA B:ALA362 4.8 35.8 1.0 CA B:GLY363 4.8 29.2 1.0 CB B:ALA362 4.8 42.7 1.0 C2 B:ISC401 4.9 37.5 1.0 C6 B:ISC401 4.9 31.4 1.0 HG3 B:GLU376 5.0 38.3 1.0 C B:ALA362 5.0 31.3 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