Iron in PDB 5jy8: An Iron-Bound Structure of the Isochorismate Synthase Entc

All present enzymatic activity of An Iron-Bound Structure of the Isochorismate Synthase Entc:
5.4.4.2;

The structure of An Iron-Bound Structure of the Isochorismate Synthase Entc, PDB code: 5jy8 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)	38.86 / 2.94
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.377, 81.377, 262.283, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.7

The binding sites of Iron atom in the An Iron-Bound Structure of the Isochorismate Synthase Entc (pdb code 5jy8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the An Iron-Bound Structure of the Isochorismate Synthase Entc, PDB code: 5jy8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the An Iron-Bound Structure of the Isochorismate Synthase Entc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of An Iron-Bound Structure of the Isochorismate Synthase Entc within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:42.0 occ:1.00 O8 A:ISJ403 2.1 39.6 1.0 OE2 A:GLU376 2.3 38.8 1.0 OE2 A:GLU241 2.4 45.4 1.0 C7 A:ISJ403 2.8 41.6 1.0 O9 A:ISJ403 2.9 47.2 1.0 CD A:GLU376 3.1 34.7 1.0 CD A:GLU241 3.1 42.5 1.0 OE1 A:GLU376 3.2 40.4 1.0 OE1 A:GLU241 3.2 39.9 1.0 HZ3 A:LYS237 3.3 46.0 1.0 HZ1 A:LYS380 3.5 43.6 1.0 H A:GLY363 3.6 44.1 1.0 HA2 A:GLY214 3.7 49.7 1.0 H A:GLY214 3.7 47.7 1.0 HZ1 A:LYS237 3.8 46.0 1.0 HB1 A:ALA362 3.9 45.6 1.0 NZ A:LYS237 3.9 38.3 1.0 HZ2 A:LYS237 4.2 46.0 1.0 O A:GLY363 4.2 36.9 1.0 N A:GLY363 4.3 36.8 1.0 C3 A:ISJ403 4.3 42.6 1.0 OE1 A:GLU373 4.3 37.8 1.0 NZ A:LYS380 4.3 36.3 1.0 HB2 A:SER215 4.3 46.0 1.0 CA A:GLY214 4.4 41.4 1.0 HZ2 A:LYS380 4.4 43.6 1.0 N A:GLY214 4.4 39.7 1.0 HG A:SER215 4.4 50.3 1.0 H A:SER215 4.4 47.7 1.0 HA A:ALA362 4.4 42.4 1.0 OD1 A:ASP238 4.4 41.7 1.0 OG A:SER215 4.4 42.0 1.0 CG A:GLU376 4.5 31.7 1.0 CG A:GLU241 4.5 43.7 1.0 N A:SER215 4.6 39.7 1.0 HG2 A:GLU376 4.6 38.0 1.0 HZ3 A:LYS380 4.6 43.6 1.0 HG2 A:GLU241 4.7 52.4 1.0 CB A:ALA362 4.7 38.0 1.0 C A:GLY214 4.8 39.1 1.0 HA3 A:GLY363 4.8 43.9 1.0 CB A:SER215 4.9 38.3 1.0 HG3 A:GLU376 4.9 38.0 1.0 H2 A:ISJ403 4.9 51.8 1.0 HG3 A:GLU241 4.9 52.4 1.0 CA A:ALA362 4.9 35.3 1.0 CA A:GLY363 4.9 36.6 1.0 HB2 A:ALA362 5.0 45.6 1.0

Iron binding site 2 out of 4 in the An Iron-Bound Structure of the Isochorismate Synthase Entc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of An Iron-Bound Structure of the Isochorismate Synthase Entc within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:58.2 occ:1.00 NE2 A:HIS261 2.2 39.8 1.0 OE2 A:GLU259 2.3 52.6 1.0 CD A:GLU259 2.6 52.9 1.0 HE1 A:HIS261 2.8 44.4 1.0 CE1 A:HIS261 2.8 37.0 1.0 OE1 A:GLU259 2.9 48.1 1.0 CD2 A:HIS261 3.4 39.6 1.0 O B:LEU16 3.4 37.8 1.0 N B:LEU16 3.5 33.4 1.0 HG3 A:GLU259 3.6 59.7 1.0 HA3 B:GLY165 3.6 47.7 1.0 CG A:GLU259 3.7 49.8 1.0 HD2 A:HIS261 3.8 47.6 1.0 C B:LEU16 3.8 37.2 1.0 OD1 B:ASP163 3.9 47.1 1.0 OD2 B:ASP163 3.9 50.5 1.0 ND1 A:HIS261 4.0 36.4 1.0 HB2 A:GLU259 4.2 56.2 1.0 HA B:ALA17 4.2 44.6 1.0 CA B:LEU16 4.3 36.8 1.0 CG B:ASP163 4.3 45.5 1.0 CG A:HIS261 4.4 37.1 1.0 HG2 A:GLU259 4.4 59.7 1.0 N B:ALA17 4.5 39.1 1.0 CB A:GLU259 4.6 46.8 1.0 CA B:GLY165 4.6 39.7 1.0 H B:GLY165 4.7 47.3 1.0 HA B:LEU16 4.7 44.2 1.0 HD1 A:HIS261 4.7 43.6 1.0 HD3 B:PRO18 4.8 45.1 1.0 CA B:ALA17 4.9 37.1 1.0

Iron binding site 3 out of 4 in the An Iron-Bound Structure of the Isochorismate Synthase Entc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of An Iron-Bound Structure of the Isochorismate Synthase Entc within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:52.9 occ:1.00 O9 B:ISJ403 2.0 46.6 1.0 O8 B:ISJ403 2.1 47.1 1.0 OE2 B:GLU241 2.2 54.7 1.0 C7 B:ISJ403 2.3 46.9 1.0 OE2 B:GLU376 2.5 43.8 1.0 OE1 B:GLU241 2.6 52.4 1.0 CD B:GLU241 2.7 54.0 1.0 OE1 B:GLU376 2.7 47.5 1.0 CD B:GLU376 2.9 43.6 1.0 HZ3 B:LYS237 3.1 53.9 1.0 H B:GLY363 3.4 49.7 1.0 HB2 B:SER215 3.6 58.6 1.0 NZ B:LYS237 3.8 44.9 1.0 HZ1 B:LYS237 3.8 53.9 1.0 H B:GLY214 3.8 60.8 1.0 C3 B:ISJ403 3.8 46.0 1.0 HZ1 B:LYS380 3.9 55.7 1.0 OE1 B:GLU373 4.0 39.8 1.0 HZ2 B:LYS237 4.0 53.9 1.0 HB1 B:ALA362 4.0 46.5 1.0 HA2 B:GLY214 4.1 59.7 1.0 CG B:GLU241 4.1 52.0 1.0 H B:SER215 4.1 61.8 1.0 N B:GLY363 4.1 41.4 1.0 OD1 B:ASP238 4.1 55.7 1.0 O B:GLY363 4.2 39.8 1.0 HG2 B:GLU241 4.2 62.4 1.0 HZ2 B:LYS380 4.4 55.7 1.0 CG B:GLU376 4.4 37.7 1.0 HA B:ALA362 4.5 50.7 1.0 HA3 B:GLY363 4.5 49.2 1.0 N B:SER215 4.5 51.5 1.0 HG3 B:GLU241 4.5 62.4 1.0 NZ B:LYS380 4.5 46.4 1.0 CB B:SER215 4.6 48.9 1.0 N B:GLY214 4.6 50.6 1.0 OE2 B:GLU373 4.6 44.0 1.0 CA B:GLY214 4.7 49.8 1.0 H4 B:ISJ403 4.7 55.2 1.0 H2 B:ISJ403 4.7 53.9 1.0 CD B:GLU373 4.7 40.2 1.0 CA B:GLY363 4.7 41.0 1.0 HG2 B:GLU376 4.7 45.3 1.0 C4 B:ISJ403 4.8 46.0 1.0 C2 B:ISJ403 4.8 44.9 1.0 HG3 B:GLU376 4.8 45.3 1.0 CB B:ALA362 4.8 38.7 1.0 C B:GLY214 4.9 49.9 1.0 C B:GLY363 4.9 40.4 1.0 HZ3 B:LYS380 4.9 55.7 1.0 HG B:SER215 5.0 54.7 1.0 CA B:ALA362 5.0 42.3 1.0

Iron binding site 4 out of 4 in the An Iron-Bound Structure of the Isochorismate Synthase Entc


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of An Iron-Bound Structure of the Isochorismate Synthase Entc within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:77.2 occ:1.00 OD2 B:ASP40 2.0 68.7 1.0 CG B:ASP40 2.4 70.0 1.0 OD1 B:ASP40 2.4 68.4 1.0 OE1 B:GLU41 2.8 66.6 1.0 CD B:GLU41 3.8 68.5 1.0 CB B:ASP40 3.8 58.2 1.0 HA B:GLU41 4.0 68.6 1.0 HB2 B:ASP40 4.0 69.9 1.0 OE2 B:GLU41 4.2 66.9 1.0 N B:GLU41 4.4 56.6 1.0 H B:ASP40 4.4 69.2 1.0 HB3 B:ASP40 4.4 69.9 1.0 C B:ASP40 4.5 54.1 1.0 H B:GLU41 4.6 67.9 1.0 CA B:GLU41 4.6 57.1 1.0 CA B:ASP40 4.7 52.9 1.0 HZ2 B:LYS56 4.8 0.8 1.0 HB2 B:GLU41 4.8 68.8 1.0 N B:ASP40 4.9 57.6 1.0 HD3 B:PRO42 5.0 63.2 1.0 O B:ASP40 5.0 55.2 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