Magnesium in PDB 6c4a: Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate

All present enzymatic activity of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate:
4.1.3.1; 4.1.3.30;

The structure of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate, PDB code: 6c4a was solved by D.F.Kreitler, S.Ray, A.S.Murkin, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.18 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	142.670, 84.320, 156.180, 90.00, 116.59, 90.00
R / Rfree (%)	16.3 / 19.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate (pdb code 6c4a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate, PDB code: 6c4a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


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 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.2 occ:1.00 O A:HOH650 2.0 23.4 1.0 O A:HOH611 2.0 25.6 1.0 OD2 A:ASP153 2.0 31.6 1.0 O A:HOH620 2.1 27.3 1.0 O2 A:PYR501 2.1 32.7 1.0 O3 A:PYR501 2.1 36.7 1.0 C2 A:PYR501 2.8 34.5 1.0 C1 A:PYR501 2.8 32.4 1.0 CG A:ASP153 3.0 28.8 1.0 HZ1 A:LYS189 3.0 35.7 1.0 HG2 A:GLU155 3.3 25.8 1.0 OZH A:EJA191 3.4 48.3 1.0 OD1 A:ASP153 3.4 27.5 1.0 H A:TRP93 3.5 36.3 1.0 H A:GLY92 3.6 41.0 1.0 HE1 A:HIS180 3.6 29.6 1.0 HA3 A:GLY92 3.6 32.5 1.0 HH12 A:ARG228 3.8 40.9 1.0 NZ A:LYS189 3.9 29.7 1.0 OD2 A:ASP108 3.9 31.1 1.0 HE3 A:LYS189 3.9 32.6 1.0 N A:TRP93 4.1 30.2 1.0 O1 A:PYR501 4.1 30.4 1.0 HE2 A:LYS189 4.2 32.6 1.0 N A:GLY92 4.2 34.1 1.0 OD1 A:ASP108 4.2 33.4 1.0 OZ A:EJA191 4.2 40.3 1.0 CA A:GLY92 4.2 27.1 1.0 HB2 A:TRP93 4.2 37.0 1.0 CG A:GLU155 4.2 21.5 1.0 NE A:EJA191 4.2 34.8 1.0 CE A:LYS189 4.2 27.2 1.0 C3 A:PYR501 4.2 34.1 1.0 HZ2 A:LYS189 4.2 35.7 1.0 NH1 A:ARG228 4.3 34.1 1.0 CB A:ASP153 4.4 25.4 1.0 HH11 A:ARG228 4.4 40.9 1.0 HA A:GLU155 4.4 33.6 1.0 HZ3 A:LYS189 4.4 35.7 1.0 OE2 A:GLU155 4.4 31.0 1.0 CG A:ASP108 4.4 29.7 1.0 OE1 A:GLU182 4.4 26.0 1.0 HB2 A:ASP153 4.5 30.5 1.0 C A:GLY92 4.5 23.4 1.0 CE1 A:HIS180 4.5 24.7 1.0 HG3 A:GLU155 4.5 25.8 1.0 H31 A:PYR501 4.6 40.9 1.0 HB3 A:ASP153 4.6 30.5 1.0 H32 A:PYR501 4.6 40.9 1.0 HG A:SER91 4.7 36.3 1.0 CD A:GLU155 4.7 31.7 1.0 HH A:TYR89 4.9 47.5 1.0 OH A:TYR89 4.9 39.6 1.0 HA A:EJA191 4.9 39.6 1.0 H33 A:PYR501 4.9 40.9 1.0 H A:GLU155 4.9 31.5 1.0

Magnesium binding site 2 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


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 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:41.3 occ:1.00 O A:ALA276 2.2 38.5 1.0 O A:HOH633 2.3 38.5 1.0 OE1 A:GLN308 2.3 31.7 1.0 O A:ALA279 2.4 26.4 1.0 O A:HOH848 2.6 29.2 1.0 O A:HOH855 2.7 37.7 1.0 H A:ALA279 3.3 30.9 1.0 C A:ALA276 3.3 30.0 1.0 CD A:GLN308 3.3 32.2 1.0 HE22 A:GLN308 3.4 39.7 1.0 C A:ALA279 3.5 31.6 1.0 HA A:ALA276 3.7 42.5 1.0 NE2 A:GLN308 3.7 33.1 1.0 HB1 A:ALA276 3.9 44.6 1.0 HA A:PRO277 3.9 43.5 1.0 O A:ASP25 3.9 41.3 1.0 N A:ALA279 4.0 25.8 1.0 CA A:ALA276 4.0 35.4 1.0 O A:HOH670 4.0 33.9 1.0 HA A:ASP280 4.1 29.6 1.0 HB2 A:ASP25 4.2 64.8 1.0 HB3 A:ASP25 4.2 64.8 1.0 N A:PRO277 4.3 31.7 1.0 CA A:ALA279 4.3 23.6 1.0 O A:HOH779 4.3 46.7 1.0 HB3 A:ALA279 4.3 28.1 1.0 CA A:PRO277 4.4 36.2 1.0 C A:PRO277 4.5 38.6 1.0 CB A:ALA276 4.5 37.2 1.0 N A:ASP280 4.5 23.7 1.0 HE21 A:GLN308 4.6 39.7 1.0 HA A:GLN308 4.6 40.7 1.0 HB2 A:GLN308 4.7 48.2 1.0 CB A:ASP25 4.7 54.0 1.0 CG A:GLN308 4.7 37.8 1.0 CA A:ASP280 4.7 24.7 1.0 N A:PHE278 4.7 31.4 1.0 H A:PHE278 4.7 37.7 1.0 HD11 A:ILE282 4.8 48.2 1.0 O A:PRO277 4.8 34.5 1.0 O A:HOH659 4.8 31.2 1.0 CB A:ALA279 4.9 23.4 1.0 C A:ASP25 4.9 46.4 1.0 HG2 A:GLN308 4.9 45.4 1.0

Magnesium binding site 3 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


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 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:79.9 occ:1.00 HH22 A:ARG386 3.5 83.4 1.0 HH12 A:ARG386 4.1 86.9 1.0 OD1 B:ASP360 4.3 49.1 1.0 NH2 A:ARG386 4.3 69.5 1.0 OE1 B:GLU375 4.3 66.9 1.0 OD2 B:ASP360 4.6 50.6 1.0 HH21 A:ARG386 4.8 83.4 1.0 CG B:ASP360 4.8 52.4 1.0 NH1 A:ARG386 4.9 72.5 1.0 O B:HOH615 4.9 51.5 1.0

Magnesium binding site 4 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:30.1 occ:1.00 O2 B:PYR503 1.9 29.7 1.0 O B:HOH606 2.0 28.9 1.0 O B:HOH661 2.0 30.0 1.0 OD2 B:ASP153 2.1 31.8 1.0 O3 B:PYR503 2.1 30.9 1.0 O B:HOH612 2.2 24.1 1.0 C1 B:PYR503 2.7 29.5 1.0 C2 B:PYR503 2.8 30.8 1.0 HZ1 B:LYS189 3.1 44.0 1.0 CG B:ASP153 3.1 27.6 1.0 HG2 B:GLU155 3.4 35.4 1.0 H B:TRP93 3.5 35.2 1.0 OD1 B:ASP153 3.5 35.7 1.0 H B:GLY92 3.6 31.2 1.0 HH12 B:ARG228 3.6 52.6 1.0 HE1 B:HIS180 3.6 35.6 1.0 HA3 B:GLY92 3.7 36.6 1.0 OD2 B:ASP108 3.8 33.0 1.0 NZ B:LYS189 3.9 36.7 1.0 HE3 B:LYS189 4.0 37.9 1.0 O1 B:PYR503 4.0 28.5 1.0 N B:TRP93 4.1 29.4 1.0 NH1 B:ARG228 4.1 43.8 1.0 OD1 B:ASP108 4.2 35.5 1.0 N B:GLY92 4.2 26.0 1.0 OZ B:EJA191 4.2 42.9 1.0 HB2 B:TRP93 4.2 40.0 1.0 NE B:EJA191 4.2 34.0 1.0 HH11 B:ARG228 4.2 52.6 1.0 C3 B:PYR503 4.2 32.4 1.0 HE2 B:LYS189 4.3 37.9 1.0 CA B:GLY92 4.3 30.5 1.0 HZ2 B:LYS189 4.3 44.0 1.0 CE B:LYS189 4.3 31.6 1.0 OZH B:EJA191 4.3 51.5 1.0 CG B:GLU155 4.3 29.5 1.0 CG B:ASP108 4.4 35.4 1.0 OE2 B:GLU155 4.4 31.2 1.0 HA B:GLU155 4.4 33.1 1.0 CB B:ASP153 4.4 33.6 1.0 HB2 B:ASP153 4.5 40.3 1.0 HZ3 B:LYS189 4.5 44.0 1.0 CE1 B:HIS180 4.5 29.6 1.0 C B:GLY92 4.5 29.5 1.0 OE1 B:GLU182 4.6 33.4 1.0 H31 B:PYR503 4.6 38.9 1.0 H32 B:PYR503 4.6 38.9 1.0 HB3 B:ASP153 4.7 40.3 1.0 HG3 B:GLU155 4.7 35.4 1.0 HG B:SER91 4.7 35.4 1.0 CD B:GLU155 4.8 33.0 1.0 HA B:EJA191 4.8 36.7 1.0 H33 B:PYR503 4.9 38.9 1.0 OH B:TYR89 4.9 31.1 1.0 HH B:TYR89 5.0 37.3 1.0

Magnesium binding site 5 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:46.1 occ:1.00 O B:ALA276 2.3 45.5 1.0 O B:HOH826 2.3 38.2 1.0 O B:ALA279 2.3 40.1 1.0 OE1 B:GLN308 2.3 45.4 1.0 O B:HOH734 2.4 43.2 1.0 O B:HOH811 2.7 42.7 1.0 HE22 B:GLN308 3.2 62.5 1.0 CD B:GLN308 3.3 45.5 1.0 H B:ALA279 3.3 46.0 1.0 C B:ALA276 3.4 41.7 1.0 C B:ALA279 3.5 42.7 1.0 NE2 B:GLN308 3.6 52.0 1.0 HA B:ALA276 3.7 55.9 1.0 HB1 B:ALA276 3.9 66.1 1.0 HA B:ASP280 4.0 52.5 1.0 N B:ALA279 4.1 38.4 1.0 CA B:ALA276 4.1 46.6 1.0 O B:HOH697 4.1 33.5 1.0 HB3 B:ALA279 4.1 59.5 1.0 O B:ASP25 4.2 50.1 1.0 HA B:PRO277 4.2 59.0 1.0 HB3 B:ASP25 4.2 76.9 1.0 CA B:ALA279 4.3 37.3 1.0 HB2 B:ASP25 4.4 76.9 1.0 N B:PRO277 4.4 46.9 1.0 N B:ASP280 4.5 37.4 1.0 HE21 B:GLN308 4.5 62.5 1.0 HA B:GLN308 4.5 57.6 1.0 CB B:ALA276 4.5 55.1 1.0 O B:HOH742 4.5 36.6 1.0 CA B:PRO277 4.6 49.1 1.0 CA B:ASP280 4.6 43.7 1.0 C B:PRO277 4.6 49.2 1.0 HB2 B:GLN308 4.7 60.3 1.0 CG B:GLN308 4.7 52.3 1.0 CB B:ALA279 4.7 49.6 1.0 CB B:ASP25 4.8 64.1 1.0 HD11 B:ILE282 4.8 70.7 1.0 N B:PHE278 4.9 43.7 1.0 H B:PHE278 4.9 52.5 1.0 HG2 B:GLN308 4.9 62.7 1.0 C B:ASP280 5.0 46.4 1.0 O B:PRO277 5.0 42.2 1.0

Magnesium binding site 6 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.7 occ:1.00 O C:HOH625 1.9 22.1 1.0 OD2 C:ASP153 2.0 29.5 1.0 O C:HOH634 2.1 24.8 1.0 O3 C:PYR501 2.1 32.3 1.0 O1 C:PYR501 2.1 29.8 1.0 O C:HOH619 2.1 24.9 1.0 C2 C:PYR501 2.8 33.7 1.0 C1 C:PYR501 2.8 32.0 1.0 CG C:ASP153 3.1 26.3 1.0 HZ1 C:LYS189 3.1 37.6 1.0 OZH C:EJA191 3.3 50.4 1.0 HG2 C:GLU155 3.4 28.1 1.0 OD1 C:ASP153 3.5 26.6 1.0 H C:TRP93 3.5 31.8 1.0 H C:GLY92 3.6 36.1 1.0 HE1 C:HIS180 3.6 30.1 1.0 HA3 C:GLY92 3.7 31.4 1.0 HH12 C:ARG228 3.8 45.5 1.0 OD2 C:ASP108 3.9 30.3 1.0 NZ C:LYS189 3.9 31.3 1.0 HE3 C:LYS189 4.0 32.0 1.0 O2 C:PYR501 4.1 30.6 1.0 OZ C:EJA191 4.1 42.0 1.0 N C:TRP93 4.1 26.5 1.0 OD1 C:ASP108 4.2 26.4 1.0 N C:GLY92 4.2 30.1 1.0 HE2 C:LYS189 4.2 32.0 1.0 NE C:EJA191 4.2 35.5 1.0 C3 C:PYR501 4.2 34.1 1.0 HB2 C:TRP93 4.2 32.4 1.0 NH1 C:ARG228 4.2 37.9 1.0 CA C:GLY92 4.3 26.2 1.0 CE C:LYS189 4.3 26.7 1.0 HZ2 C:LYS189 4.3 37.6 1.0 HH11 C:ARG228 4.3 45.5 1.0 CG C:GLU155 4.3 23.4 1.0 CB C:ASP153 4.4 24.2 1.0 HA C:GLU155 4.4 29.6 1.0 HB2 C:ASP153 4.4 29.0 1.0 OE2 C:GLU155 4.5 32.6 1.0 CG C:ASP108 4.5 28.4 1.0 HZ3 C:LYS189 4.5 37.6 1.0 CE1 C:HIS180 4.5 25.1 1.0 OE1 C:GLU182 4.5 30.4 1.0 C C:GLY92 4.6 24.9 1.0 H31 C:PYR501 4.6 41.0 1.0 H33 C:PYR501 4.6 41.0 1.0 HB3 C:ASP153 4.7 29.0 1.0 HG C:SER91 4.7 32.1 1.0 HG3 C:GLU155 4.8 28.1 1.0 CD C:GLU155 4.8 34.2 1.0 HA C:EJA191 4.9 34.7 1.0 OH C:TYR89 4.9 31.1 1.0 H32 C:PYR501 4.9 41.0 1.0 H C:GLU155 4.9 28.3 1.0 HH C:TYR89 4.9 37.3 1.0

Magnesium binding site 7 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:35.9 occ:1.00 O C:HOH744 2.2 37.5 1.0 OE1 C:GLN308 2.4 33.4 1.0 O C:ALA276 2.4 40.4 1.0 O C:HOH819 2.4 39.6 1.0 O C:HOH872 2.4 34.9 1.0 O C:ALA279 2.4 29.3 1.0 HE22 C:GLN308 3.3 40.9 1.0 CD C:GLN308 3.3 33.2 1.0 H C:ALA279 3.4 44.0 1.0 C C:ALA276 3.5 31.9 1.0 C C:ALA279 3.6 43.5 1.0 NE2 C:GLN308 3.7 34.0 1.0 HA C:ALA276 3.8 36.1 1.0 O C:HOH812 3.9 27.5 1.0 HB3 C:ASP25 4.0 62.8 1.0 O C:ASP25 4.0 40.2 1.0 HB1 C:ALA276 4.0 45.5 1.0 HA C:ASP280 4.0 41.9 1.0 O C:HOH820 4.1 45.1 1.0 HA C:PRO277 4.1 44.2 1.0 CA C:ALA276 4.1 30.1 1.0 N C:ALA279 4.2 36.6 1.0 O C:HOH838 4.2 45.0 1.0 HB3 C:ALA279 4.3 36.8 1.0 CA C:ALA279 4.4 30.0 1.0 N C:PRO277 4.4 35.8 1.0 HE21 C:GLN308 4.5 40.9 1.0 HB2 C:ASP25 4.5 62.8 1.0 HA C:GLN308 4.5 50.5 1.0 N C:ASP280 4.5 31.2 1.0 CA C:PRO277 4.6 36.9 1.0 C C:PRO277 4.6 41.9 1.0 HB2 C:GLN308 4.6 44.8 1.0 CB C:ALA276 4.6 38.0 1.0 CA C:ASP280 4.7 34.9 1.0 CG C:GLN308 4.7 40.7 1.0 CB C:ASP25 4.7 52.3 1.0 O C:HOH730 4.8 35.5 1.0 H C:PHE278 4.8 44.1 1.0 N C:PHE278 4.8 36.7 1.0 HD11 C:ILE282 4.9 57.3 1.0 CB C:ALA279 4.9 30.7 1.0 C C:ASP25 4.9 47.3 1.0 HG2 C:GLN308 5.0 48.8 1.0 O C:PRO277 5.0 36.6 1.0

Magnesium binding site 8 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:31.1 occ:1.00 OD2 D:ASP153 1.9 31.0 1.0 O3 D:PYR501 2.0 38.0 1.0 O D:HOH653 2.1 34.5 1.0 O D:HOH605 2.1 30.0 1.0 O1 D:PYR501 2.1 37.4 1.0 O D:HOH612 2.1 21.8 1.0 C2 D:PYR501 2.7 39.0 1.0 C1 D:PYR501 2.8 36.4 1.0 CG D:ASP153 2.9 31.4 1.0 HZ1 D:LYS189 3.1 42.0 1.0 OD1 D:ASP153 3.3 33.4 1.0 OZH D:EJA191 3.4 55.6 1.0 H D:TRP93 3.4 32.2 1.0 HG2 D:GLU155 3.4 36.5 1.0 H D:GLY92 3.4 34.1 1.0 HA3 D:GLY92 3.5 33.5 1.0 HE1 D:HIS180 3.6 38.1 1.0 HH12 D:ARG228 3.9 46.5 1.0 NZ D:LYS189 3.9 35.0 1.0 HE3 D:LYS189 3.9 45.8 1.0 OD2 D:ASP108 3.9 34.1 1.0 N D:TRP93 4.0 26.9 1.0 O2 D:PYR501 4.0 33.2 1.0 N D:GLY92 4.1 28.4 1.0 CA D:GLY92 4.1 27.9 1.0 HE2 D:LYS189 4.1 45.8 1.0 C3 D:PYR501 4.2 39.1 1.0 OZ D:EJA191 4.2 46.4 1.0 CB D:ASP153 4.2 29.4 1.0 HB2 D:TRP93 4.2 31.4 1.0 CE D:LYS189 4.2 38.1 1.0 OE2 D:GLU155 4.2 34.4 1.0 OD1 D:ASP108 4.2 32.3 1.0 HZ2 D:LYS189 4.3 42.0 1.0 NE D:EJA191 4.3 48.5 1.0 HA D:GLU155 4.3 31.5 1.0 HB2 D:ASP153 4.3 35.3 1.0 NH1 D:ARG228 4.3 38.7 1.0 CG D:GLU155 4.4 30.4 1.0 HH11 D:ARG228 4.4 46.5 1.0 C D:GLY92 4.4 26.2 1.0 HZ3 D:LYS189 4.4 42.0 1.0 HB3 D:ASP153 4.5 35.3 1.0 CE1 D:HIS180 4.5 31.8 1.0 CG D:ASP108 4.5 32.9 1.0 H33 D:PYR501 4.5 46.9 1.0 H31 D:PYR501 4.6 46.9 1.0 OE1 D:GLU182 4.6 30.3 1.0 CD D:GLU155 4.6 35.2 1.0 HG D:SER91 4.7 34.5 1.0 H D:GLU155 4.8 34.7 1.0 H32 D:PYR501 4.8 46.9 1.0 HG3 D:GLU155 4.9 36.5 1.0 OH D:TYR89 4.9 33.2 1.0 HA D:EJA191 4.9 54.8 1.0 HH D:TYR89 5.0 39.9 1.0 CA D:TRP93 5.0 23.5 1.0 HA2 D:GLY92 5.0 33.5 1.0

Magnesium binding site 9 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:38.2 occ:1.00 O D:HOH771 2.2 37.8 1.0 O D:ALA276 2.2 36.7 1.0 O D:HOH849 2.4 35.5 1.0 O D:ALA279 2.4 34.9 1.0 OE1 D:GLN308 2.4 32.5 1.0 O D:HOH836 2.5 37.6 1.0 H D:ALA279 3.2 41.0 1.0 HE22 D:GLN308 3.3 51.6 1.0 C D:ALA276 3.4 35.3 1.0 CD D:GLN308 3.4 37.6 1.0 C D:ALA279 3.5 40.1 1.0 NE2 D:GLN308 3.7 43.0 1.0 HA D:ALA276 3.8 39.2 1.0 HB1 D:ALA276 3.9 47.1 1.0 HB3 D:ASP25 3.9 71.3 1.0 HA D:PRO277 3.9 48.2 1.0 O D:HOH768 4.0 32.5 1.0 N D:ALA279 4.0 34.1 1.0 O D:ASP25 4.0 51.1 1.0 HA D:ASP280 4.0 36.5 1.0 CA D:ALA276 4.1 32.6 1.0 N D:PRO277 4.3 39.2 1.0 CA D:ALA279 4.3 36.3 1.0 HB3 D:ALA279 4.3 43.3 1.0 O D:HOH831 4.3 49.6 1.0 CA D:PRO277 4.4 40.2 1.0 C D:PRO277 4.4 40.4 1.0 HB2 D:ASP25 4.5 71.3 1.0 N D:ASP280 4.5 30.6 1.0 CB D:ALA276 4.5 39.3 1.0 HE21 D:GLN308 4.6 51.6 1.0 CB D:ASP25 4.6 59.4 1.0 CA D:ASP280 4.7 30.4 1.0 N D:PHE278 4.7 37.2 1.0 H D:PHE278 4.7 44.7 1.0 HB2 D:GLN308 4.7 49.9 1.0 HA D:GLN308 4.7 56.4 1.0 O D:PRO277 4.7 36.8 1.0 CG D:GLN308 4.8 38.4 1.0 CB D:ALA279 4.9 36.1 1.0 O D:HOH720 4.9 30.8 1.0 C D:ASP25 4.9 53.6 1.0 HD11 D:ILE282 5.0 58.6 1.0

Magnesium binding site 10 out of 21 in the Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of 3-Nitropropionate Modified Isocitrate Lyase From Mycobacterium Tuberculosis with Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:26.6 occ:1.00 O E:HOH664 2.0 29.9 1.0 OD2 E:ASP153 2.0 24.2 1.0 O2 E:PYR501 2.0 28.5 1.0 O E:HOH636 2.0 26.2 1.0 O E:HOH608 2.1 21.2 1.0 O3 E:PYR501 2.2 28.1 1.0 C1 E:PYR501 2.8 26.0 1.0 C2 E:PYR501 2.9 26.0 1.0 CG E:ASP153 3.0 21.9 1.0 HZ1 E:LYS189 3.1 34.0 1.0 HG2 E:GLU155 3.3 34.1 1.0 H E:GLY92 3.4 28.4 1.0 OZH E:EJA191 3.4 35.6 1.0 H E:TRP93 3.4 30.5 1.0 OD1 E:ASP153 3.5 22.3 1.0 HA3 E:GLY92 3.6 26.6 1.0 HE1 E:HIS180 3.7 26.9 1.0 OD2 E:ASP108 3.8 25.7 1.0 HH12 E:ARG228 4.0 35.6 1.0 NZ E:LYS189 4.0 28.3 1.0 N E:TRP93 4.0 25.4 1.0 HE3 E:LYS189 4.0 34.4 1.0 N E:GLY92 4.0 23.6 1.0 O1 E:PYR501 4.1 22.9 1.0 OD1 E:ASP108 4.1 26.6 1.0 HB2 E:TRP93 4.1 30.0 1.0 HE2 E:LYS189 4.1 34.4 1.0 CA E:GLY92 4.1 22.1 1.0 CG E:GLU155 4.2 28.5 1.0 OZ E:EJA191 4.2 29.6 1.0 NE E:EJA191 4.3 34.6 1.0 CE E:LYS189 4.3 28.6 1.0 OE2 E:GLU155 4.3 27.2 1.0 C3 E:PYR501 4.3 24.9 1.0 CB E:ASP153 4.3 20.6 1.0 CG E:ASP108 4.4 23.9 1.0 HZ2 E:LYS189 4.4 34.0 1.0 C E:GLY92 4.4 25.4 1.0 NH1 E:ARG228 4.4 29.6 1.0 HB2 E:ASP153 4.4 24.7 1.0 HA E:GLU155 4.5 28.8 1.0 HH11 E:ARG228 4.5 35.6 1.0 HG3 E:GLU155 4.5 34.1 1.0 HZ3 E:LYS189 4.5 34.0 1.0 CE1 E:HIS180 4.6 22.4 1.0 HB3 E:ASP153 4.6 24.7 1.0 HG E:SER91 4.6 29.6 1.0 CD E:GLU155 4.6 22.9 1.0 H31 E:PYR501 4.7 29.8 1.0 OE1 E:GLU182 4.7 23.4 1.0 H32 E:PYR501 4.7 29.8 1.0 HA E:EJA191 4.8 28.4 1.0 CB E:TRP93 4.9 25.0 1.0 CA E:TRP93 4.9 23.9 1.0 OH E:TYR89 4.9 27.7 1.0 HH E:TYR89 4.9 33.3 1.0 H33 E:PYR501 4.9 29.8 1.0 HA E:TRP93 5.0 28.7 1.0

S.Ray, D.F.Kreitler, A.M.Gulick, A.S.Murkin. The Nitro Group As A Masked Electrophile in Covalent Enzyme Inhibition. Acs Chem. Biol. V. 13 1470 2018.
ISSN: ESSN 1554-8937
PubMed: 29782144
DOI: 10.1021/ACSCHEMBIO.8B00225