Manganese in PDB 6lrt: Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion

The structure of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion, PDB code: 6lrt was solved by S.H.Lee, K.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.05 / 2.90
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	157.314, 157.314, 197.707, 90, 90, 120
R / Rfree (%)	17.6 / 24.6

The binding sites of Manganese atom in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion (pdb code 6lrt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion, PDB code: 6lrt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:86.3 occ:1.00 OD2 A:ASP148 2.6 40.3 1.0 O1 A:ICT501 2.7 54.7 1.0 O7 A:ICT501 3.0 52.0 1.0 NZ A:LYS184 3.1 39.5 1.0 CG A:ASP148 3.5 36.9 1.0 O5 A:ICT501 3.6 52.0 1.0 C1 A:ICT501 3.6 50.9 1.0 C2 A:ICT501 3.7 47.7 1.0 CE A:LYS184 3.7 38.7 1.0 OD2 A:ASP104 3.7 42.2 1.0 OD1 A:ASP148 3.8 40.0 1.0 OD1 A:ASP104 3.9 44.5 1.0 NH1 A:ARG223 4.0 35.3 1.0 OE1 A:GLU177 4.0 42.0 1.0 C3 A:ICT501 4.1 45.9 1.0 CG A:ASP104 4.2 36.6 1.0 C6 A:ICT501 4.2 48.4 1.0 CG A:GLU150 4.3 35.4 1.0 OE1 A:GLU150 4.3 39.8 1.0 OE2 A:GLU177 4.4 45.1 1.0 N A:TRP89 4.5 30.2 1.0 CA A:GLY88 4.6 31.0 1.0 CD A:GLU177 4.7 42.5 1.0 N A:GLY88 4.7 29.9 1.0 NH2 A:ARG223 4.7 33.4 1.0 CZ A:ARG223 4.7 33.7 1.0 CD A:GLU150 4.8 37.7 1.0 CE1 A:HIS175 4.8 36.5 1.0 O2 A:ICT501 4.8 60.0 1.0 CB A:ASP148 4.9 34.1 1.0 C A:GLY88 5.0 28.9 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn503 b:100.0 occ:1.00 OD2 D:ASP148 2.5 42.9 1.0 O7 D:ICT501 2.5 54.2 1.0 O1 D:ICT501 2.8 49.6 1.0 OD2 D:ASP104 3.1 49.3 1.0 CG D:ASP148 3.3 37.9 1.0 OD1 D:ASP148 3.4 39.0 1.0 OD1 D:ASP104 3.5 49.0 1.0 C2 D:ICT501 3.5 50.5 1.0 C1 D:ICT501 3.5 49.7 1.0 N D:TRP89 3.6 26.8 1.0 CG D:ASP104 3.6 45.7 1.0 CA D:GLY88 3.8 25.4 1.0 NZ D:LYS184 3.8 55.6 1.0 OE2 D:GLU150 3.9 47.4 1.0 C D:GLY88 3.9 25.6 1.0 N D:GLY88 4.0 24.2 1.0 CG D:GLU150 4.0 40.9 1.0 CE D:LYS184 4.1 52.5 1.0 C3 D:ICT501 4.3 48.4 1.0 CD D:GLU150 4.4 43.3 1.0 CA D:TRP89 4.5 26.2 1.0 CB D:ASP148 4.6 35.5 1.0 CB D:TRP89 4.7 27.2 1.0 O2 D:ICT501 4.7 46.9 1.0 O D:GLY88 4.9 22.3 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn504 b:99.3 occ:1.00 O7 G:ICT501 2.4 56.5 1.0 OD2 G:ASP148 2.6 34.6 1.0 O2 G:ICT501 3.1 50.1 1.0 OD2 G:ASP104 3.4 29.6 1.0 NZ G:LYS184 3.4 45.9 1.0 C2 G:ICT501 3.5 49.0 1.0 CG G:ASP148 3.5 30.6 1.0 CE G:LYS184 3.7 45.3 1.0 C1 G:ICT501 3.7 44.6 1.0 OD1 G:ASP148 3.7 32.3 1.0 O6 G:ICT501 3.9 49.7 1.0 OD1 G:ASP104 4.0 29.9 1.0 CG G:ASP104 4.1 30.0 1.0 C3 G:ICT501 4.2 50.9 1.0 NH1 G:ARG223 4.2 29.0 1.0 OE1 G:GLU177 4.2 50.7 1.0 OE2 G:GLU150 4.2 55.4 1.0 C6 G:ICT501 4.4 51.1 1.0 N G:TRP89 4.5 26.2 1.0 CG G:GLU150 4.6 41.2 1.0 OE2 G:GLU177 4.7 38.8 1.0 CA G:GLY88 4.7 30.8 1.0 O1 G:ICT501 4.8 39.2 1.0 N G:GLY88 4.8 29.6 1.0 CD G:GLU150 4.9 42.2 1.0 CB G:ASP148 4.9 28.0 1.0 C G:GLY88 4.9 29.2 1.0 CD G:GLU177 4.9 42.1 1.0 CZ G:ARG223 5.0 30.4 1.0 NH2 G:ARG223 5.0 32.6 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn504 b:86.4 occ:1.00 O2 J:ICT501 2.6 47.4 1.0 OD2 J:ASP148 2.7 43.3 1.0 O7 J:ICT501 2.8 51.1 1.0 OD2 J:ASP104 3.2 37.7 1.0 C1 J:ICT501 3.4 42.7 1.0 C2 J:ICT501 3.4 43.4 1.0 CG J:ASP148 3.6 40.9 1.0 NZ J:LYS184 3.6 46.1 1.0 OD1 J:ASP148 3.7 51.4 1.0 CE J:LYS184 3.8 45.8 1.0 C3 J:ICT501 3.8 39.6 1.0 O6 J:ICT501 3.8 32.3 1.0 OD1 J:ASP104 4.0 37.8 1.0 CG J:ASP104 4.0 37.3 1.0 NH1 J:ARG223 4.2 32.0 1.0 C6 J:ICT501 4.2 34.2 1.0 OE2 J:GLU150 4.3 47.7 1.0 OE1 J:GLU177 4.3 65.2 1.0 OE2 J:GLU177 4.5 55.5 1.0 CG J:GLU150 4.5 41.3 1.0 N J:TRP89 4.5 26.3 1.0 O1 J:ICT501 4.6 39.9 1.0 NH2 J:ARG223 4.7 33.7 1.0 CD J:GLU150 4.8 45.2 1.0 CZ J:ARG223 4.8 31.1 1.0 CD J:GLU177 4.9 56.6 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ M:Mn502 b:85.2 occ:1.00 O7 M:ICT501 2.1 56.5 1.0 OD2 M:ASP148 2.4 40.3 1.0 O2 M:ICT501 2.8 43.8 1.0 NZ M:LYS184 3.2 43.4 1.0 C2 M:ICT501 3.3 48.1 1.0 C1 M:ICT501 3.4 47.6 1.0 CG M:ASP148 3.5 33.9 1.0 OD2 M:ASP104 3.7 36.8 1.0 OD1 M:ASP104 3.8 41.5 1.0 OD1 M:ASP148 3.9 37.6 1.0 N M:TRP89 3.9 33.6 1.0 CE M:LYS184 4.0 39.7 1.0 CG M:ASP104 4.1 33.4 1.0 CG M:GLU150 4.1 30.0 1.0 NH2 M:ARG223 4.2 31.5 1.0 C3 M:ICT501 4.2 48.6 1.0 OE2 M:GLU150 4.2 43.6 1.0 N M:GLY88 4.2 32.4 1.0 CA M:GLY88 4.2 33.7 1.0 C M:GLY88 4.4 32.8 1.0 OE1 M:GLU177 4.6 46.2 1.0 O1 M:ICT501 4.6 55.8 1.0 CD M:GLU150 4.6 34.8 1.0 CB M:ASP148 4.7 32.9 1.0 O6 M:ICT501 4.8 53.8 1.0 CA M:TRP89 4.9 35.5 1.0 C6 M:ICT501 4.9 50.4 1.0 CB M:TRP89 5.0 35.9 1.0 OE2 M:GLU177 5.0 45.1 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn503 b:86.6 occ:1.00 OD2 P:ASP148 2.3 42.8 1.0 O7 P:ICT501 2.6 65.7 1.0 O2 P:ICT501 2.8 55.9 1.0 CG P:ASP148 3.3 38.9 1.0 OD2 P:ASP104 3.4 37.8 1.0 C1 P:ICT501 3.5 55.3 1.0 N P:TRP89 3.6 25.9 1.0 OD1 P:ASP148 3.6 43.1 1.0 C2 P:ICT501 3.6 57.2 1.0 CA P:GLY88 3.6 28.5 1.0 OE2 P:GLU150 3.7 44.5 1.0 OD1 P:ASP104 3.7 36.9 1.0 C P:GLY88 3.9 27.5 1.0 CG P:ASP104 3.9 35.3 1.0 NZ P:LYS184 3.9 49.8 1.0 N P:GLY88 3.9 26.6 1.0 CE P:LYS184 4.0 46.6 1.0 CG P:GLU150 4.1 39.6 1.0 CD P:GLU150 4.3 43.5 1.0 C3 P:ICT501 4.5 54.4 1.0 CA P:TRP89 4.6 25.9 1.0 O1 P:ICT501 4.6 53.9 1.0 CB P:ASP148 4.6 37.2 1.0 CB P:TRP89 4.8 28.4 1.0 O P:GLY88 4.8 24.7 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ S:Mn505 b:89.3 occ:1.00 O1 S:ICT501 2.4 37.6 1.0 OD2 S:ASP148 2.6 33.7 1.0 O5 S:ICT501 3.1 49.6 1.0 CG S:ASP148 3.4 30.1 1.0 OD1 S:ASP148 3.5 29.6 1.0 C1 S:ICT501 3.5 37.6 1.0 NH2 S:ARG223 3.6 41.3 1.0 O7 S:ICT501 3.6 43.3 1.0 NZ S:LYS184 3.6 44.2 1.0 CE S:LYS184 3.7 41.4 1.0 OE1 S:GLU177 3.8 45.1 1.0 OD2 S:ASP104 4.0 34.3 1.0 C6 S:ICT501 4.0 50.7 1.0 C2 S:ICT501 4.0 42.2 1.0 CG S:GLU150 4.2 40.5 1.0 OE2 S:GLU177 4.4 47.8 1.0 CE1 S:HIS175 4.5 33.6 1.0 CD S:GLU177 4.5 44.4 1.0 C3 S:ICT501 4.5 44.6 1.0 O2 S:ICT501 4.5 35.4 1.0 OE2 S:GLU150 4.5 55.6 1.0 OD1 S:ASP104 4.6 42.2 1.0 CZ S:ARG223 4.6 32.9 1.0 CA S:GLU150 4.7 32.9 1.0 CG S:ASP104 4.7 36.3 1.0 CB S:ASP148 4.8 31.0 1.0 N S:TRP89 4.8 31.6 1.0 CA S:GLY88 4.9 37.6 1.0 N S:GLY88 4.9 36.3 1.0 CD S:GLU150 4.9 44.0 1.0 CB S:GLU150 4.9 37.4 1.0 O6 S:ICT501 4.9 44.3 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Isocitrate Lyase (CAUR_3889) From Chloroflexus Aurantiacus in Complex with Isocitrate and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ V:Mn504 b:84.7 occ:1.00 O1 V:ICT501 2.5 56.5 1.0 OD2 V:ASP148 2.7 55.5 1.0 O7 V:ICT501 2.7 58.7 1.0 OD2 V:ASP104 3.2 31.6 1.0 NZ V:LYS184 3.3 47.5 1.0 OD1 V:ASP104 3.4 35.7 1.0 C1 V:ICT501 3.4 50.8 1.0 C2 V:ICT501 3.4 53.3 1.0 CG V:ASP148 3.6 47.6 1.0 CG V:ASP104 3.7 36.3 1.0 CE V:LYS184 3.9 43.0 1.0 OD1 V:ASP148 3.9 59.2 1.0 C3 V:ICT501 3.9 49.4 1.0 OE2 V:GLU150 4.0 57.6 1.0 N V:TRP89 4.2 31.5 1.0 O5 V:ICT501 4.3 45.0 1.0 NH2 V:ARG223 4.4 39.6 1.0 CG V:GLU150 4.5 44.7 1.0 O2 V:ICT501 4.5 47.9 1.0 C6 V:ICT501 4.6 43.6 1.0 CA V:GLY88 4.6 35.2 1.0 N V:GLY88 4.6 33.5 1.0 CD V:GLU150 4.7 50.0 1.0 C V:GLY88 4.7 31.8 1.0 OE1 V:GLU177 4.7 64.8 1.0 CB V:ASP148 4.9 42.3 1.0 OE2 V:GLU177 4.9 50.6 1.0 CB V:TRP89 5.0 33.1 1.0 CA V:TRP89 5.0 32.5 1.0

S.H.Lee, K.J.Kim. Structural Studies Reveal the Molecular Mechanism of Isocitrate Lyase From Chloroflexus Aurantiacus To Be Published.