Manganese in PDB 1lwd: Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria

All present enzymatic activity of Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria:
1.1.1.42;

The structure of Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria, PDB code: 1lwd was solved by C.Ceccarelli, B.J.Bahnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.23 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.860, 112.569, 66.080, 90.00, 97.00, 90.00
R / Rfree (%)	18.2 / 21

The binding sites of Manganese atom in the Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria (pdb code 1lwd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria, PDB code: 1lwd:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria


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 Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:21.9 occ:1.00 OD1 A:ASP275 2.1 21.6 1.0 O A:HOH1001 2.2 17.6 1.0 O7 A:ICT701 2.2 21.8 1.0 O A:HOH1003 2.2 28.5 1.0 OD2 B:ASP252 2.3 21.5 1.0 O2 A:ICT701 2.3 23.7 1.0 C1 A:ICT701 3.0 23.6 1.0 C2 A:ICT701 3.2 22.6 1.0 CG A:ASP275 3.2 22.8 1.0 CG B:ASP252 3.3 21.9 1.0 CB B:ASP252 3.7 20.4 1.0 OD2 A:ASP275 3.8 26.5 1.0 O A:ASP275 4.0 18.0 1.0 NZ B:LYS212 4.1 20.1 1.0 OD1 A:ASP279 4.2 29.4 1.0 OD2 A:ASP279 4.2 30.0 1.0 C6 A:ICT701 4.2 24.9 1.0 O A:HOH1005 4.3 33.6 1.0 C3 A:ICT701 4.3 23.0 1.0 NH1 A:ARG110 4.3 17.7 1.0 O1 A:ICT701 4.3 22.3 1.0 CB A:ASP275 4.4 18.8 1.0 OD1 B:ASP252 4.4 20.3 1.0 CG A:ASP279 4.4 27.3 1.0 O5 A:ICT701 4.5 25.7 1.0 C A:ASP275 4.5 17.3 1.0 CA A:ASP275 4.5 16.6 1.0 O6 A:ICT701 4.6 24.1 1.0 NH1 A:ARG133 4.7 17.5 1.0 O B:HOH1007 5.0 40.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria


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 Nadp-Dependent Isocitrate Dehydrogenase From Porcine Heart Mitochondria within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:20.4 occ:1.00 OD1 B:ASP275 2.1 19.7 1.0 O7 B:ICT702 2.2 18.0 1.0 O B:HOH1002 2.2 18.4 1.0 OD2 A:ASP252 2.3 23.4 1.0 O2 B:ICT702 2.3 19.6 1.0 O B:HOH1004 2.4 26.6 1.0 C1 B:ICT702 3.0 19.5 1.0 C2 B:ICT702 3.2 19.3 1.0 CG B:ASP275 3.2 22.8 1.0 CG A:ASP252 3.3 20.0 1.0 CB A:ASP252 3.6 18.7 1.0 OD2 B:ASP275 3.7 26.2 1.0 O B:ASP275 4.0 15.8 1.0 O B:HOH1006 4.1 26.3 1.0 NZ A:LYS212 4.1 18.7 1.0 OD2 B:ASP279 4.2 27.3 1.0 C6 B:ICT702 4.2 20.3 1.0 OD1 B:ASP279 4.2 26.9 1.0 C3 B:ICT702 4.2 20.7 1.0 O1 B:ICT702 4.3 20.1 1.0 NH1 B:ARG110 4.4 16.9 1.0 OD1 A:ASP252 4.4 23.1 1.0 CB B:ASP275 4.4 19.7 1.0 O5 B:ICT702 4.4 22.0 1.0 CG B:ASP279 4.4 25.2 1.0 C B:ASP275 4.5 17.3 1.0 O6 B:ICT702 4.5 20.2 1.0 CA B:ASP275 4.5 17.6 1.0 O B:HOH1448 4.6 38.9 1.0 NH1 B:ARG133 4.7 16.5 1.0 O A:HOH1008 4.9 40.7 1.0

C.Ceccarelli, N.B.Grodsky, N.Ariyaratne, R.F.Colman, B.J.Bahnson. Crystal Structure of Porcine Mitochondrial Nadp+-Dependent Isocitrate Dehydrogenase Complexed with MN2+ and Isocitrate J.Biol.Chem. V. 277 43454 2002.
ISSN: ISSN 0021-9258
PubMed: 12207025
DOI: 10.1074/JBC.M207306200