Calcium in PDB 8bay: Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate

All present enzymatic activity of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate:
1.1.1.42;

The structure of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate, PDB code: 8bay was solved by P.Rabe, C.J.Schofield, R.Reinbold, L.Brewitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.81 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.54, 275.78, 116.61, 90, 90, 90
R / Rfree (%)	20.1 / 22.3

The binding sites of Calcium atom in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate (pdb code 8bay). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate, PDB code: 8bay:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:67.1 occ:1.00 OD1 B:ASP275 2.4 70.7 1.0 O4 B:QDC803 2.4 71.8 0.5 OD2 A:ASP252 2.4 70.0 1.0 O B:HOH905 2.4 63.3 1.0 O B:HOH946 2.5 72.9 1.0 O4 B:QD8804 2.6 71.7 0.5 C1 B:QDC803 3.2 72.4 0.5 OD2 B:ASP279 3.2 65.6 1.0 C B:QDC803 3.3 72.1 0.5 CG A:ASP252 3.3 64.9 1.0 C B:QD8804 3.3 71.9 0.5 C1 B:QD8804 3.3 72.5 0.5 CB A:ASP252 3.4 64.5 1.0 O B:QDC803 3.5 72.7 0.5 O1 B:QD8804 3.6 72.5 0.5 CG B:ASP275 3.6 67.5 1.0 O B:QD8804 3.7 73.9 0.5 O1 B:QDC803 3.8 73.9 0.5 O B:ASP275 3.8 57.9 1.0 CG B:ASP279 3.9 65.8 1.0 OD1 B:ASP279 3.9 66.0 1.0 OD2 B:ASP275 4.2 66.1 1.0 NH1 B:ARG109 4.4 71.2 1.0 OD1 A:ASP252 4.4 65.2 1.0 C2 B:QDC803 4.5 70.9 0.5 C B:ASP275 4.6 58.7 1.0 NZ A:LYS212 4.6 60.9 1.0 C5N B:NDP801 4.6 79.8 0.8 C2 B:QD8804 4.8 70.9 0.5 O B:ALA308 4.8 102.6 1.0 CB B:ASP275 4.8 62.7 1.0 CA B:ASP275 4.8 57.4 1.0 C4N B:NDP801 4.9 80.3 0.8 CA A:ASP252 4.9 59.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:57.7 occ:1.00 O4 A:QDC704 2.4 66.2 0.5 O A:HOH803 2.4 60.5 1.0 OD1 A:ASP275 2.4 59.5 1.0 O4 A:QD8705 2.4 66.0 0.5 O A:HOH807 2.4 66.2 1.0 OD2 B:ASP252 2.6 59.0 1.0 O1 A:QDC704 2.7 64.2 0.5 O A:QD8705 2.8 65.3 0.5 C A:QDC704 3.1 64.0 0.5 C A:QD8705 3.1 64.2 0.5 C1 A:QDC704 3.1 65.0 0.5 C1 A:QD8705 3.1 64.9 0.5 OD2 A:ASP279 3.5 62.4 1.0 CG A:ASP275 3.6 59.1 1.0 CG B:ASP252 3.6 57.8 1.0 OD1 A:ASP279 3.9 57.7 1.0 CG A:ASP279 3.9 61.1 1.0 O A:QDC704 4.0 64.0 0.5 O A:ASP275 4.0 56.8 1.0 CB B:ASP252 4.0 54.5 1.0 O1 A:QD8705 4.1 65.1 0.5 O B:HOH934 4.1 70.1 1.0 NH1 A:ARG109 4.1 59.4 1.0 OD2 A:ASP275 4.1 60.1 1.0 C2 A:QDC704 4.6 62.0 0.5 C2 A:QD8705 4.6 62.3 0.5 C A:ASP275 4.7 55.1 1.0 OD1 B:ASP252 4.7 56.2 1.0 CB A:ASP275 4.8 55.3 1.0 CA A:ASP275 4.8 54.3 1.0 NZ B:LYS212 4.8 54.7 1.0 O A:ALA308 4.9 73.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca606 b:54.6 occ:1.00 O C:HOH717 2.4 54.6 1.0 OD1 C:ASP275 2.4 57.4 1.0 O4 C:QDC604 2.4 61.9 0.5 O C:HOH788 2.5 60.0 1.0 O4 C:QD8605 2.6 61.6 0.5 O1 C:QD8605 2.7 59.9 0.5 O C:QDC604 3.0 60.1 0.5 C1 C:QDC604 3.1 61.7 0.5 C C:QD8605 3.2 61.4 0.5 C1 C:QD8605 3.2 61.8 0.5 C C:QDC604 3.3 61.2 0.5 OD2 C:ASP279 3.5 60.7 1.0 CG C:ASP275 3.5 53.7 1.0 OD1 C:ASP279 3.9 57.5 1.0 CG C:ASP279 3.9 54.4 1.0 O C:ASP275 4.0 48.6 1.0 OD2 C:ASP275 4.1 54.3 1.0 NH1 C:ARG109 4.2 56.6 1.0 O1 C:QDC604 4.3 63.2 0.5 O C:QD8605 4.3 63.7 0.5 C2 C:QDC604 4.5 60.9 0.5 C C:ASP275 4.6 50.1 1.0 O C:HOH701 4.7 57.4 1.0 C2 C:QD8605 4.7 60.9 0.5 CB C:ASP275 4.7 49.6 1.0 CA C:ASP275 4.8 49.1 1.0 O C:ALA308 4.9 71.0 1.0

P.Rabe, C.J.Schofield, R.Reinbold, L.Brewitz. Crystal Structure of IDH1 Variant R132C S280F in Complex with Nadph, CA2+ and 3-Butyl-2-Oxoglutarate To Be Published.