Calcium in PDB 8vha: Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate

All present enzymatic activity of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate:
1.1.1.42;

The structure of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate, PDB code: 8vha was solved by M.Mealka, C.D.Sohl, T.Huxford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.15 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.821, 104.86, 107.711, 90, 98.19, 90
R / Rfree (%)	16.7 / 22.2

The binding sites of Calcium atom in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate (pdb code 8vha). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate, PDB code: 8vha:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


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 Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:38.5 occ:1.00 O A:HOH676 2.1 47.0 1.0 OD1 A:ASP275 2.3 31.3 1.0 O A:HOH697 2.4 41.6 1.0 OD2 A:ASP279 2.4 41.9 1.0 OD2 B:ASP252 2.5 45.0 1.0 O A:ASP275 2.7 31.8 1.0 CG A:ASP275 3.4 33.6 1.0 CG B:ASP252 3.4 37.9 1.0 CG A:ASP279 3.5 37.4 1.0 C A:ASP275 3.5 30.2 1.0 CB B:ASP252 3.7 33.8 1.0 OD1 A:ASP279 3.9 42.5 1.0 CA A:ASP275 4.0 28.1 1.0 OD2 A:ASP275 4.2 36.6 1.0 CB A:ASP275 4.2 32.6 1.0 OD1 B:ASP252 4.5 43.5 1.0 N A:VAL276 4.6 29.9 1.0 O16 A:EE1501 4.6 49.6 1.0 CB A:ASP279 4.7 31.7 1.0 O19 A:EE1501 4.8 66.2 1.0 OG A:SER278 4.9 35.4 1.0 NZ B:LYS212 4.9 32.8 1.0 CA A:VAL276 5.0 27.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


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 Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:52.6 occ:1.00 O B:HOH627 2.3 38.0 1.0 OD2 A:ASP252 2.4 52.8 1.0 OD1 B:ASP275 2.5 40.6 1.0 O B:HOH625 2.5 39.8 1.0 O5 B:AKG503 2.7 71.3 1.0 O B:HOH641 2.8 44.9 1.0 O2 B:AKG503 2.9 56.8 1.0 CG B:ASP275 3.4 32.8 1.0 C2 B:AKG503 3.5 67.9 1.0 CG A:ASP252 3.5 45.5 1.0 C1 B:AKG503 3.7 67.0 1.0 OD2 B:ASP275 3.7 35.7 1.0 OD2 B:ASP279 4.2 37.4 1.0 CB A:ASP252 4.2 38.6 1.0 O B:ASP275 4.3 26.4 1.0 NZ A:LYS212 4.4 41.5 1.0 OD1 A:ASP252 4.5 51.6 1.0 O B:HOH676 4.5 39.8 1.0 NH1 B:ARG109 4.6 49.1 1.0 O4 B:AKG503 4.6 70.3 1.0 OD1 B:ASP279 4.6 35.4 1.0 CG B:ASP279 4.7 35.4 1.0 CB B:ASP275 4.8 25.6 1.0 O1 B:AKG503 4.8 64.4 1.0 C B:ASP275 5.0 25.6 1.0 C3 B:AKG503 5.0 62.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


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 Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:59.0 occ:1.00 O C:HOH603 1.8 40.3 1.0 OD1 C:ASP275 2.2 46.7 1.0 OD2 D:ASP252 2.4 50.9 1.0 O C:HOH661 2.5 52.8 1.0 O19 C:EE1502 3.0 60.2 1.0 O16 C:EE1502 3.0 67.0 1.0 C17 C:EE1502 3.3 63.2 1.0 CG C:ASP275 3.4 46.4 1.0 C15 C:EE1502 3.5 68.6 1.0 CG D:ASP252 3.5 46.3 1.0 OD1 C:ASP279 3.8 47.4 1.0 O C:ASP275 3.8 35.4 1.0 CB D:ASP252 4.0 36.5 1.0 OD2 C:ASP275 4.0 49.2 1.0 O18 C:EE1502 4.0 60.2 1.0 H9 C:EE1502 4.0 72.6 1.0 CG C:ASP279 4.3 45.1 1.0 C C:ASP275 4.4 34.0 1.0 NZ D:LYS212 4.4 39.8 1.0 OD2 C:ASP279 4.5 57.8 1.0 CA C:ASP275 4.5 32.1 1.0 OD1 D:ASP252 4.6 47.6 1.0 CB C:ASP275 4.6 34.7 1.0 O C:ALA308 4.6 61.2 1.0 NH2 C:ARG109 4.6 63.2 1.0 C08 C:EE1502 4.6 60.5 1.0 H11 C:EE1502 4.7 74.8 1.0 C10 C:EE1502 4.8 69.1 1.0 C09 C:EE1502 5.0 62.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca503 b:53.3 occ:1.00 O D:HOH606 2.2 34.9 1.0 OD1 D:ASP275 2.3 43.6 1.0 O D:HOH704 2.5 50.4 1.0 OD2 C:ASP252 2.5 46.4 1.0 O D:HOH733 2.6 43.4 1.0 O D:HOH720 2.8 42.2 1.0 CG D:ASP275 3.4 35.9 1.0 CG C:ASP252 3.6 43.9 1.0 OD2 D:ASP275 3.8 34.7 1.0 OD2 D:ASP279 4.0 44.2 1.0 O D:ASP275 4.0 30.9 1.0 CB C:ASP252 4.2 43.1 1.0 NZ C:LYS212 4.4 39.5 1.0 OD1 D:ASP279 4.5 50.6 1.0 CG D:ASP279 4.5 42.9 1.0 O D:HOH603 4.5 39.6 1.0 OD1 C:ASP252 4.6 46.5 1.0 CB D:ASP275 4.7 29.7 1.0 C D:ASP275 4.7 28.3 1.0 CA D:ASP275 4.8 26.3 1.0 NH1 D:ARG109 4.8 48.3 1.0

M.Mealka, C.D.Sohl, T.Huxford. Active Site Remodeling in Tumor-Relevant IDH1 Mutants Drive Distinct Kinetic Features and Possible Resistance Mechanisms To Be Published.