Calcium in PDB 4kzo: Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate

All present enzymatic activity of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate:
1.1.1.42;

The structure of Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate, PDB code: 4kzo was solved by N.O.Concha, A.M.Smallwood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.77 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	96.360, 274.598, 115.990, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.1

The binding sites of Calcium atom in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate (pdb code 4kzo). 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 Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate, PDB code: 4kzo:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/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 Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:30.2 occ:1.00 OD1 A:ASP275 2.2 48.7 1.0 OD2 B:ASP252 2.3 37.2 1.0 O2 A:AKG503 2.4 41.2 1.0 OD2 A:ASP279 2.4 39.4 1.0 O A:HOH601 2.4 29.9 1.0 O A:HOH602 2.5 24.5 1.0 O A:ASP275 2.6 30.5 1.0 O5 A:AKG503 2.8 46.3 1.0 C1 A:AKG503 3.2 48.4 1.0 CG A:ASP279 3.3 39.2 1.0 CG B:ASP252 3.4 38.4 1.0 C2 A:AKG503 3.4 46.7 1.0 CG A:ASP275 3.5 46.0 1.0 C A:ASP275 3.5 26.7 1.0 OD1 A:ASP279 3.5 37.6 1.0 CB B:ASP252 3.8 31.9 1.0 NH1 A:ARG109 4.1 23.7 1.0 CA A:ASP275 4.1 27.4 1.0 OD2 A:ASP275 4.3 53.8 1.0 OG A:SER278 4.4 28.7 1.0 CB A:ASP275 4.4 30.1 1.0 O1 A:AKG503 4.4 41.9 1.0 OD1 B:ASP252 4.4 38.4 1.0 O A:ALA308 4.5 34.5 1.0 N A:VAL276 4.5 22.4 1.0 CB A:ASP279 4.6 17.9 1.0 NZ B:LYS212 4.7 41.4 1.0 CA A:VAL276 4.8 23.2 1.0 CA B:ASP252 4.8 28.1 1.0 C3 A:AKG503 4.9 38.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/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 Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:38.7 occ:1.00 OD1 B:ASP275 2.3 53.7 1.0 OD2 A:ASP252 2.3 50.7 1.0 O B:HOH601 2.4 33.0 1.0 O2 B:AKG503 2.4 63.9 1.0 O B:HOH602 2.4 44.7 1.0 OD2 B:ASP279 2.5 44.9 1.0 O B:ASP275 2.7 29.6 1.0 O5 B:AKG503 2.8 61.6 1.0 CG B:ASP279 3.3 42.9 1.0 C1 B:AKG503 3.3 64.7 1.0 OD1 B:ASP279 3.4 44.8 1.0 C2 B:AKG503 3.4 59.1 1.0 CG A:ASP252 3.5 49.0 1.0 CG B:ASP275 3.5 52.2 1.0 C B:ASP275 3.5 36.5 1.0 NH1 B:ARG109 4.0 35.1 1.0 CB A:ASP252 4.0 40.5 1.0 CA B:ASP275 4.0 36.7 1.0 OG B:SER278 4.1 31.7 1.0 OD2 B:ASP275 4.4 61.9 1.0 O B:ALA308 4.4 46.5 1.0 CB B:ASP275 4.4 42.6 1.0 O1 B:AKG503 4.5 69.5 1.0 OD1 A:ASP252 4.5 57.0 1.0 N B:VAL276 4.5 31.9 1.0 CB B:ASP279 4.6 32.1 1.0 CA B:VAL276 4.8 31.4 1.0 CA A:ASP252 4.9 36.0 1.0 C3 B:AKG503 4.9 51.2 1.0 O B:HOH696 4.9 51.5 1.0 N B:ASP279 5.0 29.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/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 Analysis of Human IDH1 Mutants in Complex with Nadp+ and CA2+/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:38.1 occ:1.00 O2 C:AKG503 2.2 46.8 1.0 OD1 C:ASP275 2.3 60.5 1.0 OD2 C:ASP279 2.3 43.8 1.0 O C:HOH602 2.5 33.5 1.0 O C:ASP275 2.5 26.6 1.0 O C:HOH601 2.6 36.0 1.0 O5 C:AKG503 3.0 51.4 1.0 C1 C:AKG503 3.2 46.7 1.0 CG C:ASP279 3.3 42.6 1.0 C C:ASP275 3.5 35.3 1.0 C2 C:AKG503 3.5 49.4 1.0 CG C:ASP275 3.5 51.1 1.0 OD1 C:ASP279 3.7 35.5 1.0 NH1 C:ARG109 4.0 37.5 1.0 CA C:ASP275 4.0 33.5 1.0 OG C:SER278 4.3 35.1 1.0 O1 C:AKG503 4.3 45.7 1.0 CB C:ASP275 4.4 39.1 1.0 OD2 C:ASP275 4.4 58.6 1.0 N C:VAL276 4.5 35.2 1.0 O C:ALA308 4.6 36.2 1.0 CB C:ASP279 4.6 31.4 1.0 CA C:VAL276 4.7 36.2 1.0

A.R.Rendina, B.Pietrak, A.Smallwood, H.Zhao, H.Qi, C.Quinn, N.D.Adams, N.Concha, C.Duraiswami, S.H.Thrall, S.Sweitzer, B.Schwartz. Mutant IDH1 Enhances the Production of 2-Hydroxyglutarate Due to Its Kinetic Mechanism. Biochemistry V. 52 4563 2013.
ISSN: ISSN 0006-2960
PubMed: 23731180
DOI: 10.1021/BI400514K