Calcium in PDB 8vhd: Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate

Enzymatic activity of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate

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

Protein crystallography data

The structure of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate, PDB code: 8vhd 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) 39.18 / 2.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.408, 103.894, 108.272, 90, 98.54, 90
R / Rfree (%) 16.9 / 22

Other elements in 8vhd:

The structure of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate also contains other interesting chemical elements:

Iodine (I) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate (pdb code 8vhd). 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 Isocitrate, PDB code: 8vhd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8vhd

Go back to Calcium Binding Sites List in 8vhd
Calcium binding site 1 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:34.5
occ:1.00
 OD1 A:ASP275 2.3 30.3 1.0
OD2 A:ASP279 2.3 32.4 1.0
O A:HOH791 2.4 34.4 1.0
OD1 B:ASP252 2.5 41.1 1.0
O A:HOH768 2.5 37.8 1.0
O A:ASP275 2.8 17.5 1.0
CG B:ASP252 3.2 29.5 1.0
CG A:ASP275 3.2 28.7 1.0
CG A:ASP279 3.4 32.8 1.0
C A:ASP275 3.6 19.2 1.0
OD1 A:ASP279 3.7 28.8 1.0
CB B:ASP252 3.8 17.7 1.0
OD2 A:ASP275 3.9 30.8 1.0
CA A:ASP275 4.0 18.5 1.0
O A:HOH644 4.0 36.7 1.0
OD2 B:ASP252 4.0 38.7 1.0
CB A:ASP275 4.1 21.4 1.0
OG A:SER278 4.5 34.6 1.0
CB A:ASP279 4.7 21.6 1.0
N A:VAL276 4.7 16.6 1.0
CA B:ASP252 4.9 19.1 1.0

Calcium binding site 2 out of 4 in 8vhd

Go back to Calcium Binding Sites List in 8vhd
Calcium binding site 2 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:36.5
occ:1.00
 OD1 B:ASP275 2.4 26.0 1.0
O B:HOH601 2.4 15.6 1.0
OD2 A:ASP252 2.4 36.0 1.0
O B:HOH744 2.5 31.4 1.0
O A:HOH806 2.5 38.2 1.0
O B:HOH759 2.5 39.5 1.0
CG B:ASP275 3.2 20.2 1.0
O B:HOH739 3.3 40.0 1.0
OD2 B:ASP275 3.4 21.9 1.0
CG A:ASP252 3.5 32.2 1.0
CB A:ASP252 4.0 23.5 1.0
OD2 B:ASP279 4.1 30.2 1.0
NZ A:LYS212 4.2 30.4 1.0
O B:ASP275 4.3 15.1 1.0
OD1 A:ASP252 4.5 46.2 1.0
CB B:ASP275 4.6 17.1 1.0
CG B:ASP279 4.7 27.4 1.0
O B:HOH621 4.7 29.3 1.0
OD1 B:ASP279 4.7 26.4 1.0
NH1 B:ARG109 4.7 32.0 1.0
C B:ASP275 4.9 18.1 1.0
O A:HOH655 4.9 27.8 1.0
CA B:ASP275 4.9 14.5 1.0

Calcium binding site 3 out of 4 in 8vhd

Go back to Calcium Binding Sites List in 8vhd
Calcium binding site 3 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca505

b:32.9
occ:1.00
 O7 C:ICT501 2.2 41.4 1.0
O1 C:ICT501 2.3 43.0 1.0
OD1 C:ASP275 2.3 40.7 1.0
O C:HOH615 2.3 17.2 1.0
OD2 D:ASP252 2.4 28.2 1.0
O C:HOH638 2.4 19.7 1.0
C2 C:ICT501 2.9 50.0 1.0
C1 C:ICT501 3.0 48.0 1.0
CG C:ASP275 3.4 33.6 1.0
CG D:ASP252 3.5 21.2 1.0
OD2 C:ASP275 3.8 35.6 1.0
CB D:ASP252 3.9 20.7 1.0
OD1 C:ASP279 4.0 25.4 1.0
O C:ALA308 4.0 38.5 1.0
O C:ASP275 4.0 21.7 1.0
NH1 C:ARG109 4.1 37.9 1.0
C5N C:NAP503 4.2 28.6 1.0
O2 C:ICT501 4.2 46.5 1.0
O C:HOH719 4.2 19.9 1.0
O D:HOH689 4.3 24.7 1.0
C3 C:ICT501 4.4 46.7 1.0
CG C:ASP279 4.4 21.4 1.0
NZ D:LYS212 4.4 20.2 1.0
C4N C:NAP503 4.5 28.2 1.0
OD2 C:ASP279 4.5 22.6 1.0
OD1 D:ASP252 4.5 24.2 1.0
CB C:ASP275 4.6 23.3 1.0
C6 C:ICT501 4.6 51.9 1.0
O6 C:ICT501 4.7 57.1 1.0
C C:ASP275 4.8 26.1 1.0
O C:HOH643 4.8 35.1 1.0
O D:HOH676 4.8 24.3 1.0
CA C:ASP275 4.8 19.2 1.0
NH2 C:ARG109 4.9 45.9 1.0
CZ C:ARG109 5.0 40.4 1.0

Calcium binding site 4 out of 4 in 8vhd

Go back to Calcium Binding Sites List in 8vhd
Calcium binding site 4 out of 4 in the Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Isocitrate


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 Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca505

b:36.5
occ:1.00
 OD1 D:ASP275 2.3 26.7 1.0
O D:HOH623 2.3 29.7 1.0
OD2 C:ASP252 2.4 30.6 1.0
O D:HOH730 2.4 35.2 1.0
O C:HOH727 2.4 47.6 1.0
O D:HOH723 2.4 39.7 1.0
CG D:ASP275 3.2 22.4 1.0
O D:ASP275 3.3 28.4 1.0
CG C:ASP252 3.3 32.1 1.0
OD2 D:ASP275 3.5 23.9 1.0
CB C:ASP252 3.6 31.4 1.0
OD2 D:ASP279 3.6 32.9 1.0
CG D:ASP279 4.0 28.6 1.0
OD1 D:ASP279 4.1 30.7 1.0
C D:ASP275 4.2 19.7 1.0
O D:HOH717 4.2 38.7 1.0
OD1 C:ASP252 4.4 29.1 1.0
CB D:ASP275 4.4 20.8 1.0
NZ C:LYS212 4.5 29.4 1.0
CA D:ASP275 4.6 18.2 1.0
NH1 D:ARG109 4.7 36.6 1.0
CA C:ASP252 4.9 21.4 1.0

Reference:

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.
Page generated: Fri Jul 19 12:33:28 2024

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