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

Enzymatic activity of 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;

Protein crystallography data

The structure of Crystal Structure of Human IDH1 R132Q in Complex with Nadph and Alpha- Ketoglutarate, PDB code: 8vhb 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) 39.63 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.404, 105.807, 109.782, 90, 98.44, 90
R / Rfree (%) 16.7 / 20.6

Other elements in 8vhb:

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

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 8vhb

Go back to Calcium Binding Sites List in 8vhb
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:Ca510

b:29.1
occ:1.00
 O A:HOH634 2.1 23.7 1.0
OD1 A:ASP275 2.3 28.1 1.0
OD2 B:ASP252 2.4 38.3 1.0
O2 A:AKG501 2.4 34.2 1.0
O A:HOH711 2.5 30.0 1.0
O A:HOH691 2.5 34.0 1.0
O5 A:AKG501 2.6 41.9 1.0
C1 A:AKG501 3.3 44.6 1.0
C2 A:AKG501 3.3 46.5 1.0
CG A:ASP275 3.4 27.8 1.0
CG B:ASP252 3.6 38.1 1.0
OD2 A:ASP275 3.8 29.6 1.0
CB B:ASP252 4.3 27.6 1.0
NH1 A:ARG109 4.3 30.0 1.0
O A:ASP275 4.3 21.9 1.0
NZ B:LYS212 4.4 39.1 1.0
OD2 A:ASP279 4.5 33.3 1.0
OD1 A:ASP279 4.5 32.4 1.0
O1 A:AKG501 4.5 43.0 1.0
OD1 B:ASP252 4.5 38.0 1.0
O A:HOH720 4.6 28.7 1.0
CB A:ASP275 4.7 19.7 1.0
CG A:ASP279 4.8 32.6 1.0
O A:HOH794 4.8 40.8 1.0
C3 A:AKG501 4.8 43.4 1.0
C A:ASP275 4.9 23.0 1.0
CA A:ASP275 4.9 20.1 1.0

Calcium binding site 2 out of 4 in 8vhb

Go back to Calcium Binding Sites List in 8vhb
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
A:Ca511

b:37.2
occ:1.00
 O B:HOH603 2.2 19.4 1.0
O19 B:EE1501 2.3 45.1 1.0
O B:HOH762 2.4 43.2 1.0
O B:HOH605 2.5 36.8 1.0
OD2 A:ASP252 2.5 31.1 0.5
OD1 B:ASP275 2.5 27.9 1.0
O B:HOH785 2.6 49.8 1.0
OD2 A:ASP252 2.7 30.0 0.5
O16 B:EE1501 3.1 48.5 1.0
C17 B:EE1501 3.1 43.6 1.0
C15 B:EE1501 3.2 40.5 1.0
CG B:ASP275 3.6 32.1 1.0
CG A:ASP252 3.6 28.2 0.5
CG A:ASP252 3.7 29.0 0.5
OD2 B:ASP279 3.9 40.2 1.0
OD2 B:ASP275 4.0 33.1 1.0
CB A:ASP252 4.1 26.9 0.5
CB A:ASP252 4.2 26.3 0.5
NZ A:LYS212 4.2 28.2 1.0
O B:ASP275 4.3 20.2 1.0
O18 B:EE1501 4.3 39.9 1.0
C10 B:EE1501 4.4 44.9 1.0
NH1 B:ARG109 4.4 34.0 1.0
O A:HOH609 4.4 43.1 1.0
OD1 A:ASP252 4.5 26.5 0.5
C11 B:EE1501 4.6 38.7 1.0
OD1 A:ASP252 4.7 28.5 0.5
CG B:ASP279 4.7 33.1 1.0
OD1 B:ASP279 4.8 30.4 1.0
CB B:ASP275 4.9 23.0 1.0
C B:ASP275 4.9 23.5 1.0

Calcium binding site 3 out of 4 in 8vhb

Go back to Calcium Binding Sites List in 8vhb
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:Ca507

b:33.3
occ:1.00
 O C:HOH649 2.2 30.9 1.0
O C:HOH679 2.2 35.5 1.0
OD1 C:ASP275 2.4 38.0 1.0
O2 C:AKG501 2.4 40.2 1.0
OD2 D:ASP252 2.4 26.7 0.5
O C:HOH685 2.4 37.9 1.0
OD2 D:ASP252 2.5 29.2 0.5
O5 C:AKG501 2.7 43.2 1.0
C1 C:AKG501 3.3 49.0 1.0
CG C:ASP275 3.4 36.9 1.0
C2 C:AKG501 3.4 50.5 1.0
CG D:ASP252 3.6 29.4 0.5
CG D:ASP252 3.6 29.3 0.5
OD2 C:ASP275 3.8 36.3 1.0
CB D:ASP252 4.0 27.9 0.5
CB D:ASP252 4.1 27.4 0.5
O C:ASP275 4.2 31.3 1.0
OD2 C:ASP279 4.2 36.3 1.0
NZ D:LYS212 4.3 34.8 1.0
NH1 C:ARG109 4.3 38.5 1.0
O C:HOH688 4.4 35.8 1.0
O1 C:AKG501 4.4 49.6 1.0
OD1 C:ASP279 4.5 36.7 1.0
OD1 D:ASP252 4.6 25.3 0.5
OD1 D:ASP252 4.6 27.1 0.5
CG C:ASP279 4.7 33.6 1.0
CB C:ASP275 4.7 28.8 1.0
C C:ASP275 4.8 28.5 1.0
CA C:ASP275 4.9 28.7 1.0
C3 C:AKG501 4.9 49.2 1.0

Calcium binding site 4 out of 4 in 8vhb

Go back to Calcium Binding Sites List in 8vhb
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:Ca509

b:32.8
occ:1.00
 O D:HOH613 2.2 21.4 1.0
OD1 D:ASP275 2.3 33.0 1.0
O18 D:EE1501 2.4 46.8 0.4
O18 D:EE1501 2.4 34.8 0.5
O D:HOH730 2.4 38.9 1.0
OD2 C:ASP252 2.5 44.8 1.0
O D:HOH604 2.5 38.7 1.0
O16 D:EE1501 2.6 41.9 0.5
C15 D:EE1501 3.2 41.2 0.5
C17 D:EE1501 3.2 39.6 0.5
C17 D:EE1501 3.2 46.9 0.4
O16 D:EE1501 3.2 45.8 0.4
C15 D:EE1501 3.3 43.4 0.4
CG D:ASP275 3.4 35.6 1.0
CG C:ASP252 3.7 39.7 1.0
OD2 D:ASP275 3.9 30.9 1.0
NZ C:LYS212 4.3 44.0 1.0
CB C:ASP252 4.3 31.9 1.0
O D:ASP275 4.3 25.1 1.0
NH1 D:ARG109 4.3 34.0 1.0
O19 D:EE1501 4.3 50.0 0.4
OD2 D:ASP279 4.4 38.3 1.0
O19 D:EE1501 4.4 37.0 0.5
C10 D:EE1501 4.4 46.9 0.4
C11 D:EE1501 4.5 44.2 0.5
C10 D:EE1501 4.5 46.4 0.5
C11 D:EE1501 4.5 45.3 0.4
O D:HOH807 4.5 39.1 1.0
OD1 C:ASP252 4.6 38.9 1.0
OD1 D:ASP279 4.6 31.8 1.0
O03 D:EE1501 4.7 43.4 0.5
CB D:ASP275 4.7 23.4 1.0
O D:HOH718 4.8 36.0 1.0
CG D:ASP279 4.8 31.5 1.0
O D:HOH634 4.8 32.5 1.0
C D:ASP275 4.9 25.1 1.0
CA D:ASP275 4.9 24.8 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 12:32:49 2024

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