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Calcium in PDB 6ajc: Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+

Enzymatic activity of Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+

All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+, PDB code: 6ajc was solved by X.Wang, D.K.Inaoka, T.Shiba, E.O.Balogun, N.Ziebart, S.Allman, Y.Watanabe, T.Nozaki, M.Boshart, F.Bringaud, S.Harada, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 123.765, 123.485, 127.040, 90.00, 105.96, 90.00
R / Rfree (%) 20.2 / 28.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ (pdb code 6ajc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+, PDB code: 6ajc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6ajc

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Calcium binding site 1 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


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 Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:43.5
occ:1.00
 O4 A:ICT503 2.3 33.6 1.0
OD2 A:ASP274 2.4 33.8 1.0
OD2 B:ASP251 2.4 41.1 1.0
OD2 A:ASP278 2.7 43.4 1.0
O A:ASP274 3.0 32.1 1.0
OD1 A:ASP278 3.3 48.1 1.0
CG A:ASP278 3.3 43.3 1.0
C5 A:ICT503 3.5 35.8 1.0
CG B:ASP251 3.5 36.5 1.0
CG A:ASP274 3.6 33.8 1.0
NH2 A:ARG109 3.6 27.2 1.0
C A:ASP274 3.8 32.0 1.0
CA A:ASP274 4.0 33.4 1.0
C4 A:ICT503 4.1 39.5 1.0
CB B:ASP251 4.2 33.2 1.0
O A:ALA307 4.3 31.6 1.0
O7 A:ICT503 4.3 47.7 1.0
CB A:ASP274 4.4 33.2 1.0
O3 A:ICT503 4.4 34.9 1.0
OD1 A:ASP274 4.5 35.3 1.0
OD1 B:ASP251 4.5 37.9 1.0
OG A:SER277 4.6 34.5 1.0
CB A:ASP278 4.7 39.1 1.0
CZ A:ARG109 4.7 27.2 1.0
C3 A:ICT503 4.8 45.3 1.0
N A:VAL275 4.9 31.1 1.0
NH1 A:ARG132 4.9 27.0 1.0

Calcium binding site 2 out of 8 in 6ajc

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Calcium binding site 2 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


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 Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:36.4
occ:1.00
 O3 B:ICT503 2.3 47.0 1.0
OD2 A:ASP251 2.4 45.0 1.0
OD2 B:ASP278 2.4 27.8 1.0
OD2 B:ASP274 2.4 33.5 1.0
O B:HOH602 2.5 23.7 1.0
O B:ASP274 2.7 32.6 1.0
CG A:ASP251 3.0 44.5 1.0
OD1 A:ASP251 3.0 42.9 1.0
CG B:ASP278 3.4 27.4 1.0
C B:ASP274 3.4 31.2 1.0
CG B:ASP274 3.5 29.9 1.0
C5 B:ICT503 3.5 49.1 1.0
OD1 B:ASP278 3.7 26.7 1.0
CA B:ASP274 3.8 29.9 1.0
NH2 B:ARG109 3.8 38.2 1.0
OG B:SER277 4.1 29.5 1.0
O B:ALA307 4.2 38.2 1.0
CB B:ASP274 4.2 30.3 1.0
OD1 B:ASP274 4.3 29.1 1.0
O4 B:ICT503 4.3 45.0 1.0
C4 B:ICT503 4.3 52.9 1.0
CB A:ASP251 4.4 42.1 1.0
N B:VAL275 4.5 32.2 1.0
CB B:ASP278 4.6 27.6 1.0
NZ A:LYS211 4.8 30.7 1.0
C3 B:ICT503 4.8 56.0 1.0
CA B:VAL275 4.9 33.6 1.0
N B:ASP278 5.0 29.2 1.0

Calcium binding site 3 out of 8 in 6ajc

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Calcium binding site 3 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


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 Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:39.0
occ:1.00
 OD2 C:ASP278 2.2 35.5 1.0
OD2 C:ASP274 2.3 40.0 1.0
OD2 D:ASP251 2.5 31.9 1.0
O3 C:ICT503 2.5 34.8 1.0
O C:ASP274 2.6 30.1 1.0
CG C:ASP278 3.3 34.6 1.0
CG C:ASP274 3.4 36.8 1.0
C5 C:ICT503 3.5 38.4 1.0
C C:ASP274 3.5 31.3 1.0
CG D:ASP251 3.6 32.0 1.0
NH2 C:ARG109 3.6 49.3 1.0
OD1 C:ASP278 3.9 38.2 1.0
CA C:ASP274 3.9 30.8 1.0
CB D:ASP251 4.0 32.1 1.0
C4 C:ICT503 4.1 43.4 1.0
OD1 C:ASP274 4.3 36.6 1.0
CB C:ASP274 4.3 34.5 1.0
O C:ALA307 4.4 35.4 1.0
OG C:SER277 4.4 31.3 1.0
O4 C:ICT503 4.5 37.9 1.0
CB C:ASP278 4.5 31.7 1.0
C3 C:ICT503 4.5 46.0 1.0
OD1 D:ASP251 4.6 35.1 1.0
N C:VAL275 4.6 30.2 1.0
NZ D:LYS211 4.8 31.2 1.0
CZ C:ARG109 4.9 46.3 1.0
CA D:ASP251 4.9 31.7 1.0

Calcium binding site 4 out of 8 in 6ajc

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Calcium binding site 4 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


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 Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:35.5
occ:1.00
 OD2 D:ASP274 2.3 31.4 1.0
OD2 D:ASP278 2.4 42.7 1.0
O4 D:ICT503 2.5 36.1 1.0
OD2 C:ASP251 2.5 43.7 1.0
O D:ASP274 2.9 33.0 1.0
CG D:ASP278 3.3 36.4 1.0
OD1 D:ASP278 3.5 38.7 1.0
CG D:ASP274 3.5 32.7 1.0
C5 D:ICT503 3.6 39.1 1.0
CG C:ASP251 3.7 37.4 1.0
C D:ASP274 3.7 31.3 1.0
NH2 D:ARG109 3.7 30.6 1.0
CA D:ASP274 4.0 31.4 1.0
CB C:ASP251 4.2 34.0 1.0
C4 D:ICT503 4.2 42.2 1.0
OG D:SER277 4.2 24.2 1.0
O D:ALA307 4.2 24.3 1.0
CB D:ASP274 4.4 33.9 1.0
OD1 D:ASP274 4.4 31.9 1.0
O3 D:ICT503 4.6 36.1 1.0
CB D:ASP278 4.6 32.9 1.0
OD1 C:ASP251 4.7 37.8 1.0
CZ D:ARG109 4.8 28.6 1.0
N D:VAL275 4.8 30.8 1.0
C3 D:ICT503 5.0 45.5 1.0
NZ C:LYS211 5.0 31.3 1.0

Calcium binding site 5 out of 8 in 6ajc

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Calcium binding site 5 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:40.2
occ:1.00
 OD2 F:ASP251 2.3 25.9 1.0
OD2 E:ASP278 2.4 37.3 1.0
O3 E:ICT503 2.5 32.8 1.0
OD2 E:ASP274 2.7 29.8 1.0
O E:ASP274 2.8 26.4 1.0
CG E:ASP278 3.3 37.3 1.0
OD1 E:ASP278 3.5 37.4 1.0
CG F:ASP251 3.6 26.2 1.0
C5 E:ICT503 3.7 35.9 1.0
NH2 E:ARG109 3.7 28.2 1.0
C E:ASP274 3.8 26.5 1.0
CG E:ASP274 3.9 27.2 1.0
O E:ALA307 4.0 35.4 1.0
OG E:SER277 4.1 33.0 1.0
C4 E:ICT503 4.2 39.0 1.0
CB F:ASP251 4.2 25.9 1.0
CA E:ASP274 4.3 27.3 1.0
OD1 F:ASP251 4.5 26.4 1.0
CB E:ASP278 4.6 35.8 1.0
O4 E:ICT503 4.7 35.1 1.0
CB E:ASP274 4.7 28.5 1.0
OD1 E:ASP274 4.7 24.9 1.0
NZ F:LYS211 4.8 28.4 1.0
C3 E:ICT503 4.8 41.5 1.0
CZ E:ARG109 4.8 24.7 1.0
C E:ALA307 4.9 30.1 1.0
N E:VAL275 4.9 24.5 1.0

Calcium binding site 6 out of 8 in 6ajc

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Calcium binding site 6 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca502

b:42.3
occ:1.00
 OD2 E:ASP251 2.2 40.4 1.0
OD2 F:ASP278 2.4 31.6 1.0
OD2 F:ASP274 2.6 30.1 1.0
O4 F:ICT503 2.6 65.0 1.0
O F:ASP274 3.0 27.0 1.0
CG F:ASP278 3.2 30.7 1.0
CG E:ASP251 3.3 36.3 1.0
OD1 F:ASP278 3.4 31.1 1.0
NH2 F:ARG109 3.6 40.4 1.0
CG F:ASP274 3.7 28.1 1.0
C5 F:ICT503 3.8 65.9 1.0
C F:ASP274 3.9 25.9 1.0
OG F:SER277 4.1 28.0 1.0
CB E:ASP251 4.1 34.3 1.0
O F:ALA307 4.2 36.5 1.0
OD1 E:ASP251 4.2 38.4 1.0
CA F:ASP274 4.3 25.6 1.0
OD1 F:ASP274 4.4 26.8 1.0
CB F:ASP278 4.5 30.2 1.0
O3 F:ICT503 4.5 61.8 1.0
CB F:ASP274 4.6 26.5 1.0
C4 F:ICT503 4.8 65.2 1.0
CZ F:ARG109 4.8 41.4 1.0
N F:ASP278 4.9 27.4 1.0
C F:ALA307 5.0 35.1 1.0
NH1 F:ARG132 5.0 26.8 1.0
CA E:ASP251 5.0 31.8 1.0
N F:VAL275 5.0 24.5 1.0

Calcium binding site 7 out of 8 in 6ajc

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Calcium binding site 7 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca502

b:36.1
occ:1.00
 OD2 H:ASP251 2.3 38.2 1.0
OD2 G:ASP278 2.5 46.8 1.0
OD2 G:ASP274 2.5 32.0 1.0
O4 G:ICT503 2.6 39.7 1.0
O G:HOH608 2.9 28.1 1.0
O G:ASP274 3.0 32.6 1.0
CG G:ASP278 3.3 42.8 1.0
CG H:ASP251 3.5 39.9 1.0
OD1 G:ASP278 3.5 44.2 1.0
C G:ASP274 3.7 28.9 1.0
CG G:ASP274 3.7 31.4 1.0
NH2 G:ARG109 3.7 32.1 1.0
C5 G:ICT503 3.8 42.2 1.0
CA G:ASP274 4.0 30.2 1.0
OG G:SER277 4.1 26.9 1.0
CB H:ASP251 4.2 39.3 1.0
C4 G:ICT503 4.4 43.7 1.0
CB G:ASP274 4.4 31.3 1.0
OD1 H:ASP251 4.4 43.0 1.0
O G:ALA307 4.4 31.7 1.0
CB G:ASP278 4.5 37.2 1.0
OD1 G:ASP274 4.7 30.0 1.0
O3 G:ICT503 4.7 43.3 1.0
N G:VAL275 4.7 29.7 1.0
N G:ASP278 4.9 32.0 1.0
CZ G:ARG109 4.9 30.6 1.0
NH1 G:ARG132 5.0 32.7 1.0

Calcium binding site 8 out of 8 in 6ajc

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Calcium binding site 8 out of 8 in the Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Trypanosoma Cruzi Cytosolic Isocitrate Dehydrogenase in Complex with Nadp+, Isocitrate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca502

b:44.6
occ:1.00
 OD2 G:ASP251 2.1 42.7 1.0
OD2 H:ASP278 2.3 42.9 1.0
OD2 H:ASP274 2.3 32.7 1.0
O3 H:ICT503 2.4 39.6 1.0
O H:ASP274 3.0 34.5 1.0
CG G:ASP251 3.3 39.5 1.0
CG H:ASP278 3.3 45.9 1.0
CG H:ASP274 3.4 32.0 1.0
C5 H:ICT503 3.4 45.4 1.0
C H:ASP274 3.7 33.7 1.0
OD1 H:ASP278 3.7 49.0 1.0
C4 H:ICT503 3.8 46.9 1.0
CB G:ASP251 3.9 35.8 1.0
CA H:ASP274 4.0 33.9 1.0
OD1 H:ASP274 4.2 29.6 1.0
CB H:ASP274 4.3 33.6 1.0
OD1 G:ASP251 4.3 44.0 1.0
NH1 H:ARG109 4.3 39.0 1.0
C3 H:ICT503 4.4 50.5 1.0
OG H:SER277 4.5 38.7 1.0
O4 H:ICT503 4.6 42.6 1.0
O H:ALA307 4.6 42.1 1.0
NZ G:LYS211 4.6 40.1 1.0
CB H:ASP278 4.6 44.1 1.0
N H:VAL275 4.7 32.8 1.0
NH1 H:ARG132 4.8 42.4 1.0
CA G:ASP251 5.0 36.6 1.0

Reference:

X.Wang, D.K.Inaoka, T.Shiba, E.O.Balogun, N.Ziebart, S.Allman, Y.Watanabe, T.Nozaki, M.Boshart, F.Bringaud, S.Harada, K.Kita. Biochemical Characterization of A Novel Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase with Dual Coenzyme Specificity (Nadp+/Nad+) To Be Published.
Page generated: Wed Jul 9 12:28:43 2025

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