Atomistry » Calcium » PDB 6ahg-6b1v » 6ajc
Atomistry »
  Calcium »
    PDB 6ahg-6b1v »
      6ajc »

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

Go back to Calcium Binding Sites List in 6ajc
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

Go back to Calcium Binding Sites List in 6ajc
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

Go back to Calcium Binding Sites List in 6ajc
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

Go back to Calcium Binding Sites List in 6ajc
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

Go back to Calcium Binding Sites List in 6ajc
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

Go back to Calcium Binding Sites List in 6ajc
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

Go back to Calcium Binding Sites List in 6ajc
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

Go back to Calcium Binding Sites List in 6ajc
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: Mon Jul 15 16:29:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy