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Calcium in PDB 6aja: Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+, PDB code: 6aja 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) 19.93 / 2.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 120.894, 70.455, 122.052, 90.00, 113.39, 90.00
R / Rfree (%) 19.8 / 28.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+ (pdb code 6aja). 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 Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+, PDB code: 6aja:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6aja

Go back to Calcium Binding Sites List in 6aja
Calcium binding site 1 out of 4 in the Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate 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 Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:86.6
occ:1.00
 OD1 A:ASP274 2.7 58.4 1.0
O A:ASP274 2.8 57.1 1.0
OD2 B:ASP251 3.0 66.0 1.0
OD1 A:ASP278 3.1 74.1 1.0
CG A:ASP278 3.6 75.6 1.0
CG A:ASP274 3.6 59.1 1.0
C A:ASP274 3.7 54.3 1.0
OD2 A:ASP278 3.7 79.3 1.0
CA A:ASP274 4.0 54.3 1.0
CG B:ASP251 4.0 64.5 1.0
CB B:ASP251 4.3 59.8 1.0
OD2 A:ASP274 4.4 58.6 1.0
CB A:ASP274 4.4 57.1 1.0
NH2 A:ARG132 4.6 44.9 1.0
CB A:ASP278 4.7 71.7 1.0
N A:VAL275 4.9 51.5 1.0

Calcium binding site 2 out of 4 in 6aja

Go back to Calcium Binding Sites List in 6aja
Calcium binding site 2 out of 4 in the Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate 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 Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:66.0
occ:1.00
 OD1 B:ASP274 2.5 44.1 1.0
OD2 A:ASP251 2.8 66.8 1.0
OD1 B:ASP278 3.1 50.9 1.0
CG B:ASP274 3.7 41.9 1.0
CG B:ASP278 3.9 50.3 1.0
CG A:ASP251 3.9 63.0 1.0
OD2 B:ASP278 4.0 49.5 1.0
O B:ASP274 4.2 50.2 1.0
OD2 B:ASP274 4.3 41.1 1.0
CB A:ASP251 4.5 57.9 1.0
C B:ASP274 4.9 45.0 1.0
CB B:ASP274 4.9 41.4 1.0
OD1 A:ASP251 4.9 64.7 1.0
CA B:ASP274 5.0 42.1 1.0

Calcium binding site 3 out of 4 in 6aja

Go back to Calcium Binding Sites List in 6aja
Calcium binding site 3 out of 4 in the Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate 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 Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:75.2
occ:1.00
 OD2 C:ASP278 2.6 66.3 1.0
OD1 C:ASP274 3.0 54.8 1.0
O C:ASP274 3.4 53.0 1.0
CG C:ASP278 3.5 63.9 1.0
CG C:ASP274 3.6 51.8 1.0
OD1 C:ASP278 3.6 62.2 1.0
OD2 C:ASP274 3.8 51.3 1.0
CB D:ASP251 3.8 56.9 1.0
CG D:ASP251 3.8 60.6 1.0
OD2 D:ASP251 4.1 62.8 1.0
OD1 D:ASP251 4.2 61.4 1.0
C C:ASP274 4.3 51.0 1.0
CA C:ASP274 4.7 49.1 1.0
CB C:ASP274 4.7 50.9 1.0
CB C:ASP278 4.9 58.6 1.0

Calcium binding site 4 out of 4 in 6aja

Go back to Calcium Binding Sites List in 6aja
Calcium binding site 4 out of 4 in the Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate 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 Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadph, Alpha-Ketoglutarate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:66.0
occ:1.00
 O5 D:AKG503 2.5 83.1 1.0
O2 D:AKG503 2.6 75.1 1.0
OD1 D:ASP274 2.6 55.7 1.0
OD2 D:ASP278 2.8 50.9 1.0
C1 D:AKG503 3.1 81.4 1.0
C2 D:AKG503 3.2 82.5 1.0
CG D:ASP274 3.5 57.3 1.0
NH2 D:ARG109 3.6 54.6 1.0
CB C:ASP251 3.7 58.6 1.0
O D:ALA307 3.8 55.8 1.0
OD2 D:ASP274 3.8 63.3 1.0
OD2 C:ASP251 3.8 77.7 1.0
CG C:ASP251 3.9 69.7 1.0
CG D:ASP278 4.0 50.3 1.0
O D:ASP274 4.0 46.2 1.0
O1 D:AKG503 4.1 85.6 1.0
OD1 D:ASP278 4.4 49.6 1.0
NH2 D:ARG132 4.4 58.8 1.0
C5N D:NAP501 4.5 49.6 1.0
CA D:ASP274 4.6 50.8 1.0
C D:ASP274 4.6 49.0 1.0
CB D:ASP274 4.6 53.3 1.0
C3 D:AKG503 4.7 83.6 1.0
C4N D:NAP501 4.7 48.3 1.0
OD1 C:ASP251 4.7 73.4 1.0
NZ C:LYS211 4.8 55.6 1.0
CZ D:ARG109 4.9 52.6 1.0
C D:ALA307 4.9 53.3 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 16:29:12 2024

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