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

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

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadh, 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 Nadh, Alpha-Ketoglutarate and CA2+, PDB code: 6ajb 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) 19.98 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 120.520, 70.464, 121.929, 90.00, 113.42, 90.00
R / Rfree (%) 19.2 / 28.4

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 6ajb

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

b:64.6
occ:1.00
 OD1 A:ASP274 2.3 49.1 1.0
O A:ASP274 3.0 46.8 1.0
OD2 B:ASP251 3.0 56.5 1.0
OD1 A:ASP278 3.1 67.2 1.0
CG A:ASP278 3.5 68.7 1.0
CG A:ASP274 3.5 48.5 1.0
CB B:ASP251 3.7 54.2 1.0
CG B:ASP251 3.8 55.2 1.0
C A:ASP274 3.9 44.6 1.0
CB A:ASP278 3.9 66.7 1.0
OD2 A:ASP278 4.2 71.7 1.0
CA A:ASP274 4.3 45.6 1.0
OD2 A:ASP274 4.3 51.6 1.0
CB A:ASP274 4.5 47.2 1.0
N A:ASP278 4.8 57.6 1.0
CA A:ASP278 4.9 62.0 1.0
NH2 A:ARG132 5.0 46.0 1.0

Calcium binding site 2 out of 4 in 6ajb

Go back to Calcium Binding Sites List in 6ajb
Calcium binding site 2 out of 4 in the Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadh, 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 Nadh, Alpha-Ketoglutarate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:94.4
occ:1.00
 OD1 B:ASP274 2.4 52.7 1.0
OD2 B:ASP278 2.7 58.0 1.0
CG B:ASP278 3.5 59.6 1.0
OD1 B:ASP278 3.5 58.2 1.0
CG B:ASP274 3.6 52.9 1.0
OD2 A:ASP251 3.9 60.1 1.0
O B:ASP274 3.9 54.3 1.0
CG A:ASP251 4.1 55.8 1.0
OD2 B:ASP274 4.2 54.1 1.0
CB A:ASP251 4.3 53.4 1.0
OD1 A:ASP251 4.7 56.6 1.0
C B:ASP274 4.8 52.1 1.0
CB B:ASP274 4.9 51.9 1.0
CA B:ASP274 4.9 50.5 1.0
CB B:ASP278 4.9 59.4 1.0

Calcium binding site 3 out of 4 in 6ajb

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

b:70.0
occ:1.00
 OD2 C:ASP278 2.4 51.7 1.0
OD2 C:ASP274 2.5 61.4 1.0
O C:ASP274 3.3 52.2 1.0
CG C:ASP278 3.3 52.0 1.0
OD1 C:ASP278 3.5 53.5 1.0
CG C:ASP274 3.5 57.2 1.0
C C:ASP274 4.0 52.1 1.0
CB D:ASP251 4.1 70.5 1.0
CA C:ASP274 4.2 50.7 1.0
OD1 C:ASP274 4.2 58.6 1.0
CG D:ASP251 4.2 75.9 1.0
CB C:ASP274 4.5 54.2 1.0
OD1 D:ASP251 4.5 80.5 1.0
OD2 D:ASP251 4.6 79.1 1.0
CB C:ASP278 4.8 49.6 1.0
NH2 C:ARG132 4.8 40.4 1.0

Calcium binding site 4 out of 4 in 6ajb

Go back to Calcium Binding Sites List in 6ajb
Calcium binding site 4 out of 4 in the Crystal Structure of Trypanosoma Brucei Glycosomal Isocitrate Dehydrogenase in Complex with Nadh, 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 Nadh, Alpha-Ketoglutarate and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:59.9
occ:1.00
 OD1 D:ASP274 2.3 50.8 1.0
O2 D:AKG502 2.6 61.5 1.0
O5 D:AKG502 2.8 62.9 1.0
C1 D:AKG502 3.4 62.2 1.0
OD2 D:ASP278 3.4 53.4 1.0
C2 D:AKG502 3.4 62.6 1.0
CG D:ASP274 3.5 50.2 1.0
OD1 D:ASP278 3.6 51.7 1.0
O D:ASP274 3.6 46.2 1.0
O D:ALA307 3.7 48.4 1.0
CG D:ASP278 3.7 50.9 1.0
CB C:ASP251 3.8 64.6 1.0
CG C:ASP251 3.9 69.5 1.0
NH2 D:ARG109 3.9 49.1 1.0
OD2 C:ASP251 4.0 69.4 1.0
OD2 D:ASP274 4.2 51.9 1.0
OD1 C:ASP251 4.3 76.3 1.0
C D:ASP274 4.5 46.6 1.0
C5N D:NAD501 4.5 59.8 1.0
CA D:ASP274 4.6 47.7 1.0
O1 D:AKG502 4.6 63.0 1.0
CB D:ASP274 4.6 48.7 1.0
C4N D:NAD501 4.8 57.3 1.0
CB D:ASP278 4.8 48.2 1.0
C D:ALA307 4.9 52.1 1.0
C3 D:AKG502 4.9 61.9 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 16:29:13 2024

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