Atomistry » Calcium » PDB 6ai0-6b40 » 6ajb
Atomistry »
  Calcium »
    PDB 6ai0-6b40 »
      6ajb »

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: Wed Jul 9 12:28:41 2025

Last articles

Mg in 8CGI
Mg in 8CF8
Mg in 8CGA
Mg in 8CEP
Mg in 8CF1
Mg in 8CAH
Mg in 8CE5
Mg in 8CDQ
Mg in 8CE2
Mg in 8CCO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy