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Cobalt in PDB 5e93: Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071

Enzymatic activity of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071

All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071:
1.3.98.1;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071, PDB code: 5e93 was solved by J.R.Rocha, D.K.Inaoka, J.Cheleski, T.Shiba, S.Harada, C.A.Montanari, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.325, 71.789, 124.343, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 16.8

Other elements in 5e93:

The structure of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071 also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071 (pdb code 5e93). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071, PDB code: 5e93:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 5e93

Go back to Cobalt Binding Sites List in 5e93
Cobalt binding site 1 out of 4 in the Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co409

b:36.1
occ:1.00
 CO A:NCO409 0.0 36.1 1.0
N5 A:NCO409 2.0 38.1 1.0
N4 A:NCO409 2.0 39.6 1.0
N3 A:NCO409 2.0 43.3 1.0
N6 A:NCO409 2.0 39.4 1.0
N1 A:NCO409 2.0 34.4 1.0
N2 A:NCO409 2.0 39.0 1.0
O A:LYS296 3.9 19.9 1.0
O A:HOH648 3.9 43.0 1.0
O A:HOH732 4.0 22.9 1.0
O B:HOH554 4.2 31.7 1.0

Cobalt binding site 2 out of 4 in 5e93

Go back to Cobalt Binding Sites List in 5e93
Cobalt binding site 2 out of 4 in the Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co409

b:13.4
occ:1.00
 CO B:NCO409 0.0 13.4 1.0
N4 B:NCO409 2.0 12.9 1.0
N1 B:NCO409 2.0 13.3 1.0
N2 B:NCO409 2.0 13.3 1.0
N6 B:NCO409 2.1 14.5 1.0
N3 B:NCO409 2.1 14.8 1.0
N5 B:NCO409 2.2 14.5 1.0
O B:GLN275 3.8 11.1 1.0
C2 B:PEG423 4.1 17.3 1.0
O B:GLU276 4.2 11.9 1.0
O B:HOH743 4.3 30.8 1.0
O B:HOH729 4.3 30.3 1.0
O B:HOH668 4.4 19.8 1.0
O B:HOH763 4.4 35.5 1.0
O B:HOH716 4.5 25.8 1.0
C1 B:PEG423 4.6 20.6 1.0
O2 B:PEG423 4.8 26.0 1.0
C B:GLU276 4.9 10.6 1.0

Cobalt binding site 3 out of 4 in 5e93

Go back to Cobalt Binding Sites List in 5e93
Cobalt binding site 3 out of 4 in the Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co410

b:21.4
occ:0.50
 CO B:NCO410 0.0 21.4 0.5
N3 B:NCO410 2.0 25.5 0.5
N1 B:NCO410 2.0 23.4 0.5
N5 B:NCO410 2.0 24.3 0.5
N4 B:NCO410 2.0 23.4 0.5
N2 B:NCO410 2.0 22.4 0.5
N6 B:NCO410 2.0 24.2 0.5
N4 B:NCO410 2.3 26.5 0.5
N2 B:NCO410 2.6 22.1 0.5
CO B:NCO410 3.3 21.9 0.5
N5 B:NCO410 3.4 20.4 0.5
O B:HOH751 4.2 31.4 1.0
N3 B:NCO410 4.3 22.9 0.5
N1 B:NCO410 4.8 25.9 0.5
OE1 B:GLU205 4.9 16.9 0.5
N6 B:NCO410 5.0 24.1 0.5

Cobalt binding site 4 out of 4 in 5e93

Go back to Cobalt Binding Sites List in 5e93
Cobalt binding site 4 out of 4 in the Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Trypanosoma Cruzi Dihydroorotate Dehydrogenase in Complex with NEQ0071 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co410

b:21.9
occ:0.50
 CO B:NCO410 0.0 21.9 0.5
N3 B:NCO410 2.0 22.9 0.5
N4 B:NCO410 2.0 26.5 0.5
N1 B:NCO410 2.0 25.9 0.5
N6 B:NCO410 2.0 24.1 0.5
N2 B:NCO410 2.0 22.1 0.5
N5 B:NCO410 2.1 20.4 0.5
N3 B:NCO410 2.2 25.5 0.5
N6 B:NCO410 2.7 24.2 0.5
O B:HOH503 3.2 40.7 1.0
CO B:NCO410 3.3 21.4 0.5
N2 B:NCO410 3.4 22.4 0.5
OE1 B:GLU205 3.9 16.9 0.5
O B:HOH759 4.2 28.8 1.0
OD1 B:ASP203 4.3 18.6 1.0
N1 B:NCO410 4.3 23.4 0.5
OD2 B:ASP203 4.4 18.6 1.0
CG B:ASP203 4.7 16.2 1.0
N4 B:NCO410 4.8 23.4 0.5
O B:HOH751 5.0 31.4 1.0

Reference:

J.R.Rocha, J.Cheleski, D.K.Inaoka, L.A.Avelar, J.F.R.Ribeiro, H.J.Wiggers, S.Albuquerque, T.Shiba, S.Harada, K.Kita, A.B.F.Silva, C.A.Montanari. Exploring Trypanosoma Cruzi Dihydroorotate Dehydrogenase Active Site Plasticity For the Discovery of Potent and Selective Inhibitors with Trypanocidal Activity To Be Published.
Page generated: Tue Jul 30 17:49:47 2024

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