Calcium in PDB 8ctm: Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.

Enzymatic activity of Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.

All present enzymatic activity of Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.:
3.2.2.1;

Protein crystallography data

The structure of Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani., PDB code: 8ctm was solved by Y.Chen, W.D.Tolbert, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.87 / 1.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.221, 79.111, 107.621, 90, 90.77, 90
R / Rfree (%) 17.4 / 20.7

Other elements in 8ctm:

The structure of Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani. (pdb code 8ctm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani., PDB code: 8ctm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8ctm

Go back to Calcium Binding Sites List in 8ctm
Calcium binding site 1 out of 5 in the Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.


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 the Nucleoside Hydrolase From Leishmania Donovani. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:10.6
occ:1.00
 OD2 A:ASP241 2.4 11.8 1.0
O A:THR126 2.4 10.9 1.0
OD1 A:ASP10 2.4 11.5 1.0
O A:HOH673 2.4 18.6 1.0
OD1 A:ASP15 2.5 11.6 1.0
O A:HOH532 2.5 14.4 1.0
OD2 A:ASP15 2.5 13.1 1.0
O3 A:GOL401 2.6 13.6 1.0
CG A:ASP15 2.8 12.8 1.0
CG A:ASP241 3.4 16.3 1.0
CG A:ASP10 3.5 13.4 1.0
C A:THR126 3.6 10.0 1.0
OD1 A:ASP241 3.7 20.0 1.0
C3 A:GOL401 3.8 16.8 1.0
OD2 A:ASP10 4.0 13.2 1.0
OG1 A:THR126 4.3 17.9 1.0
CA A:GLY127 4.3 8.7 1.0
CB A:ASP15 4.3 10.0 1.0
N A:GLY127 4.3 9.2 1.0
O A:ASP10 4.4 10.5 1.0
CB A:THR126 4.4 15.8 1.0
OD1 A:ASN168 4.4 11.4 1.0
O2 A:GOL401 4.5 22.6 1.0
N A:ASP10 4.5 11.0 1.0
ND2 A:ASN168 4.5 11.3 1.0
CA A:THR126 4.6 10.2 1.0
C2 A:GOL401 4.6 17.8 1.0
N A:ASP15 4.6 12.0 1.0
C A:ASP10 4.7 8.9 1.0
CB A:ASP241 4.8 9.2 1.0
O A:HOH514 4.8 15.1 1.0
CB A:ASP10 4.8 11.2 1.0
CB A:ASP14 4.8 13.6 1.0
CA A:ASP15 4.9 9.5 1.0
CG A:ASN168 4.9 12.8 1.0
CA A:ASP10 4.9 11.8 1.0

Calcium binding site 2 out of 5 in 8ctm

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Calcium binding site 2 out of 5 in the Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.


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 the Nucleoside Hydrolase From Leishmania Donovani. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:16.8
occ:1.00
 O B:THR126 2.4 14.6 1.0
OD2 B:ASP241 2.4 18.6 1.0
OD1 B:ASP10 2.5 14.4 1.0
O1 B:GOL401 2.5 19.1 1.0
O B:HOH536 2.5 22.4 1.0
OD2 B:ASP15 2.5 15.0 1.0
O B:HOH524 2.5 16.6 1.0
OD1 B:ASP15 2.5 16.1 1.0
CG B:ASP15 2.8 12.3 1.0
CG B:ASP241 3.4 20.3 1.0
C B:THR126 3.6 11.4 1.0
CG B:ASP10 3.6 19.1 1.0
OD1 B:ASP241 3.7 19.6 1.0
C1 B:GOL401 3.9 28.6 1.0
OD2 B:ASP10 4.1 16.5 1.0
CA B:GLY127 4.3 11.4 1.0
OG1 B:THR126 4.3 18.8 1.0
N B:GLY127 4.3 14.0 1.0
CB B:ASP15 4.3 14.7 1.0
O2 B:GOL401 4.4 34.3 1.0
ND2 B:ASN168 4.4 14.3 1.0
CB B:THR126 4.4 18.5 1.0
OD1 B:ASP14 4.4 38.7 1.0
OD1 B:ASN168 4.4 13.7 1.0
O B:ASP10 4.5 15.1 1.0
N B:ASP10 4.5 13.4 1.0
C2 B:GOL401 4.6 36.5 1.0
CA B:THR126 4.6 12.3 1.0
OD2 B:ASP14 4.7 46.5 1.0
CB B:ASP241 4.7 15.0 1.0
N B:ASP15 4.8 17.8 1.0
C B:ASP10 4.8 11.4 1.0
CG B:ASP14 4.8 30.6 1.0
CB B:ASP10 4.9 14.7 1.0
CG B:ASN168 4.9 17.1 1.0
CA B:ASP15 4.9 14.3 1.0
CA B:ASP10 5.0 14.3 1.0

Calcium binding site 3 out of 5 in 8ctm

Go back to Calcium Binding Sites List in 8ctm
Calcium binding site 3 out of 5 in the Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.


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 the Nucleoside Hydrolase From Leishmania Donovani. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:17.8
occ:1.00
 O C:HOH539 2.3 26.9 1.0
OD1 C:ASP10 2.4 19.4 1.0
OD2 C:ASP241 2.4 18.2 1.0
O C:THR126 2.4 17.6 1.0
O C:HOH532 2.4 17.1 1.0
OD1 C:ASP15 2.5 19.7 1.0
OD2 C:ASP15 2.5 20.7 1.0
O3 C:GOL401 2.5 22.6 1.0
CG C:ASP15 2.8 21.6 1.0
CG C:ASP241 3.4 20.3 1.0
CG C:ASP10 3.5 20.4 1.0
C C:THR126 3.6 18.7 1.0
OD1 C:ASP241 3.8 27.0 1.0
C3 C:GOL401 3.8 31.2 1.0
OD2 C:ASP10 4.0 19.3 1.0
OG1 C:THR126 4.2 23.1 1.0
CB C:ASP15 4.3 15.1 1.0
CA C:GLY127 4.4 15.7 1.0
N C:GLY127 4.4 16.7 1.0
CB C:THR126 4.4 19.5 1.0
OD1 C:ASN168 4.5 15.3 1.0
N C:ASP10 4.5 14.7 1.0
O C:ASP10 4.5 18.4 1.0
ND2 C:ASN168 4.5 16.2 1.0
O2 C:GOL401 4.5 39.2 1.0
CA C:THR126 4.6 17.5 1.0
C2 C:GOL401 4.6 31.6 1.0
N C:ASP15 4.7 18.9 1.0
O C:HOH508 4.7 27.2 1.0
C C:ASP10 4.7 16.2 1.0
CB C:ASP10 4.8 18.7 1.0
CB C:ASP241 4.8 19.4 1.0
CA C:ASP10 4.9 19.1 1.0
CA C:ASP15 4.9 17.9 1.0
CG C:ASN168 4.9 13.1 1.0

Calcium binding site 4 out of 5 in 8ctm

Go back to Calcium Binding Sites List in 8ctm
Calcium binding site 4 out of 5 in the Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.


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 the Nucleoside Hydrolase From Leishmania Donovani. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:46.6
occ:1.00
 ND1 C:HIS23 3.4 31.0 1.0
CB C:LEU30 3.9 25.1 1.0
N C:LEU30 4.0 24.9 1.0
CE1 C:HIS23 4.1 28.4 1.0
CA C:HIS23 4.3 23.4 1.0
O C:HIS23 4.5 33.0 1.0
CG2 C:VAL61 4.5 23.6 1.0
CG C:HIS23 4.5 22.6 1.0
CA C:LEU30 4.6 22.9 1.0
CD2 C:LEU30 4.7 24.9 1.0
O C:LEU30 4.7 25.4 1.0
O C:ALA22 4.7 23.7 1.0
CA C:GLU29 4.8 30.6 1.0
CB C:HIS23 4.8 21.7 1.0
C C:GLU29 4.9 26.3 1.0
C C:HIS23 4.9 25.2 1.0
CG C:LEU30 5.0 40.6 1.0

Calcium binding site 5 out of 5 in 8ctm

Go back to Calcium Binding Sites List in 8ctm
Calcium binding site 5 out of 5 in the Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani.


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 the Nucleoside Hydrolase From Leishmania Donovani. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca404

b:17.1
occ:1.00
 O D:HOH587 2.3 20.6 1.0
O D:THR126 2.4 16.1 1.0
OD2 D:ASP241 2.4 22.2 1.0
O D:HOH547 2.4 18.6 1.0
OD1 D:ASP10 2.5 21.6 1.0
OD1 D:ASP15 2.6 17.0 1.0
OD2 D:ASP15 2.6 19.5 1.0
O3 D:GOL401 2.6 22.3 1.0
CG D:ASP15 2.9 14.4 1.0
CG D:ASP241 3.3 23.4 1.0
C D:THR126 3.6 15.3 1.0
CG D:ASP10 3.6 21.0 1.0
OD1 D:ASP241 3.6 23.5 1.0
C3 D:GOL401 3.8 45.1 1.0
OD2 D:ASP10 4.1 18.0 1.0
CA D:GLY127 4.3 15.0 1.0
OD2 D:ASP14 4.3 54.4 1.0
N D:GLY127 4.3 16.8 1.0
OG1 D:THR126 4.3 24.3 1.0
CB D:ASP15 4.3 17.7 1.0
O2 D:GOL401 4.4 56.4 1.0
OD1 D:ASN168 4.4 15.7 1.0
CB D:THR126 4.4 24.1 1.0
ND2 D:ASN168 4.4 13.7 1.0
OD1 D:ASP14 4.4 38.6 1.0
O D:ASP10 4.5 17.9 1.0
N D:ASP10 4.5 15.2 1.0
C2 D:GOL401 4.6 33.7 1.0
CA D:THR126 4.6 13.9 1.0
CG D:ASP14 4.7 33.6 1.0
N D:ASP15 4.7 19.8 1.0
CB D:ASP241 4.7 19.0 1.0
C D:ASP10 4.9 17.1 1.0
CG D:ASN168 4.9 17.3 1.0
CA D:ASP15 4.9 18.3 1.0
CB D:ASP10 4.9 14.3 1.0

Reference:

Y.Chen, W.D.Tolbert, M.Pazgier. Crystal Structure of the Nucleoside Hydrolase From Leishmania Donovani. To Be Published.
Page generated: Wed Jul 26 13:07:19 2023

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