Calcium in PDB 8oic: Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)

The structure of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged), PDB code: 8oic was solved by M.Patrone, B.J.Stockman, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	116.42 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.055, 94.665, 120.589, 105.08, 89.96, 93.83
R / Rfree (%)	20.9 / 25.1

The binding sites of Calcium atom in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) (pdb code 8oic). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged), PDB code: 8oic:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:55.9 occ:1.00 OD2 A:ASP263 2.4 47.8 1.0 O A:HOH505 2.4 61.1 1.0 O A:HOH514 2.4 68.7 1.0 OD1 A:ASP15 2.4 63.3 1.0 O A:THR142 2.4 52.9 1.0 O4 A:BCN401 2.5 56.5 1.0 OD2 A:ASP15 2.5 59.9 1.0 OD2 A:ASP10 2.6 65.7 1.0 CG A:ASP15 2.8 58.2 1.0 C4 A:BCN401 3.0 62.6 1.0 CG A:ASP263 3.4 45.3 1.0 C A:THR142 3.6 49.8 1.0 OD1 A:ASP263 3.7 45.2 1.0 CG A:ASP10 3.7 61.8 1.0 C3 A:BCN401 4.0 63.3 1.0 OG1 A:THR142 4.0 41.0 1.0 OD1 A:ASP10 4.2 68.0 1.0 CB A:ASP15 4.3 55.8 1.0 ND2 A:ASN39 4.3 82.0 1.0 OD2 A:ASP14 4.3 74.0 1.0 N A:GLY143 4.3 48.6 1.0 CA A:GLY143 4.3 49.8 1.0 CB A:THR142 4.4 46.1 1.0 CA A:THR142 4.6 47.5 1.0 OD1 A:ASN184 4.6 44.5 1.0 O A:ASP10 4.6 48.2 1.0 N A:ASP10 4.7 55.0 1.0 CB A:ASP263 4.7 44.8 1.0 N A:ASP15 4.7 57.2 1.0 ND2 A:ASN184 4.7 48.8 1.0 C A:ASP10 4.9 50.1 1.0 CA A:ASP15 4.9 55.3 1.0 CB A:ASP10 5.0 56.2 1.0

Calcium binding site 2 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca400 b:56.4 occ:1.00 O B:THR142 2.4 46.7 1.0 O B:HOH510 2.4 78.0 1.0 OD2 B:ASP263 2.4 63.6 1.0 OD2 B:ASP15 2.4 63.3 1.0 OD1 B:ASP15 2.4 68.9 1.0 O4 B:BCN401 2.5 74.3 1.0 OD2 B:ASP10 2.5 58.1 1.0 CG B:ASP15 2.8 63.0 1.0 C4 B:BCN401 3.2 81.6 1.0 CG B:ASP263 3.4 56.7 1.0 C B:THR142 3.5 48.6 1.0 OD1 B:ASP263 3.7 58.6 1.0 CG B:ASP10 3.7 63.0 1.0 C3 B:BCN401 3.8 81.3 1.0 OG1 B:THR142 4.0 47.6 1.0 OD1 B:ASP10 4.2 64.0 1.0 CB B:ASP15 4.3 58.4 1.0 N B:GLY143 4.3 47.1 1.0 ND2 B:ASN39 4.3 79.9 1.0 CA B:GLY143 4.3 45.9 1.0 CB B:THR142 4.3 46.1 1.0 OD2 B:ASP14 4.4 69.2 1.0 CA B:THR142 4.5 46.4 1.0 OD1 B:ASN184 4.5 57.8 1.0 O B:ASP10 4.6 58.5 1.0 N B:ASP10 4.7 52.3 1.0 ND2 B:ASN184 4.7 59.1 1.0 CB B:ASP263 4.7 53.5 1.0 N B:ASP15 4.8 55.3 1.0 C B:ASP10 4.9 57.3 1.0 CA B:ASP15 4.9 53.0 1.0 CB B:ASP10 4.9 57.7 1.0

Calcium binding site 3 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca400 b:68.6 occ:1.00 O C:THR142 2.4 63.3 1.0 O4 C:BCN401 2.4 80.5 1.0 OD2 C:ASP15 2.4 68.1 1.0 OD2 C:ASP10 2.4 52.7 1.0 O C:HOH506 2.4 58.0 1.0 O C:HOH508 2.4 54.1 1.0 OD1 C:ASP15 2.4 69.2 1.0 OD2 C:ASP263 2.5 56.2 1.0 CG C:ASP15 2.7 66.2 1.0 C C:THR142 3.4 61.2 1.0 CG C:ASP263 3.5 60.5 1.0 CG C:ASP10 3.6 58.8 1.0 C4 C:BCN401 3.7 85.6 1.0 OD1 C:ASP263 3.8 63.1 1.0 OG1 C:THR142 4.0 64.9 1.0 OD1 C:ASP10 4.1 65.1 1.0 CA C:GLY143 4.2 60.6 1.0 N C:GLY143 4.2 61.6 1.0 C3 C:BCN401 4.2 85.9 1.0 CB C:ASP15 4.2 66.7 1.0 CB C:THR142 4.3 61.5 1.0 ND2 C:ASN39 4.3 103.0 1.0 CA C:THR142 4.5 58.1 1.0 OD2 C:ASP14 4.5 71.1 1.0 OD1 C:ASN184 4.5 54.1 1.0 N C:ASP10 4.5 59.3 1.0 O C:ASP10 4.6 62.6 1.0 ND2 C:ASN184 4.7 57.4 1.0 CB C:ASP263 4.8 62.5 1.0 C C:ASP10 4.8 59.8 1.0 N C:ASP15 4.8 63.7 1.0 CB C:ASP10 4.8 57.1 1.0 CA C:ASP15 4.9 67.4 1.0 CA C:ASP10 5.0 57.9 1.0

Calcium binding site 4 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca400 b:62.1 occ:1.00 O D:THR142 2.4 57.5 1.0 O D:HOH501 2.4 54.9 1.0 OD2 D:ASP263 2.4 64.9 1.0 O D:HOH506 2.4 53.7 1.0 O4 D:BCN401 2.4 86.9 1.0 OD1 D:ASP15 2.6 76.8 1.0 OD2 D:ASP15 2.6 73.1 1.0 OD2 D:ASP10 2.7 47.9 1.0 CG D:ASP15 2.9 75.9 1.0 CG D:ASP263 3.3 63.5 1.0 C4 D:BCN401 3.4 92.1 1.0 C D:THR142 3.5 64.7 1.0 OD1 D:ASP263 3.5 62.0 1.0 CG D:ASP10 3.8 60.0 1.0 OG1 D:THR142 4.1 52.4 1.0 OD1 D:ASP10 4.3 55.5 1.0 OD2 D:ASP14 4.3 101.1 1.0 CB D:THR142 4.3 60.4 1.0 N D:GLY143 4.3 66.0 1.0 CA D:GLY143 4.3 67.6 1.0 ND2 D:ASN39 4.4 78.6 1.0 OD1 D:ASN184 4.4 63.8 1.0 CB D:ASP15 4.4 78.2 1.0 C3 D:BCN401 4.5 83.2 1.0 CA D:THR142 4.5 64.4 1.0 ND2 D:ASN184 4.5 76.8 1.0 CB D:ASP263 4.7 64.3 1.0 O D:ASP10 4.8 54.3 1.0 N D:ASP10 4.8 62.4 1.0 N D:ASP15 4.9 84.0 1.0 CG D:ASN184 4.9 69.1 1.0

Calcium binding site 5 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca400 b:55.3 occ:1.00 O E:HOH514 2.4 53.1 1.0 OD2 E:ASP263 2.4 48.1 1.0 O4 E:BCN401 2.4 62.7 1.0 O E:HOH513 2.4 48.7 1.0 O E:THR142 2.4 48.7 1.0 OD1 E:ASP15 2.4 60.0 1.0 OD2 E:ASP15 2.5 55.0 1.0 OD2 E:ASP10 2.6 53.2 1.0 CG E:ASP15 2.8 57.2 1.0 CG E:ASP263 3.4 46.4 1.0 C E:THR142 3.5 47.8 1.0 OD1 E:ASP263 3.7 46.8 1.0 C4 E:BCN401 3.7 68.0 1.0 CG E:ASP10 3.8 57.6 1.0 OG1 E:THR142 4.0 46.3 1.0 C3 E:BCN401 4.1 70.3 1.0 CB E:ASP15 4.3 56.0 1.0 OD2 E:ASP14 4.3 70.7 1.0 N E:GLY143 4.3 52.6 1.0 OD1 E:ASP10 4.3 57.1 1.0 CA E:GLY143 4.3 55.3 1.0 CB E:THR142 4.3 47.4 1.0 OD1 E:ASN184 4.5 46.8 1.0 CA E:THR142 4.5 45.0 1.0 O E:ASP10 4.7 58.5 1.0 ND2 E:ASN184 4.7 51.7 1.0 CB E:ASP263 4.7 46.0 1.0 N E:ASP10 4.7 54.3 1.0 N E:ASP15 4.7 54.7 1.0 CA E:ASP15 4.9 54.1 1.0 C E:ASP10 4.9 56.5 1.0

Calcium binding site 6 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca400 b:55.1 occ:1.00 O F:THR142 2.4 55.0 1.0 OD2 F:ASP15 2.4 56.4 1.0 O F:HOH505 2.4 52.1 1.0 OD1 F:ASP15 2.4 59.7 1.0 O4 F:BCN401 2.4 63.0 1.0 OD2 F:ASP263 2.4 60.6 1.0 O F:HOH519 2.4 41.3 1.0 OD2 F:ASP10 2.5 50.7 1.0 CG F:ASP15 2.7 63.9 1.0 CG F:ASP263 3.4 59.7 1.0 C F:THR142 3.5 53.0 1.0 C4 F:BCN401 3.6 67.5 1.0 CG F:ASP10 3.7 52.6 1.0 OD1 F:ASP263 3.7 61.4 1.0 OG1 F:THR142 4.0 40.3 1.0 C3 F:BCN401 4.2 69.6 1.0 OD1 F:ASP10 4.2 54.8 1.0 CB F:ASP15 4.2 61.7 1.0 N F:GLY143 4.3 54.6 1.0 CA F:GLY143 4.3 57.4 1.0 CB F:THR142 4.3 47.4 1.0 ND2 F:ASN39 4.3 79.4 1.0 OD2 F:ASP14 4.4 71.0 1.0 CA F:THR142 4.5 51.1 1.0 OD1 F:ASN184 4.6 61.3 1.0 O F:ASP10 4.6 52.0 1.0 N F:ASP10 4.6 53.2 1.0 CB F:ASP263 4.7 58.0 1.0 ND2 F:ASN184 4.7 71.2 1.0 N F:ASP15 4.7 57.5 1.0 C F:ASP10 4.8 51.9 1.0 CA F:ASP15 4.9 56.6 1.0 CB F:ASP10 4.9 52.3 1.0

Calcium binding site 7 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca400 b:49.1 occ:1.00 O G:HOH505 2.4 49.0 1.0 O G:THR142 2.4 54.4 1.0 O4 G:BCN401 2.4 72.2 1.0 OD1 G:ASP15 2.4 57.3 1.0 OD2 G:ASP263 2.4 57.1 1.0 OD2 G:ASP15 2.5 55.3 1.0 O G:HOH502 2.5 43.4 1.0 OD2 G:ASP10 2.5 46.8 1.0 CG G:ASP15 2.8 54.2 1.0 C4 G:BCN401 2.9 77.8 1.0 CG G:ASP263 3.4 57.2 1.0 C G:THR142 3.5 51.5 1.0 CG G:ASP10 3.7 53.4 1.0 OD1 G:ASP263 3.7 56.3 1.0 C3 G:BCN401 3.8 74.7 1.0 OG1 G:THR142 4.0 44.9 1.0 OD1 G:ASP10 4.2 53.9 1.0 CB G:ASP15 4.2 55.2 1.0 N G:GLY143 4.3 53.5 1.0 CA G:GLY143 4.3 57.4 1.0 ND2 G:ASN39 4.3 81.7 1.0 OD2 G:ASP14 4.3 67.9 1.0 CB G:THR142 4.3 47.7 1.0 OD1 G:ASN184 4.5 51.6 1.0 CA G:THR142 4.6 50.0 1.0 O G:ASP10 4.6 62.4 1.0 N G:ASP10 4.7 55.7 1.0 ND2 G:ASN184 4.7 55.2 1.0 CB G:ASP263 4.7 56.0 1.0 N G:ASP15 4.8 60.9 1.0 C G:ASP10 4.9 59.3 1.0 CA G:ASP15 4.9 58.9 1.0 CB G:ASP10 4.9 56.5 1.0

Calcium binding site 8 out of 8 in the Trichomonas Vaginalis Riboside Hydrolase (His-Tagged)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Trichomonas Vaginalis Riboside Hydrolase (His-Tagged) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca400 b:58.9 occ:1.00 OD2 H:ASP15 2.3 58.3 1.0 OD1 H:ASP15 2.4 59.6 1.0 O H:HOH504 2.4 49.8 1.0 O H:THR142 2.4 55.8 1.0 O4 H:BCN401 2.4 90.1 1.0 OD2 H:ASP263 2.4 64.6 1.0 O H:HOH509 2.4 40.6 1.0 OD2 H:ASP10 2.4 58.9 1.0 CG H:ASP15 2.7 58.3 1.0 CG H:ASP263 3.4 61.9 1.0 C H:THR142 3.5 54.1 1.0 CG H:ASP10 3.6 64.3 1.0 C4 H:BCN401 3.6 88.8 1.0 OD1 H:ASP263 3.7 60.8 1.0 OG1 H:THR142 3.9 46.9 1.0 CB H:ASP15 4.2 59.7 1.0 OD1 H:ASP10 4.2 61.7 1.0 N H:GLY143 4.2 52.6 1.0 CA H:GLY143 4.3 55.6 1.0 CB H:THR142 4.3 52.6 1.0 ND2 H:ASN39 4.3 91.3 1.0 OD2 H:ASP14 4.4 77.0 1.0 CA H:THR142 4.5 54.7 1.0 N H:ASP10 4.5 59.0 1.0 O H:ASP10 4.6 73.3 1.0 OD1 H:ASN184 4.6 52.1 1.0 C3 H:BCN401 4.6 85.5 1.0 CB H:ASP263 4.7 62.2 1.0 N H:ASP15 4.7 60.8 1.0 ND2 H:ASN184 4.8 67.5 1.0 C H:ASP10 4.8 66.2 1.0 CA H:ASP15 4.8 60.0 1.0 CB H:ASP10 4.9 68.4 1.0 CA H:ASP10 5.0 63.8 1.0

M.Patrone, G.S.Galasyn, F.Kerin, M.M.Nyitray, D.W.Parkin, B.J.Stockman, M.Degano. A Riboside Hydrolase That Salvages Both Nucleobases and Nicotinamide in the Auxotrophic Parasite Trichomonas Vaginalis. J.Biol.Chem. 05077 2023.
ISSN: ESSN 1083-351X
PubMed: 37482279
DOI: 10.1016/J.JBC.2023.105077