Calcium in PDB 8cp0: Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form)

The structure of Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form), PDB code: 8cp0 was solved by M.Martinez, A.Bouillon, F.Batista, P.M.Alzari, J.C.Barale, A.Haouz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.15 / 3.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.15, 89.15, 119.078, 90, 90, 120
R / Rfree (%)	19.6 / 24.2

The binding sites of Calcium atom in the Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form) (pdb code 8cp0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form), PDB code: 8cp0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:41.9 occ:1.00 OD2 A:ASP281 2.2 66.6 1.0 O A:VAL383 2.2 45.5 1.0 OD1 A:ASP325 2.3 52.8 1.0 O A:ILE388 2.5 51.0 1.0 OD2 A:ASP325 2.5 54.8 1.0 OD1 A:ASN386 2.5 53.9 1.0 O A:ILE390 2.6 48.2 1.0 CG A:ASP325 2.7 52.8 1.0 C A:VAL383 3.4 45.2 1.0 CG A:ASP281 3.4 64.6 1.0 CG A:ASN386 3.5 52.8 1.0 C A:ILE388 3.6 50.8 1.0 C A:ILE390 3.8 48.1 1.0 ND2 A:ASN386 3.8 53.3 1.0 N A:ILE390 3.9 48.7 1.0 C A:GLY389 4.1 49.6 1.0 CB A:ASP325 4.2 50.0 1.0 CB A:ASP281 4.3 61.5 1.0 CA A:VAL383 4.3 44.7 1.0 CA A:GLY389 4.3 50.1 1.0 OD1 A:ASP281 4.3 64.5 1.0 N A:GLY384 4.3 45.4 1.0 N A:GLY389 4.4 50.2 1.0 CA A:GLY384 4.4 46.2 1.0 CA A:ILE390 4.4 48.3 1.0 CB A:VAL383 4.5 45.1 1.0 N A:VAL383 4.5 44.6 1.0 O A:GLY389 4.7 49.9 1.0 CA A:ILE388 4.7 51.0 1.0 N A:ILE388 4.8 51.1 1.0 N A:VAL391 4.8 47.8 1.0 CB A:ASN386 4.8 50.1 1.0 CG1 A:ILE388 4.9 52.0 1.0 C A:GLY384 4.9 46.9 1.0 N A:ASN386 4.9 48.4 1.0 CA A:ASP325 5.0 49.1 1.0

Calcium binding site 2 out of 3 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:72.8 occ:1.00 OD1 A:ASP346 2.1 82.6 1.0 OE2 A:GLU336 2.1 85.9 1.0 OD1 A:ASN348 2.1 74.2 1.0 OD1 A:ASP353 2.3 69.2 1.0 OD1 A:ASP344 2.4 84.8 1.0 O A:VAL350 2.5 66.0 1.0 CG A:ASN348 3.1 73.4 1.0 CD A:GLU336 3.2 84.5 1.0 CG A:ASP346 3.3 81.8 1.0 CG A:ASP353 3.4 68.1 1.0 CG A:GLU336 3.6 80.1 1.0 ND2 A:ASN348 3.6 73.8 1.0 CG A:ASP344 3.6 84.1 1.0 C A:VAL350 3.6 65.8 1.0 OD2 A:ASP346 3.8 83.6 1.0 OD2 A:ASP353 3.8 70.0 1.0 N A:ASN348 4.2 71.0 1.0 CA A:ASP344 4.2 78.6 1.0 N A:ASP346 4.3 76.2 1.0 N A:VAL350 4.3 66.4 1.0 OE1 A:GLU336 4.3 85.3 1.0 CB A:ASN348 4.3 71.2 1.0 CA A:VAL350 4.4 65.9 1.0 OD2 A:ASP344 4.4 85.8 1.0 C A:ASP344 4.4 78.2 1.0 CB A:ASP344 4.4 80.2 1.0 CB A:ASP346 4.5 77.6 1.0 CB A:VAL350 4.5 65.8 1.0 N A:SER347 4.6 73.8 1.0 N A:ASP353 4.6 61.9 1.0 N A:VAL351 4.7 65.2 1.0 CA A:ASN348 4.7 70.5 1.0 CA A:ASP346 4.7 75.8 1.0 N A:ASP345 4.7 77.5 1.0 CB A:ASP353 4.7 63.5 1.0 N A:ASP352 4.7 63.5 1.0 C A:ASP346 4.8 75.0 1.0 CA A:VAL351 4.8 65.1 1.0 ND2 A:ASN333 4.8 70.9 1.0 O A:ASP344 4.9 78.3 1.0 C A:ASN348 5.0 69.8 1.0

Calcium binding site 3 out of 3 in the Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Catalytic Domain of P. Vivax SUB1 (Trigonal Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:73.4 occ:1.00 OD1 A:ASP345 2.2 83.5 1.0 OE1 A:GLU336 2.4 85.3 1.0 O A:ARG340 2.4 81.0 1.0 OD1 A:ASP352 2.5 69.0 1.0 O A:VAL343 2.5 79.1 1.0 CG A:ASP345 3.4 82.9 1.0 C A:ARG340 3.5 80.9 1.0 CD A:GLU336 3.6 84.5 1.0 C A:VAL343 3.7 79.0 1.0 CG A:ASP352 3.7 68.6 1.0 O A:GLU336 4.0 76.8 1.0 N A:ARG340 4.0 81.2 1.0 CA A:ASP352 4.1 63.2 1.0 N A:VAL343 4.1 79.2 1.0 CB A:VAL343 4.2 79.9 1.0 C A:GLY339 4.2 81.5 1.0 OD2 A:ASP345 4.2 84.9 1.0 CA A:VAL343 4.2 79.2 1.0 N A:ASP352 4.3 63.5 1.0 OE2 A:GLU336 4.3 85.9 1.0 CB A:ASP352 4.4 64.8 1.0 N A:ASP345 4.4 77.5 1.0 CB A:ASP345 4.4 78.9 1.0 CA A:ARG340 4.4 81.2 1.0 CA A:GLU336 4.4 75.3 1.0 N A:LYS341 4.4 80.5 1.0 O A:GLY339 4.5 81.7 1.0 CB A:GLU336 4.5 76.8 1.0 CA A:LYS341 4.5 80.4 1.0 CA A:GLY339 4.6 81.4 1.0 CG A:GLU336 4.6 80.1 1.0 OD2 A:ASP352 4.6 70.7 1.0 C A:GLU336 4.7 76.6 1.0 CG1 A:VAL343 4.7 80.5 1.0 N A:ASP344 4.8 78.6 1.0 C A:LYS341 4.9 80.2 1.0 N A:GLY342 5.0 79.7 1.0

M.Martinez, F.A.Batista, M.Maurel, A.Bouillon, L.Ortega Varga, A.M.Wehenkel, L.Le Chevalier-Sontag, A.Blondel, A.Haouz, J.F.Hernandez, P.M.Alzari, J.C.Barale. 3D Structures of the Plasmodium Vivax Subtilisin-Like Drug Target SUB1 Reveal Conformational Changes to Accommodate A Substrate-Derived Alpha-Ketoamide Inhibitor. Acta Crystallogr D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37428845
DOI: 10.1107/S2059798323004710