Calcium in PDB 4tr2: Crystal Structure of PVSUB1

The structure of Crystal Structure of PVSUB1, PDB code: 4tr2 was solved by D.Giganti, A.Bouillon, M.Martinez, P.Weber, C.Girard-Blanc, S.Petres, A.Haouz, J.C.Barale, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.10 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.000, 95.000, 287.760, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.4

The binding sites of Calcium atom in the Crystal Structure of PVSUB1 (pdb code 4tr2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of PVSUB1, PDB code: 4tr2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of PVSUB1


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 PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:45.5 occ:1.00 O A:VAL383 2.1 46.6 1.0 O A:ILE390 2.2 40.7 1.0 OD2 A:ASP281 2.2 68.6 1.0 OD1 A:ASN386 2.4 52.2 1.0 O A:ILE388 2.4 47.0 1.0 OD1 A:ASP325 2.5 48.4 1.0 OD2 A:ASP325 2.6 49.4 1.0 CG A:ASP325 2.9 46.9 1.0 CG A:ASP281 3.2 65.5 1.0 C A:VAL383 3.3 46.2 1.0 C A:ILE390 3.4 40.5 1.0 CG A:ASN386 3.4 61.3 1.0 C A:ILE388 3.7 46.8 1.0 CB A:ASP281 3.7 56.3 1.0 N A:ILE390 3.8 37.6 1.0 ND2 A:ASN386 3.9 50.1 1.0 C A:GLY389 4.1 44.2 1.0 CA A:ILE390 4.2 35.6 1.0 N A:GLY384 4.2 44.3 1.0 CA A:GLY384 4.2 45.1 1.0 OD1 A:ASP281 4.3 67.9 1.0 CA A:VAL383 4.3 38.8 1.0 N A:VAL383 4.4 38.8 1.0 CB A:ASP325 4.4 46.2 1.0 N A:VAL391 4.4 35.6 1.0 O A:GLY389 4.5 45.9 1.0 N A:GLY389 4.5 41.0 1.0 CA A:GLY389 4.5 40.1 1.0 N A:ILE388 4.7 47.7 1.0 CA A:ILE388 4.7 46.3 1.0 CB A:ASN386 4.7 49.6 1.0 CG1 A:ILE388 4.7 49.2 1.0 N A:ASN386 4.7 48.6 1.0 C A:GLY384 4.7 52.5 1.0 CA A:VAL391 4.8 34.6 1.0 CA A:ASP281 4.8 55.5 1.0 CB A:VAL383 4.8 41.8 1.0 N A:ASN385 4.9 49.6 1.0 C A:ALA382 4.9 42.0 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of PVSUB1


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 PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:0.7 occ:1.00 O A:ASN130 2.4 79.8 1.0 O A:PRO135 2.6 87.4 1.0 O A:GLY190 2.9 80.9 1.0 O A:THR133 3.0 94.8 1.0 OE1 A:GLU129 3.1 76.1 1.0 OG1 A:THR133 3.1 94.2 1.0 C A:THR133 3.4 95.5 1.0 C A:ASN130 3.5 78.8 1.0 CA A:GLY190 3.5 82.5 1.0 C A:GLY190 3.6 82.7 1.0 C A:PRO135 3.7 89.4 1.0 N A:SER134 3.9 93.7 1.0 CA A:THR133 4.1 88.8 1.0 CA A:SER134 4.2 94.1 1.0 CD A:GLU129 4.2 80.2 1.0 CB A:THR133 4.2 94.8 1.0 CA A:SER136 4.2 79.6 1.0 N A:ASN130 4.2 70.2 1.0 CA A:ASN130 4.2 70.8 1.0 CB A:ASN130 4.3 71.5 1.0 N A:SER136 4.3 83.7 1.0 N A:THR133 4.4 87.3 1.0 N A:PHE137 4.5 74.0 1.0 N A:HIS131 4.6 76.7 1.0 C A:SER134 4.7 97.3 1.0 CG A:GLU129 4.7 67.9 1.0 CA A:PRO135 4.8 90.4 1.0 C A:SER136 4.8 81.2 1.0 CA A:HIS131 4.8 78.5 1.0 N A:PRO135 4.9 91.9 1.0 N A:GLY190 4.9 84.6 1.0 N A:ALA191 5.0 77.8 1.0 C A:HIS131 5.0 85.3 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of PVSUB1


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 PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:50.6 occ:1.00 O A:VAL350 2.1 56.8 1.0 OD1 A:ASN348 2.3 50.8 1.0 OD1 A:ASP353 2.4 59.5 1.0 OE2 A:GLU336 2.5 49.7 1.0 OD1 A:ASP344 2.5 65.3 1.0 OD1 A:ASP346 2.5 60.3 1.0 CG A:ASP344 3.2 62.0 1.0 CG A:ASN348 3.2 61.3 1.0 C A:VAL350 3.2 58.5 1.0 CD A:GLU336 3.4 71.6 1.0 CG A:ASP353 3.5 57.3 1.0 CG A:ASP346 3.7 63.7 1.0 CG A:GLU336 3.7 59.6 1.0 ND2 A:ASN348 3.8 54.0 1.0 OD2 A:ASP344 3.8 59.5 1.0 CB A:ASP344 4.0 61.0 1.0 N A:VAL350 4.0 57.2 1.0 CA A:VAL350 4.0 55.5 1.0 CA A:ASP344 4.0 60.6 1.0 OD2 A:ASP353 4.0 60.2 1.0 OD2 A:ASP346 4.2 73.6 1.0 N A:ASN348 4.2 60.3 1.0 N A:VAL351 4.3 54.4 1.0 CB A:ASN348 4.4 50.0 1.0 CB A:VAL350 4.4 57.1 1.0 C A:ASP344 4.4 67.5 1.0 ND2 A:ASN333 4.5 56.7 1.0 N A:ASP353 4.5 52.2 1.0 N A:ASP352 4.5 58.2 1.0 CA A:VAL351 4.5 54.0 1.0 OE1 A:GLU336 4.6 78.8 1.0 N A:ASP346 4.7 63.5 1.0 CA A:ASN348 4.7 57.8 1.0 CB A:ASP353 4.7 50.7 1.0 N A:SER347 4.7 61.7 1.0 C A:VAL351 4.8 59.3 1.0 O A:ASP344 4.9 69.0 1.0 N A:GLY349 4.9 56.7 1.0 N A:ASP345 4.9 64.1 1.0 CB A:ASP346 4.9 61.6 1.0 C A:ASN348 5.0 62.0 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of PVSUB1


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 PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:71.6 occ:1.00 OD1 A:ASP345 2.1 77.7 1.0 O A:ARG340 2.3 72.2 1.0 OE1 A:GLU336 2.4 78.8 1.0 OD1 A:ASP352 2.4 77.2 1.0 O A:VAL343 2.8 67.5 1.0 CG A:ASP345 3.3 76.1 1.0 C A:ARG340 3.3 73.2 1.0 CG A:ASP352 3.6 75.1 1.0 CD A:GLU336 3.6 71.6 1.0 O A:GLU336 3.7 60.4 1.0 C A:GLY339 3.8 71.2 1.0 N A:ARG340 3.8 69.1 1.0 C A:VAL343 3.9 68.9 1.0 OD2 A:ASP345 4.0 79.2 1.0 O A:GLY339 4.1 72.5 1.0 CA A:ASP352 4.1 57.9 1.0 CA A:ARG340 4.2 70.7 1.0 CA A:GLY339 4.2 61.5 1.0 CB A:ASP352 4.2 60.7 1.0 N A:LYS341 4.2 69.3 1.0 OE2 A:GLU336 4.3 49.7 1.0 CA A:GLU336 4.3 56.0 1.0 N A:ASP352 4.4 58.2 1.0 N A:VAL343 4.4 69.5 1.0 CA A:LYS341 4.4 68.5 1.0 CB A:ASP345 4.5 64.6 1.0 C A:GLU336 4.5 60.0 1.0 OD2 A:ASP352 4.6 78.5 1.0 N A:ASP345 4.6 64.1 1.0 CA A:VAL343 4.6 68.4 1.0 CB A:GLU336 4.6 56.0 1.0 CG A:GLU336 4.6 59.6 1.0 CB A:VAL343 4.7 73.5 1.0 N A:GLY339 4.9 60.0 1.0 N A:GLY342 4.9 69.4 1.0 C A:LYS341 5.0 73.7 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of PVSUB1


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 PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:69.0 occ:1.00 OD1 B:ASN386 2.1 73.8 1.0 OD2 B:ASP281 2.2 68.2 1.0 O B:VAL383 2.3 62.7 1.0 O B:ILE388 2.3 64.4 1.0 OD1 B:ASP325 2.3 63.1 1.0 O B:ILE390 2.6 57.4 1.0 OD2 B:ASP325 2.8 63.6 1.0 CG B:ASP325 2.9 61.6 1.0 CG B:ASN386 3.2 82.3 1.0 CG B:ASP281 3.4 66.7 1.0 C B:ILE388 3.5 63.7 1.0 C B:VAL383 3.5 62.8 1.0 ND2 B:ASN386 3.6 74.7 1.0 C B:ILE390 3.7 56.5 1.0 N B:ILE390 3.8 51.3 1.0 CB B:ASP281 4.0 62.1 1.0 C B:GLY389 4.1 57.9 1.0 N B:GLY389 4.3 58.6 1.0 CA B:ILE390 4.4 49.8 1.0 OD1 B:ASP281 4.4 66.8 1.0 CA B:GLY389 4.4 56.1 1.0 N B:GLY384 4.4 61.1 1.0 CB B:ASP325 4.4 53.0 1.0 CA B:GLY384 4.4 62.4 1.0 CD1 B:ILE388 4.5 57.5 1.0 N B:ILE388 4.5 62.8 1.0 CB B:ASN386 4.5 61.3 1.0 CA B:VAL383 4.5 58.0 1.0 CA B:ILE388 4.5 60.7 1.0 O B:GLY389 4.6 58.8 1.0 N B:VAL383 4.6 57.3 1.0 N B:ASN386 4.6 64.2 1.0 CG1 B:ILE388 4.7 60.5 1.0 N B:VAL391 4.8 52.9 1.0 CB B:VAL383 4.8 61.6 1.0 C B:GLY384 4.9 66.8 1.0 CA B:ASN386 4.9 63.6 1.0 CA B:ASP281 4.9 62.9 1.0 N B:ASN385 5.0 66.0 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of PVSUB1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:66.3 occ:1.00 O B:ASN130 2.4 70.1 1.0 O B:PRO135 2.7 64.7 1.0 O B:GLY190 2.8 56.1 1.0 OE2 B:GLU129 2.9 56.5 1.0 O B:THR133 3.1 72.1 1.0 OG1 B:THR133 3.2 75.2 1.0 CA B:GLY190 3.4 56.1 1.0 C B:THR133 3.5 73.8 1.0 C B:GLY190 3.5 58.2 1.0 C B:ASN130 3.6 69.3 1.0 C B:PRO135 3.7 64.9 1.0 N B:SER134 3.9 71.2 1.0 CD B:GLU129 4.0 62.4 1.0 CA B:SER136 4.1 54.9 1.0 N B:ASN130 4.1 61.0 1.0 CB B:ASN130 4.2 62.8 1.0 CA B:SER134 4.2 70.7 1.0 CA B:THR133 4.2 70.7 1.0 CA B:ASN130 4.2 62.3 1.0 CB B:THR133 4.2 76.1 1.0 N B:SER136 4.3 58.0 1.0 N B:PHE137 4.4 54.4 1.0 N B:THR133 4.5 71.0 1.0 CG B:GLU129 4.5 51.1 1.0 N B:HIS131 4.6 65.9 1.0 C B:SER134 4.7 73.3 1.0 C B:SER136 4.7 59.0 1.0 N B:ALA191 4.8 55.4 1.0 N B:GLY190 4.8 58.1 1.0 CA B:PRO135 4.8 64.9 1.0 N B:PRO135 4.9 67.4 1.0 CA B:HIS131 4.9 65.9 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of PVSUB1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:45.0 occ:1.00 OD1 B:ASN348 2.1 52.0 1.0 O B:VAL350 2.2 49.4 1.0 OD1 B:ASP344 2.2 59.2 1.0 OE2 B:GLU336 2.3 45.5 1.0 OD1 B:ASP353 2.3 50.7 1.0 OD1 B:ASP346 2.5 57.1 1.0 CG B:ASN348 3.1 60.7 1.0 CG B:ASP344 3.2 57.6 1.0 C B:VAL350 3.3 49.0 1.0 CD B:GLU336 3.4 56.8 1.0 CG B:ASP353 3.4 47.7 1.0 ND2 B:ASN348 3.6 54.8 1.0 CG B:ASP346 3.6 57.2 1.0 CG B:GLU336 3.8 50.6 1.0 N B:VAL350 4.0 42.0 1.0 OD2 B:ASP353 4.0 47.5 1.0 CA B:VAL350 4.0 42.3 1.0 OD2 B:ASP344 4.1 62.0 1.0 OD2 B:ASP346 4.1 63.8 1.0 CB B:ASP344 4.1 50.0 1.0 CA B:ASP344 4.1 49.3 1.0 N B:ASN348 4.2 44.4 1.0 CB B:ASN348 4.3 39.9 1.0 CB B:VAL350 4.3 44.7 1.0 N B:VAL351 4.4 46.7 1.0 OE1 B:GLU336 4.5 57.5 1.0 N B:ASP353 4.5 41.6 1.0 C B:ASP344 4.5 53.7 1.0 CB B:ASP353 4.6 41.6 1.0 ND2 B:ASN333 4.6 40.1 1.0 N B:ASP352 4.6 45.6 1.0 CA B:ASN348 4.6 43.2 1.0 CA B:VAL351 4.7 47.4 1.0 N B:ASP346 4.7 46.1 1.0 N B:SER347 4.8 44.9 1.0 N B:GLY349 4.8 43.0 1.0 CB B:ASP346 4.9 45.7 1.0 C B:VAL351 4.9 51.1 1.0 C B:ASN348 4.9 46.2 1.0 O B:ASP344 4.9 53.4 1.0 N B:ASP345 4.9 51.2 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of PVSUB1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of PVSUB1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca804 b:60.7 occ:1.00 O B:HOH904 2.1 81.5 1.0 OD1 B:ASP345 2.3 55.2 1.0 O B:VAL343 2.3 57.2 1.0 OD1 B:ASP352 2.3 61.4 1.0 O B:ARG340 2.4 64.8 1.0 OE1 B:GLU336 2.5 57.5 1.0 C B:ARG340 3.4 65.8 1.0 CG B:ASP345 3.5 57.9 1.0 CG B:ASP352 3.5 60.3 1.0 C B:VAL343 3.5 58.0 1.0 CD B:GLU336 3.8 56.8 1.0 N B:ARG340 3.9 60.6 1.0 CA B:ASP352 3.9 45.0 1.0 N B:VAL343 3.9 59.2 1.0 CB B:ASP352 4.1 47.2 1.0 N B:ASP352 4.1 45.6 1.0 C B:GLY339 4.1 63.3 1.0 OD2 B:ASP345 4.1 62.4 1.0 CA B:ARG340 4.2 61.0 1.0 CA B:VAL343 4.2 57.1 1.0 O B:GLU336 4.2 50.4 1.0 N B:ASP345 4.4 51.2 1.0 N B:LYS341 4.4 62.8 1.0 OE2 B:GLU336 4.4 45.5 1.0 O B:GLY339 4.4 64.1 1.0 OD2 B:ASP352 4.5 65.8 1.0 CB B:VAL343 4.5 61.2 1.0 N B:ASP344 4.6 51.9 1.0 CA B:GLY339 4.6 56.6 1.0 CB B:ASP345 4.6 52.4 1.0 CA B:GLU336 4.6 48.3 1.0 N B:GLY342 4.7 62.4 1.0 C B:LYS341 4.7 68.5 1.0 CA B:LYS341 4.8 62.8 1.0 CB B:GLU336 4.8 48.5 1.0 CG B:GLU336 4.8 50.6 1.0 CA B:ASP344 4.9 49.3 1.0 C B:GLU336 4.9 52.2 1.0 CB B:ARG340 5.0 60.0 1.0 C B:GLY342 5.0 65.5 1.0

D.Giganti, A.Bouillon, L.Tawk, F.Robert, M.Martinez, E.Crublet, P.Weber, C.Girard-Blanc, S.Petres, A.Haouz, J.F.Hernandez, O.Mercereau-Puijalon, P.M.Alzari, J.C.Barale. A Novel Plasmodium-Specific Prodomain Fold Regulates the Malaria Drug Target SUB1 Subtilase. Nat Commun V. 5 4833 2014.
ISSN: ESSN 2041-1723
PubMed: 25204226
DOI: 10.1038/NCOMMS5833