Calcium in PDB 4lvn: Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex

All present enzymatic activity of Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex:
3.4.21.61;

The structure of Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex, PDB code: 4lvn was solved by C.Withers-Martinez, M.J.Blackman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.500, 74.790, 78.850, 90.00, 103.33, 90.00
R / Rfree (%)	19.5 / 23.7

The structure of Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex (pdb code 4lvn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex, PDB code: 4lvn:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex


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 PFSUB1-Prodomain-Nimp.M7 Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:33.3 occ:1.00 O A:ILE439 2.3 36.1 1.0 O A:VAL446 2.3 32.9 1.0 OD1 A:ASN442 2.4 34.1 1.0 OD1 A:ASP381 2.4 34.2 1.0 O A:ILE444 2.4 40.9 1.0 OE2 A:GLU338 2.5 45.8 1.0 OD2 A:ASP381 2.7 30.3 1.0 CG A:ASP381 2.9 35.4 1.0 CG A:ASN442 3.3 35.5 1.0 C A:VAL446 3.5 29.4 1.0 C A:ILE439 3.5 34.6 1.0 CD A:GLU338 3.5 48.9 1.0 N A:VAL446 3.6 25.8 1.0 C A:ILE444 3.6 43.0 1.0 ND2 A:ASN442 3.7 34.7 1.0 CG A:GLU338 3.9 50.5 1.0 C A:GLY445 4.0 35.4 1.0 CB A:GLU338 4.1 52.7 1.0 CA A:VAL446 4.2 28.9 1.0 CA A:GLY445 4.4 38.5 1.0 CG1 A:ILE444 4.4 37.9 1.0 CB A:ASP381 4.4 34.9 1.0 N A:GLY440 4.4 34.4 1.0 CA A:GLY440 4.4 41.2 1.0 CA A:ILE439 4.4 31.0 1.0 N A:GLY445 4.4 43.2 1.0 N A:ILE439 4.4 26.6 1.0 N A:VAL447 4.6 30.0 1.0 OE1 A:GLU338 4.6 49.3 1.0 O A:GLY445 4.6 35.8 1.0 CA A:ILE444 4.7 43.2 1.0 N A:ASN442 4.7 34.7 1.0 N A:ILE444 4.7 47.5 1.0 CB A:ASN442 4.7 35.2 1.0 CB A:ILE439 4.8 45.0 1.0 C A:GLY440 4.8 42.7 1.0 CA A:VAL447 4.8 35.2 1.0 C A:ALA438 4.9 29.9 1.0 CG2 A:ILE439 5.0 42.4 1.0 N A:ASN441 5.0 41.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex


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 PFSUB1-Prodomain-Nimp.M7 Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:31.2 occ:1.00 OD1 A:ASP401 2.2 37.6 1.0 O A:ARG396 2.3 32.8 1.0 OD1 A:ASP408 2.3 32.6 1.0 O A:HOH891 2.4 21.1 1.0 O A:PHE399 2.4 37.1 1.0 OE1 A:GLU392 2.4 41.5 1.0 C A:ARG396 3.3 29.6 1.0 CG A:ASP401 3.4 37.0 1.0 CG A:ASP408 3.5 38.4 1.0 C A:PHE399 3.5 35.8 1.0 CD A:GLU392 3.6 26.0 1.0 N A:ARG396 3.7 28.6 1.0 N A:PHE399 4.0 36.5 1.0 CA A:ASP408 4.0 35.1 1.0 N A:ASP408 4.0 34.2 1.0 OE2 A:GLU392 4.1 26.6 1.0 CA A:ARG396 4.1 36.0 1.0 OD2 A:ASP401 4.1 35.8 1.0 CA A:PHE399 4.2 39.7 1.0 O A:GLU392 4.2 30.8 1.0 N A:LYS397 4.2 39.4 1.0 N A:ASP401 4.3 35.1 1.0 CB A:ASP408 4.3 36.3 1.0 C A:GLY395 4.3 36.2 1.0 CB A:PHE399 4.3 42.0 1.0 OD2 A:ASP408 4.4 39.7 1.0 CA A:LYS397 4.4 30.2 1.0 CB A:ASP401 4.4 37.7 1.0 CA A:GLU392 4.5 29.7 1.0 OH C:TYR54 4.5 37.3 1.0 CA A:GLY395 4.6 27.1 1.0 N A:ASP400 4.6 36.4 1.0 CB A:GLU392 4.6 24.5 1.0 N A:GLY398 4.7 31.2 1.0 C A:LYS397 4.7 34.8 1.0 CG A:GLU392 4.7 24.9 1.0 C A:GLU392 4.8 31.8 1.0 CA A:ASP400 4.9 39.6 1.0 CA A:ASP401 5.0 39.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of PFSUB1-Prodomain-Nimp.M7 Fab Complex


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 PFSUB1-Prodomain-Nimp.M7 Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:31.4 occ:1.00 OD1 A:ASP402 2.3 35.2 1.0 OD1 A:ASP400 2.3 35.2 1.0 OE2 A:GLU392 2.3 26.6 1.0 OD1 A:ASP409 2.3 37.1 1.0 OD1 A:ASN404 2.4 29.7 1.0 O A:ILE406 2.4 37.9 1.0 CG A:ASN404 3.0 30.1 1.0 CD A:GLU392 3.2 26.0 1.0 ND2 A:ASN404 3.2 25.9 1.0 CG A:ASP409 3.3 34.5 1.0 CG A:ASP402 3.4 37.4 1.0 CG A:ASP400 3.5 38.8 1.0 C A:ILE406 3.5 37.4 1.0 CG A:GLU392 3.6 24.9 1.0 OD2 A:ASP409 3.7 33.5 1.0 OD2 A:ASP402 3.7 38.1 1.0 CA A:ASP400 4.2 39.6 1.0 OE1 A:GLU392 4.2 41.5 1.0 CA A:ILE406 4.3 39.9 1.0 N A:ILE406 4.3 41.0 1.0 OD2 A:ASP400 4.3 37.2 1.0 CB A:ASN404 4.3 33.8 1.0 N A:ASN404 4.3 35.1 1.0 CB A:ASP400 4.4 41.3 1.0 N A:ASP402 4.4 37.4 1.0 CB A:ILE406 4.4 37.7 1.0 C A:ASP400 4.5 38.0 1.0 N A:ASP401 4.5 35.1 1.0 N A:ASP409 4.5 27.3 1.0 N A:VAL407 4.6 35.8 1.0 N A:ASP408 4.6 34.2 1.0 CB A:ASP409 4.6 31.7 1.0 CB A:ASP402 4.7 35.9 1.0 ND2 A:ASN389 4.7 25.7 1.0 CA A:ASN404 4.8 38.6 1.0 CA A:VAL407 4.8 35.9 1.0 CG2 A:ILE406 4.8 35.0 1.0 N A:ASN403 4.8 40.9 1.0 CA A:ASP402 4.9 38.3 1.0 C A:VAL407 4.9 35.8 1.0 C A:ASP402 4.9 40.7 1.0

C.Withers-Martinez, M.Strath, F.Hackett, L.F.Haire, S.A.Howell, P.A.Walker, C.Evangelos, G.G.Dodson, M.J.Blackman. The Malaria Parasite Egress Protease SUB1 Is A Calcium-Dependent Redox Switch Subtilisin. Nat Commun V. 5 3726 2014.
ISSN: ESSN 2041-1723
PubMed: 24785947
DOI: 10.1038/NCOMMS4726