Calcium in PDB 3w57: Structure of A C2 Domain

The structure of Structure of A C2 Domain, PDB code: 3w57 was solved by D.A.K.Traore, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.01 / 1.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.803, 52.751, 49.055, 90.00, 107.15, 90.00
R / Rfree (%)	15.9 / 18.2

The binding sites of Calcium atom in the Structure of A C2 Domain (pdb code 3w57). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of A C2 Domain, PDB code: 3w57:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A C2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:6.3 occ:1.00 OD2 A:ASP35 2.3 9.1 1.0 O A:GLU89 2.4 9.0 1.0 OD1 A:ASP90 2.4 10.4 1.0 OD2 A:ASP41 2.5 6.2 1.0 OD1 A:ASP88 2.5 5.8 1.0 O A:HOH325 2.6 11.3 1.0 OD2 A:ASP88 2.6 9.2 1.0 CG A:ASP88 2.9 8.7 1.0 CG A:ASP90 3.3 11.9 1.0 CG A:ASP35 3.3 9.8 1.0 C A:GLU89 3.5 8.1 1.0 CG A:ASP41 3.5 6.7 1.0 OD1 A:ASP35 3.8 9.2 1.0 CB A:ASP41 3.9 7.3 1.0 O A:HOH303 3.9 9.2 1.0 OD2 A:ASP90 4.0 12.6 1.0 CA A:ASP90 4.1 7.8 1.0 N A:ASP90 4.2 8.1 1.0 O A:HOH349 4.3 18.5 1.0 N A:ASP41 4.3 5.1 1.0 CB A:ASP90 4.3 9.9 1.0 CA A:CA202 4.4 8.3 1.0 N A:GLU89 4.4 5.5 1.0 CB A:ASP88 4.4 5.9 1.0 O A:HOH346 4.4 13.8 1.0 CA A:GLU89 4.5 6.2 1.0 O A:HOH376 4.5 17.4 1.0 CB A:ASP35 4.6 8.7 1.0 CA A:CA203 4.6 8.0 1.0 C A:ASP88 4.6 7.7 1.0 OD1 A:ASP41 4.6 7.5 1.0 O A:HOH327 4.8 12.6 1.0 CA A:ASP41 4.8 4.7 1.0 O A:HOH367 4.8 20.4 1.0 O A:ASP88 5.0 7.0 1.0 CA A:ASP88 5.0 6.0 1.0

Calcium binding site 2 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A C2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:8.3 occ:1.00 OD2 A:ASP90 2.4 12.6 1.0 OD2 A:ASP95 2.4 12.3 1.0 OD1 A:ASP35 2.4 9.2 1.0 O A:HOH305 2.5 9.3 1.0 O A:HOH329 2.5 11.5 1.0 OD2 A:ASP88 2.5 9.2 1.0 O A:HOH312 2.6 12.3 1.0 CG A:ASP90 3.3 11.9 1.0 CG A:ASP95 3.5 13.1 1.0 CG A:ASP35 3.5 9.8 1.0 CG A:ASP88 3.6 8.7 1.0 OD1 A:ASP90 3.6 10.4 1.0 OD2 A:ASP35 4.0 9.1 1.0 CB A:ASP95 4.1 8.0 1.0 CB A:ASP88 4.2 5.9 1.0 CA A:CA201 4.4 6.3 1.0 N A:LEU36 4.5 10.8 1.0 O A:HOH339 4.5 10.7 1.0 OD1 A:ASP95 4.6 14.5 1.0 O A:HOH372 4.6 25.4 1.0 O A:HOH338 4.6 12.5 1.0 OD1 A:ASP88 4.6 5.8 1.0 CB A:ASP90 4.6 9.9 1.0 O A:HOH346 4.7 13.8 1.0 CB A:ASP35 4.7 8.7 1.0 CA A:ASP35 4.8 9.7 1.0 O A:HOH358 4.9 19.5 1.0 CB A:LEU36 5.0 10.9 1.0

Calcium binding site 3 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A C2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:8.0 occ:1.00 OD1 A:ASN61 2.4 10.6 1.0 O A:ILE39 2.4 7.8 1.0 O A:HOH303 2.4 9.2 1.0 OD1 A:ASP41 2.5 7.5 1.0 O A:HOH327 2.5 12.6 1.0 O A:HOH317 2.5 12.2 1.0 OD2 A:ASP41 2.6 6.2 1.0 CG A:ASP41 2.9 6.7 1.0 CG A:ASN61 3.5 11.1 1.0 C A:ILE39 3.6 7.1 1.0 O A:HOH325 4.1 11.3 1.0 N A:ILE39 4.2 7.7 1.0 OD2 A:ASP35 4.2 9.1 1.0 ND2 A:ASN61 4.3 13.7 1.0 CA A:ASN61 4.3 6.5 1.0 N A:ASN61 4.3 5.6 1.0 CB A:ASP41 4.4 7.3 1.0 O A:HOH314 4.4 14.2 1.0 CA A:ILE39 4.4 7.4 1.0 O A:MET37 4.4 17.0 1.0 O A:HOH323 4.4 14.7 1.0 CB A:ASN61 4.5 8.6 1.0 C A:THR40 4.5 6.7 1.0 O A:HOH451 4.5 28.7 1.0 N A:THR40 4.5 5.7 1.0 CA A:CA201 4.6 6.3 1.0 N A:ASP41 4.6 5.1 1.0 CA A:THR40 4.7 5.3 1.0 O A:HOH426 4.7 25.3 1.0 O A:THR40 4.7 6.8 1.0 O A:HOH424 4.7 25.0 1.0 C A:GLY38 4.8 7.4 1.0 O A:HOH367 4.9 20.4 1.0 CB A:ILE39 5.0 9.9 1.0 CA A:ASP41 5.0 4.7 1.0

Calcium binding site 4 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A C2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:9.5 occ:1.00 OD1 B:ASP35 2.3 13.2 1.0 O B:GLU89 2.4 8.9 1.0 OD1 B:ASP90 2.4 10.2 1.0 O B:HOH317 2.5 14.0 1.0 OD2 B:ASP41 2.5 9.2 1.0 OD1 B:ASP88 2.5 8.3 1.0 OD2 B:ASP88 2.6 10.9 1.0 CG B:ASP88 2.9 10.8 1.0 CG B:ASP35 3.4 13.1 1.0 C B:GLU89 3.4 10.4 1.0 CG B:ASP90 3.5 11.2 1.0 CG B:ASP41 3.6 9.8 1.0 OD2 B:ASP35 3.9 12.6 1.0 O B:HOH312 3.9 13.0 1.0 CB B:ASP41 4.0 10.6 1.0 O B:HOH370 4.1 19.2 1.0 CA B:ASP90 4.1 9.8 1.0 N B:ASP90 4.1 8.2 1.0 CA B:CA203 4.1 11.1 1.0 OD2 B:ASP90 4.3 14.1 1.0 N B:ASP41 4.3 9.1 1.0 N B:GLU89 4.3 8.1 1.0 CB B:ASP88 4.4 7.7 1.0 CB B:ASP90 4.4 11.4 1.0 CB B:ASP35 4.5 11.8 1.0 CA B:GLU89 4.5 7.9 1.0 O B:HOH411 4.5 28.0 1.0 CA B:CA202 4.5 11.2 1.0 O B:HOH377 4.5 19.0 1.0 C B:ASP88 4.5 10.6 1.0 OD1 B:ASP41 4.7 10.8 1.0 CA B:ASP41 4.8 7.5 1.0 O B:ILE39 4.9 12.7 1.0 O B:ASP88 4.9 10.3 1.0 CA B:ASP88 5.0 7.0 1.0

Calcium binding site 5 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A C2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:11.2 occ:1.00 O B:HOH312 2.4 13.0 1.0 O B:ILE39 2.4 12.7 1.0 OD1 B:ASN61 2.4 11.4 1.0 OD1 B:ASP41 2.5 10.8 1.0 O B:HOH363 2.5 21.5 1.0 O B:HOH319 2.6 13.7 1.0 OD2 B:ASP41 2.7 9.2 1.0 CG B:ASP41 2.9 9.8 1.0 C B:ILE39 3.6 11.3 1.0 CG B:ASN61 3.6 12.7 1.0 N B:ILE39 4.0 16.0 1.0 OD1 B:ASP35 4.2 13.2 1.0 O B:HOH317 4.3 14.0 1.0 CA B:ILE39 4.3 13.3 1.0 O B:HOH351 4.3 19.7 1.0 ND2 B:ASN61 4.4 16.4 1.0 CA B:ASN61 4.4 8.8 1.0 N B:ASN61 4.4 9.4 1.0 CB B:ASP41 4.4 10.6 1.0 O B:HOH347 4.4 16.7 1.0 C B:THR40 4.5 9.2 1.0 CA B:CA201 4.5 9.5 1.0 CB B:ASN61 4.6 10.0 1.0 O B:HOH416 4.6 25.2 1.0 N B:THR40 4.6 8.3 1.0 N B:ASP41 4.6 9.1 1.0 CB B:ILE39 4.6 12.2 1.0 O B:HOH348 4.7 18.6 1.0 O B:THR40 4.7 10.0 1.0 O B:HOH485 4.8 34.5 1.0 CA B:THR40 4.8 10.4 1.0 C B:GLY38 5.0 17.0 1.0

Calcium binding site 6 out of 6 in the Structure of A C2 Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A C2 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:11.1 occ:1.00 OD2 B:ASP35 2.4 12.6 1.0 OD2 B:ASP88 2.4 10.9 1.0 O B:HOH305 2.4 11.6 1.0 OD2 B:ASP95 2.4 17.4 1.0 OD2 B:ASP90 2.5 14.1 1.0 O B:HOH383 2.6 22.5 1.0 O B:HOH385 2.6 23.5 1.0 OD1 B:ASP90 3.2 10.2 1.0 CG B:ASP90 3.2 11.2 1.0 CG B:ASP35 3.4 13.1 1.0 CG B:ASP88 3.6 10.8 1.0 CG B:ASP95 3.6 17.4 1.0 OD1 B:ASP35 3.8 13.2 1.0 CA B:CA201 4.1 9.5 1.0 CB B:ASP95 4.1 14.1 1.0 CB B:ASP88 4.2 7.7 1.0 O B:HOH362 4.3 22.1 1.0 O B:HOH411 4.4 28.0 1.0 OD1 B:ASP88 4.5 8.3 1.0 OD1 B:ASP95 4.6 18.3 1.0 O B:HOH314 4.6 12.2 1.0 CB B:ASP90 4.6 11.4 1.0 CB B:ASP35 4.6 11.8 1.0 O B:HOH337 4.7 16.7 1.0 O B:HOH449 4.9 30.7 1.0 CA B:ASP35 4.9 15.0 1.0

D.A.Traore, A.J.Brennan, R.H.Law, C.Dogovski, M.A.Perugini, N.Lukoyanova, E.W.Leung, R.S.Norton, J.A.Lopez, K.A.Browne, H.Yagita, G.J.Lloyd, A.Ciccone, S.Verschoor, J.A.Trapani, J.C.Whisstock, I.Voskoboinik. Defining the Interaction of Perforin with Calcium and the Phospholipid Membrane. Biochem.J. V. 456 323 2013.
ISSN: ISSN 0264-6021
PubMed: 24070258
DOI: 10.1042/BJ20130999