Calcium in PDB 3aaj: Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122

The structure of Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122, PDB code: 3aaj was solved by H.Suzuki, T.Inuzuka, M.Kawasaki, H.Shibata, S.Wakatsuki, M.Maki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.28 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.580, 78.940, 60.333, 90.00, 104.58, 90.00
R / Rfree (%)	19.6 / 26.6

The binding sites of Calcium atom in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122 (pdb code 3aaj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122, PDB code: 3aaj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122


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 CA2+-Bound Form of DES3-23ALG-2DELTAGF122 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca991 b:37.3 occ:1.00 OD1 A:ASP36 2.2 36.6 1.0 OE1 A:GLU47 2.4 31.2 1.0 O A:VAL42 2.4 27.6 1.0 OD2 A:ASP38 2.5 38.6 1.0 OG A:SER40 2.5 34.7 1.0 OE2 A:GLU47 2.6 28.8 1.0 CD A:GLU47 2.8 30.4 1.0 CG A:ASP38 3.4 39.2 1.0 CG A:ASP36 3.5 37.3 1.0 C A:VAL42 3.6 28.1 1.0 CB A:SER40 3.6 35.9 1.0 N A:SER40 3.8 37.2 1.0 OD1 A:ASP38 3.8 41.9 1.0 O A:HOH201 4.1 28.3 1.0 CA A:SER40 4.2 35.2 1.0 OD2 A:ASP36 4.3 37.2 1.0 N A:VAL42 4.3 29.4 1.0 CA A:ASP36 4.3 38.1 1.0 CG A:GLU47 4.3 30.1 1.0 N A:ASP38 4.4 38.5 1.0 CA A:ILE43 4.4 26.6 1.0 CB A:ASP36 4.4 37.7 1.0 N A:ILE43 4.4 27.5 1.0 CB A:ASP38 4.5 38.9 1.0 C A:ASP36 4.5 37.7 1.0 CA A:VAL42 4.5 28.3 1.0 N A:SER44 4.5 26.9 1.0 N A:ARG39 4.6 39.6 1.0 CA A:ASP38 4.7 39.0 1.0 N A:GLY41 4.7 33.9 1.0 N A:LYS37 4.8 37.7 1.0 O A:HOH17 4.8 41.2 1.0 C A:SER40 4.8 34.3 1.0 O A:ASP36 4.9 37.3 1.0 C A:ASP38 4.9 39.3 1.0 C A:ILE43 4.9 26.9 1.0 C A:ARG39 4.9 39.1 1.0 OG A:SER44 5.0 28.7 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122


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 CA2+-Bound Form of DES3-23ALG-2DELTAGF122 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca992 b:34.7 occ:1.00 OD1 A:ASP103 2.3 29.8 1.0 OE2 A:GLU114 2.4 38.7 1.0 OE1 A:GLU114 2.4 36.8 1.0 OD2 A:ASP105 2.4 37.1 1.0 O A:MET109 2.5 33.8 1.0 OG A:SER107 2.6 33.6 1.0 CD A:GLU114 2.8 34.7 1.0 CG A:ASP105 3.4 36.1 1.0 CG A:ASP103 3.5 29.9 1.0 OD1 A:ASP105 3.7 35.5 1.0 C A:MET109 3.7 34.2 1.0 CB A:SER107 3.8 34.2 1.0 N A:SER107 4.2 35.5 1.0 CG A:GLU114 4.3 32.0 1.0 OD2 A:ASP103 4.4 29.9 1.0 CA A:ASP103 4.4 28.2 1.0 CB A:ASP103 4.5 27.2 1.0 CA A:ILE110 4.5 32.0 1.0 N A:MET109 4.5 34.5 1.0 CA A:SER107 4.5 34.6 1.0 N A:ILE110 4.6 33.5 1.0 N A:ASP105 4.6 31.8 1.0 N A:ASP111 4.6 31.0 1.0 C A:ASP103 4.7 29.1 1.0 CA A:MET109 4.7 34.7 1.0 CB A:ASP105 4.7 34.0 1.0 OE1 A:GLN143 4.8 46.2 1.0 O A:HOH19 4.8 38.0 1.0 N A:ARG104 4.8 30.0 1.0 CG A:ASP111 4.9 32.1 1.0 C A:SER107 5.0 34.5 1.0 OD2 A:ASP111 5.0 31.1 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122


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 CA2+-Bound Form of DES3-23ALG-2DELTAGF122 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca993 b:32.5 occ:1.00 OD1 A:ASP167 2.2 25.1 1.0 O A:HOH208 2.3 31.4 1.0 O A:TRP173 2.4 30.1 1.0 OD1 A:ASP169 2.5 42.5 1.0 OD1 A:ASP171 2.5 38.0 1.0 O A:HOH207 2.7 43.7 1.0 CG A:ASP167 3.4 31.6 1.0 C A:TRP173 3.4 29.1 1.0 CG A:ASP171 3.5 36.2 1.0 CG A:ASP169 3.5 39.6 1.0 OD2 A:ASP169 3.8 38.7 1.0 OD2 A:ASP171 4.0 38.2 1.0 N A:TRP173 4.0 30.4 1.0 CA A:TRP173 4.1 29.9 1.0 OD2 A:ASP167 4.2 31.1 1.0 CA A:ASP167 4.2 34.5 1.0 CB A:TRP173 4.3 28.8 1.0 CB A:ASP167 4.3 32.5 1.0 N A:ASP171 4.3 34.7 1.0 N A:ILE174 4.5 29.0 1.0 CA A:ILE174 4.6 27.9 1.0 CB A:ASP171 4.7 33.3 1.0 C A:ASP167 4.7 35.1 1.0 N A:GLN170 4.7 38.9 1.0 N A:ASP169 4.8 38.4 1.0 CB A:ASP169 4.8 38.3 1.0 N A:GLY172 4.9 32.0 1.0 CA A:ASP171 4.9 33.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122


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 CA2+-Bound Form of DES3-23ALG-2DELTAGF122 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca991 b:33.6 occ:1.00 OD1 B:ASP103 2.2 36.3 1.0 O B:MET109 2.3 31.5 1.0 OE2 B:GLU114 2.4 33.7 1.0 OD2 B:ASP105 2.4 40.5 1.0 OE1 B:GLU114 2.4 30.2 1.0 OG B:SER107 2.5 35.7 1.0 CD B:GLU114 2.7 29.2 1.0 CG B:ASP105 3.2 41.7 1.0 OD1 B:ASP105 3.4 39.2 1.0 CB B:SER107 3.4 34.5 1.0 CG B:ASP103 3.4 35.5 1.0 C B:MET109 3.6 31.5 1.0 OD2 B:ASP111 3.9 41.2 1.0 N B:SER107 4.1 35.8 1.0 CA B:ASP103 4.2 35.6 1.0 N B:MET109 4.2 32.5 1.0 CG B:GLU114 4.3 28.1 1.0 CB B:ASP103 4.3 35.0 1.0 OD2 B:ASP103 4.3 38.1 1.0 CA B:SER107 4.3 34.7 1.0 N B:ASP111 4.3 29.7 1.0 O B:HOH7 4.4 32.9 1.0 CA B:ILE110 4.4 29.1 1.0 C B:ASP103 4.5 36.8 1.0 N B:ILE110 4.5 30.8 1.0 CA B:MET109 4.5 32.0 1.0 CG B:ASP111 4.6 35.1 1.0 N B:GLY108 4.6 34.0 1.0 CB B:ASP105 4.6 40.1 1.0 N B:ASP105 4.6 40.0 1.0 C B:SER107 4.8 34.4 1.0 O B:ASP103 4.8 36.3 1.0 C B:ILE110 4.8 29.7 1.0 N B:ARG104 4.9 38.3 1.0 N B:ASN106 5.0 39.9 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122


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 CA2+-Bound Form of DES3-23ALG-2DELTAGF122 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca992 b:50.0 occ:1.00 O B:HOH194 2.0 40.2 1.0 OD1 B:ASP36 2.1 50.0 1.0 OE2 B:GLU47 2.5 44.0 1.0 OD1 B:ASP38 2.5 54.0 1.0 O B:VAL42 2.5 46.6 1.0 OE1 B:GLU47 2.6 41.6 1.0 CD B:GLU47 2.9 44.6 1.0 OG B:SER40 3.0 53.9 1.0 CG B:ASP36 3.4 51.8 1.0 CG B:ASP38 3.5 53.3 1.0 C B:VAL42 3.5 47.2 1.0 OD2 B:ASP38 3.8 52.4 1.0 CB B:SER40 3.9 52.7 1.0 N B:SER40 4.1 53.3 1.0 OD2 B:ASP36 4.1 51.5 1.0 CA B:ASP36 4.2 52.5 1.0 N B:VAL42 4.3 49.9 1.0 N B:ILE43 4.3 45.1 1.0 CA B:ILE43 4.3 42.8 1.0 CB B:ASP36 4.3 52.1 1.0 CA B:SER40 4.4 52.9 1.0 CG B:GLU47 4.4 41.2 1.0 CA B:VAL42 4.5 48.5 1.0 N B:LYS37 4.5 53.6 1.0 C B:ASP36 4.6 53.0 1.0 N B:ASP38 4.6 53.6 1.0 N B:SER44 4.6 41.6 1.0 N B:GLY41 4.8 52.3 1.0 C B:SER40 4.8 52.6 1.0 N B:ARG39 4.8 54.5 1.0 CB B:ASP38 4.8 53.5 1.0 C B:ASP38 4.9 54.4 1.0 C B:ILE43 5.0 42.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of CA2+-Bound Form of DES3-23ALG-2DELTAGF122


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 CA2+-Bound Form of DES3-23ALG-2DELTAGF122 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca993 b:45.6 occ:1.00 OD1 B:ASP167 2.2 34.7 1.0 OD1 B:ASP171 2.3 44.5 1.0 O B:TRP173 2.3 34.0 1.0 OD1 B:ASP169 2.4 49.9 1.0 O B:HOH198 3.1 48.3 1.0 CG B:ASP169 3.3 44.1 1.0 CG B:ASP171 3.4 43.1 1.0 CG B:ASP167 3.4 39.0 1.0 OD2 B:ASP169 3.4 45.6 1.0 C B:TRP173 3.5 34.2 1.0 OD2 B:ASP171 4.1 43.4 1.0 CA B:ASP167 4.2 41.2 1.0 N B:TRP173 4.2 36.6 1.0 OD2 B:ASP167 4.2 38.0 1.0 CB B:ASP167 4.3 38.8 1.0 CA B:TRP173 4.3 34.8 1.0 OE1 B:GLN175 4.3 46.1 1.0 CB B:ASP171 4.4 41.9 1.0 N B:ILE174 4.5 33.5 1.0 N B:ASP171 4.5 42.1 1.0 C B:ASP167 4.6 42.5 1.0 CA B:ILE174 4.6 32.9 1.0 CB B:ASP169 4.6 42.0 1.0 CG2 B:ILE174 4.7 33.1 1.0 N B:ASP169 4.7 42.6 1.0 O B:ASP167 4.8 42.8 1.0 CB B:TRP173 4.8 34.0 1.0 N B:GLN170 4.9 43.7 1.0 CA B:ASP171 4.9 41.0 1.0 N B:GLY172 5.0 40.3 1.0

T.Inuzuka, H.Suzuki, M.Kawasaki, H.Shibata, S.Wakatsuki, M.Maki. Molecular Basis For Defect in Alix-Binding By Alternatively Spliced Isoform of Alg-2 (Alg-2DELTAGF122) and Structural Roles of F122 in Target Recognition Bmc Struct.Biol. V. 10 25 2010.
ISSN: ESSN 1472-6807
PubMed: 20691033
DOI: 10.1186/1472-6807-10-25