Calcium in PDB 2zn9: Crystal Structure of CA2+-Bound Form of DES3-20ALG-2

The structure of Crystal Structure of CA2+-Bound Form of DES3-20ALG-2, PDB code: 2zn9 was solved by H.Suzuki, M.Kawasaki, T.Inuzuka, T.Kakiuchi, 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)	38.66 / 2.40
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	72.024, 72.024, 91.663, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 29.8

The binding sites of Calcium atom in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2 (pdb code 2zn9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2, PDB code: 2zn9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2


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 DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:58.6 occ:1.00 OD2 A:ASP38 2.2 60.0 1.0 O A:HOH927 2.2 50.4 1.0 OD1 A:ASP36 2.3 52.9 1.0 O A:VAL42 2.4 50.2 1.0 OE2 A:GLU47 2.5 46.6 1.0 OG A:SER40 2.8 51.5 1.0 OE1 A:GLU47 2.8 46.1 1.0 CD A:GLU47 3.1 46.9 1.0 CG A:ASP38 3.2 58.2 1.0 CG A:ASP36 3.5 54.4 1.0 C A:VAL42 3.6 50.1 1.0 OD1 A:ASP38 3.6 58.8 1.0 N A:SER40 3.7 53.9 1.0 CB A:SER40 3.9 53.3 1.0 CA A:ASP36 4.1 54.0 1.0 N A:ARG39 4.2 55.8 1.0 CA A:SER40 4.3 53.1 1.0 CB A:ASP36 4.3 54.0 1.0 N A:ASP38 4.3 56.0 1.0 O A:HOH909 4.3 46.8 1.0 C A:ASP36 4.3 54.5 1.0 N A:ILE43 4.4 49.7 1.0 N A:VAL42 4.4 50.6 1.0 CA A:ILE43 4.4 48.9 1.0 CB A:ASP38 4.4 56.4 1.0 OD2 A:ASP36 4.4 55.3 1.0 N A:LYS37 4.5 55.1 1.0 CA A:VAL42 4.5 50.2 1.0 CG A:GLU47 4.6 46.1 1.0 N A:GLY41 4.6 52.7 1.0 C A:ASP38 4.6 56.0 1.0 CA A:ASP38 4.7 56.4 1.0 C A:ARG39 4.7 54.9 1.0 CA A:ARG39 4.7 55.4 1.0 N A:SER44 4.8 50.1 1.0 C A:SER40 4.8 53.2 1.0 O A:ASP36 4.9 54.5 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2


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 DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:38.9 occ:1.00 OD1 A:ASP103 2.3 34.1 1.0 O A:MET109 2.3 40.3 1.0 OE1 A:GLU114 2.4 39.2 1.0 OD2 A:ASP105 2.5 42.5 1.0 OE2 A:GLU114 2.5 37.6 1.0 OG A:SER107 2.6 38.8 1.0 CD A:GLU114 2.8 40.8 1.0 CG A:ASP105 3.5 39.6 1.0 CG A:ASP103 3.5 35.5 1.0 C A:MET109 3.6 40.4 1.0 CB A:SER107 3.8 38.1 1.0 OD1 A:ASP105 3.9 42.1 1.0 N A:SER107 4.0 37.7 1.0 CA A:ASP103 4.2 36.1 1.0 N A:MET109 4.2 39.2 1.0 C A:ASP103 4.3 36.5 1.0 CG A:GLU114 4.3 40.7 1.0 CB A:ASP103 4.3 36.0 1.0 OD2 A:ASP103 4.4 34.9 1.0 CA A:ILE110 4.4 40.2 1.0 N A:ASP105 4.4 38.5 1.0 CA A:SER107 4.4 38.1 1.0 N A:ILE110 4.4 40.2 1.0 N A:ASP111 4.5 40.9 1.0 N A:ARG104 4.5 37.7 1.0 CA A:MET109 4.5 40.0 1.0 N A:ASN106 4.6 37.4 1.0 N A:GLY108 4.6 38.5 1.0 CB A:ASP105 4.7 38.7 1.0 OD2 A:ASP111 4.8 41.3 1.0 O A:ASP103 4.8 35.7 1.0 C A:SER107 4.9 38.2 1.0 C A:ILE110 4.9 40.6 1.0 CA A:ASP105 4.9 38.9 1.0 C A:ASP105 4.9 38.5 1.0 OE1 A:GLN145 4.9 52.0 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2


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 DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:58.7 occ:1.00 OD1 A:ASP173 2.2 54.9 1.0 OD2 A:ASP171 2.3 57.9 1.0 OD1 A:ASP169 2.4 48.6 1.0 O A:TRP175 2.5 57.6 1.0 O A:HOH924 2.5 43.2 1.0 O A:HOH928 2.5 69.1 1.0 CG A:ASP173 3.4 55.4 1.0 CG A:ASP171 3.5 57.3 1.0 CG A:ASP169 3.5 52.0 1.0 C A:TRP175 3.7 57.5 1.0 OD1 A:ASP171 4.0 58.6 1.0 OD2 A:ASP173 4.1 55.6 1.0 OD2 A:ASP169 4.2 49.2 1.0 N A:ASP171 4.3 56.4 1.0 CA A:ASP169 4.4 54.5 1.0 N A:ASP173 4.4 54.8 1.0 CB A:ASP173 4.4 54.9 1.0 N A:TRP175 4.4 57.2 1.0 N A:THR170 4.5 55.9 1.0 CB A:ASP169 4.5 53.6 1.0 CA A:TRP175 4.5 57.5 1.0 C A:ASP169 4.6 55.4 1.0 N A:ILE176 4.6 57.1 1.0 CB A:ASP171 4.6 56.5 1.0 CA A:ILE176 4.7 56.4 1.0 CG2 A:ILE176 4.7 56.0 1.0 CB A:TRP175 4.8 58.3 1.0 CA A:ASP171 4.8 56.2 1.0 N A:GLN172 4.8 55.1 1.0 C A:ASP171 4.8 55.8 1.0 CA A:ASP173 4.9 54.8 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2


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 DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:43.1 occ:1.00 OD1 A:ASN106 2.5 39.2 1.0 O A:HOH920 2.9 35.6 1.0 CG A:ASN106 3.6 38.9 1.0 ND2 A:ASN106 4.1 38.9 1.0 O A:ASP103 4.2 35.7 1.0 O A:ARG100 4.3 36.2 1.0 O A:ARG104 4.8 39.5 1.0 CB A:ASN106 4.8 37.4 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2


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 DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:54.0 occ:1.00 OD1 B:ASP36 2.1 50.3 1.0 O B:HOH915 2.3 45.3 1.0 OD1 B:ASP38 2.3 60.6 1.0 O B:VAL42 2.5 50.0 1.0 OE2 B:GLU47 2.5 49.6 1.0 OE1 B:GLU47 2.9 47.0 1.0 CD B:GLU47 3.1 47.9 1.0 OG B:SER40 3.1 53.6 1.0 CG B:ASP38 3.2 59.2 1.0 CG B:ASP36 3.4 52.6 1.0 OD2 B:ASP38 3.4 59.1 1.0 C B:VAL42 3.6 50.3 1.0 CB B:SER40 3.8 55.0 1.0 N B:SER40 3.8 56.0 1.0 OD2 B:ASP36 4.2 53.0 1.0 CA B:ASP36 4.2 53.3 1.0 CA B:SER40 4.2 55.0 1.0 N B:VAL42 4.3 51.3 1.0 CB B:ASP36 4.4 53.4 1.0 N B:ASP38 4.4 57.2 1.0 N B:ILE43 4.4 49.9 1.0 C B:ASP36 4.4 54.1 1.0 CB B:ASP38 4.5 57.8 1.0 CA B:ILE43 4.5 49.0 1.0 N B:ARG39 4.5 57.6 1.0 O B:HOH916 4.5 47.1 1.0 CG B:GLU47 4.6 46.4 1.0 N B:LYS37 4.6 55.0 1.0 CA B:VAL42 4.6 50.4 1.0 N B:GLY41 4.6 54.4 1.0 C B:SER40 4.7 55.0 1.0 N B:SER44 4.7 49.9 1.0 C B:ASP38 4.8 57.8 1.0 CA B:ASP38 4.8 57.9 1.0 C B:ARG39 4.9 56.8 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2


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 DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:36.6 occ:1.00 OD1 B:ASP103 2.3 32.8 1.0 O B:MET109 2.3 39.3 1.0 OE1 B:GLU114 2.4 38.7 1.0 OE2 B:GLU114 2.4 35.2 1.0 OD2 B:ASP105 2.6 41.7 1.0 OG B:SER107 2.7 38.8 1.0 CD B:GLU114 2.7 39.3 1.0 CG B:ASP103 3.5 35.3 1.0 C B:MET109 3.6 39.4 1.0 CG B:ASP105 3.6 39.7 1.0 CB B:SER107 3.8 37.6 1.0 OD1 B:ASP105 4.0 42.8 1.0 N B:SER107 4.0 37.8 1.0 CA B:ASP103 4.1 35.5 1.0 CG B:GLU114 4.2 39.2 1.0 CA B:ILE110 4.3 38.6 1.0 N B:MET109 4.3 38.3 1.0 C B:ASP103 4.3 35.8 1.0 CB B:ASP103 4.4 35.5 1.0 OD2 B:ASP103 4.4 33.4 1.0 N B:ILE110 4.4 38.8 1.0 CA B:SER107 4.4 37.9 1.0 N B:ASP111 4.5 39.7 1.0 N B:ASP105 4.5 37.8 1.0 CA B:MET109 4.6 39.3 1.0 N B:ARG104 4.6 36.9 1.0 N B:ASN106 4.6 37.5 1.0 N B:GLY108 4.7 37.8 1.0 O B:ASP103 4.8 35.5 1.0 CB B:ASP105 4.8 38.5 1.0 C B:ILE110 4.8 39.3 1.0 C B:SER107 4.8 37.8 1.0 OD2 B:ASP111 4.9 41.1 1.0 C B:ASP105 4.9 38.2 1.0 CA B:ASP105 5.0 38.5 1.0 CG1 B:ILE110 5.0 37.0 1.0 CG B:ASP111 5.0 40.0 1.0 OE1 B:GLN145 5.0 54.6 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of CA2+-Bound Form of DES3-20ALG-2


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 CA2+-Bound Form of DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:56.9 occ:1.00 OD1 B:ASP173 2.2 53.6 1.0 OD1 B:ASP169 2.4 49.8 1.0 O B:HOH914 2.4 41.4 1.0 O B:TRP175 2.6 56.9 1.0 OD1 B:ASP171 2.6 54.3 1.0 O B:HOH925 2.8 56.7 1.0 CG B:ASP173 3.4 54.7 1.0 CG B:ASP171 3.5 55.6 1.0 CG B:ASP169 3.6 52.5 1.0 C B:TRP175 3.8 56.7 1.0 OD2 B:ASP171 4.0 57.8 1.0 OD2 B:ASP173 4.1 53.7 1.0 CA B:ASP169 4.3 54.6 1.0 N B:ASP171 4.3 55.8 1.0 OD2 B:ASP169 4.3 50.5 1.0 N B:ASP173 4.4 54.6 1.0 CB B:ASP173 4.4 54.4 1.0 CG2 B:ILE176 4.5 55.2 1.0 CB B:ASP169 4.5 53.6 1.0 C B:ASP169 4.6 55.2 1.0 N B:THR170 4.6 55.5 1.0 N B:TRP175 4.6 57.0 1.0 CA B:ILE176 4.7 55.6 1.0 CA B:TRP175 4.7 56.9 1.0 N B:ILE176 4.7 56.3 1.0 CB B:ASP171 4.7 55.5 1.0 N B:GLN172 4.8 54.6 1.0 CA B:ASP171 4.8 55.5 1.0 CA B:ASP173 4.9 54.6 1.0 C B:ASP171 4.9 55.1 1.0 CB B:TRP175 4.9 57.5 1.0

H.Suzuki, M.Kawasaki, T.Inuzuka, M.Okumura, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki. Structural Basis For Ca(2+)-Dependent Formation of Alg-2/Alix Peptide Complex: Ca(2+)/EF3-Driven Arginine Switch Mechanism Structure V. 16 1562 2008.
ISSN: ISSN 0969-2126
PubMed: 18940611
DOI: 10.1016/J.STR.2008.07.012