Calcium in PDB 3als: Crystal Structure of Cel-IV

The structure of Crystal Structure of Cel-IV, PDB code: 3als was solved by T.Hatakeyama, T.Hozawa, K.Ishii, T.Kamiya, S.Goda, M.Kusunoki, H.Unno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.03 / 3.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	86.065, 86.065, 375.321, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 21.5

The binding sites of Calcium atom in the Crystal Structure of Cel-IV (pdb code 3als). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Cel-IV, PDB code: 3als:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Cel-IV


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 Cel-IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca158 b:33.3 occ:1.00 OD1 A:ASN116 2.2 40.7 1.0 OE2 A:GLU113 2.3 33.6 1.0 O A:ASP136 2.5 34.5 1.0 OD1 A:ASP136 2.5 30.2 1.0 O A:HOH162 2.6 9.4 1.0 OD1 A:ASN115 2.9 48.2 1.0 CD A:GLU113 3.1 34.7 1.0 OE1 A:GLU113 3.3 33.6 1.0 CG A:ASN116 3.4 42.7 1.0 C A:ASP136 3.6 34.1 1.0 CG A:ASP136 3.7 34.6 1.0 CG A:ASN115 3.7 44.0 1.0 N A:ASP136 3.8 32.6 1.0 ND2 A:ASN115 4.0 43.1 1.0 CA A:ASP136 4.1 33.8 1.0 ND2 A:ASN116 4.3 40.6 1.0 CB A:ASN116 4.5 43.7 1.0 CB A:ASP136 4.5 33.9 1.0 CG A:GLU113 4.6 34.8 1.0 OD2 A:ASP136 4.6 33.5 1.0 N A:ASN116 4.6 43.8 1.0 C A:ALA135 4.7 32.2 1.0 CB A:ALA135 4.8 31.7 1.0 N A:VAL137 4.8 34.4 1.0 N A:ASN115 4.8 41.8 1.0 C A:ASN115 4.9 43.1 1.0 CB A:ASN115 4.9 42.2 1.0 CA A:ALA135 5.0 31.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Cel-IV


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 Cel-IV within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca158 b:35.2 occ:1.00 OD1 B:ASN116 2.0 40.3 1.0 OE2 B:GLU113 2.4 33.2 1.0 OD1 B:ASP136 2.4 30.8 1.0 O B:ASP136 2.5 34.4 1.0 O B:HOH160 2.5 11.8 1.0 OD1 B:ASN115 2.5 48.4 1.0 CG B:ASN116 3.2 42.7 1.0 CD B:GLU113 3.2 34.5 1.0 OE1 B:GLU113 3.3 34.3 1.0 CG B:ASN115 3.5 44.1 1.0 CG B:ASP136 3.6 34.6 1.0 C B:ASP136 3.6 33.8 1.0 N B:ASP136 3.8 32.3 1.0 ND2 B:ASN115 3.9 42.9 1.0 ND2 B:ASN116 4.1 40.8 1.0 CA B:ASP136 4.1 33.4 1.0 CB B:ASN116 4.2 43.8 1.0 OD2 B:ASP136 4.4 33.5 1.0 CB B:ASP136 4.5 33.6 1.0 N B:ASN116 4.5 43.7 1.0 N B:ASN115 4.6 41.6 1.0 CG B:GLU113 4.7 34.7 1.0 N B:VAL137 4.7 34.3 1.0 CB B:ASN115 4.8 42.5 1.0 C B:ALA135 4.8 31.8 1.0 C B:ASN115 4.8 43.1 1.0 CA B:ASN115 5.0 42.7 1.0 CA B:ASN116 5.0 44.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Cel-IV


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 Cel-IV within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca158 b:33.4 occ:1.00 OD1 C:ASN116 2.1 40.3 1.0 OE2 C:GLU113 2.4 33.5 1.0 O C:HOH163 2.4 11.4 1.0 OD1 C:ASP136 2.4 30.8 1.0 O C:ASP136 2.5 34.2 1.0 OD1 C:ASN115 2.6 48.3 1.0 CG C:ASN116 3.2 42.6 1.0 CD C:GLU113 3.3 34.8 1.0 OE1 C:GLU113 3.4 34.6 1.0 CG C:ASN115 3.5 44.1 1.0 CG C:ASP136 3.6 34.7 1.0 C C:ASP136 3.6 33.8 1.0 N C:ASP136 3.8 32.4 1.0 ND2 C:ASN115 3.9 42.8 1.0 ND2 C:ASN116 4.1 40.8 1.0 CA C:ASP136 4.2 33.4 1.0 CB C:ASN116 4.2 43.6 1.0 OD2 C:ASP136 4.5 33.6 1.0 CB C:ASP136 4.5 33.7 1.0 N C:ASN116 4.5 43.6 1.0 N C:ASN115 4.7 41.5 1.0 N C:VAL137 4.7 34.3 1.0 CG C:GLU113 4.7 34.5 1.0 C C:ALA135 4.8 31.9 1.0 CB C:ASN115 4.8 42.5 1.0 C C:ASN115 4.9 43.1 1.0 CA C:ASN115 5.0 42.7 1.0 CA C:ASN116 5.0 44.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Cel-IV


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 Cel-IV within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca158 b:33.0 occ:1.00 OE2 D:GLU113 2.2 33.7 1.0 OD1 D:ASN116 2.3 40.6 1.0 O D:ASP136 2.5 34.5 1.0 OD1 D:ASP136 2.5 30.2 1.0 O D:HOH159 2.7 6.8 1.0 OD1 D:ASN115 2.9 48.3 1.0 CD D:GLU113 3.1 34.6 1.0 OE1 D:GLU113 3.3 33.6 1.0 CG D:ASN116 3.5 42.7 1.0 C D:ASP136 3.6 34.1 1.0 CG D:ASP136 3.7 34.7 1.0 CG D:ASN115 3.7 44.1 1.0 N D:ASP136 3.7 32.7 1.0 ND2 D:ASN115 4.0 43.1 1.0 CA D:ASP136 4.1 33.8 1.0 ND2 D:ASN116 4.3 40.6 1.0 CB D:ASP136 4.5 33.8 1.0 CB D:ASN116 4.5 43.7 1.0 OD2 D:ASP136 4.6 33.6 1.0 CG D:GLU113 4.6 34.8 1.0 CB D:ALA135 4.7 31.6 1.0 C D:ALA135 4.7 32.2 1.0 N D:ASN116 4.7 43.8 1.0 N D:VAL137 4.7 34.4 1.0 N D:ASN115 4.9 41.7 1.0 CA D:ALA135 4.9 31.9 1.0 C D:ASN115 4.9 43.0 1.0 CB D:ASN115 5.0 42.2 1.0

T.Hatakeyama, T.Kamiya, M.Kusunoki, S.Nakamura-Tsuruta, J.Hirabayashi, S.Goda, H.Unno. Galactose Recognition By A Tetrameric C-Type Lectin, Cel-IV, Containing the Epn Carbohydrate Recognition Motif J.Biol.Chem. V. 286 10305 2011.
ISSN: ISSN 0021-9258
PubMed: 21247895
DOI: 10.1074/JBC.M110.200576