Calcium in PDB 3alu: Crystal Structure of Cel-IV Complexed with Raffinose

The structure of Crystal Structure of Cel-IV Complexed with Raffinose, PDB code: 3alu 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)	40.16 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.808, 78.159, 102.883, 90.00, 96.82, 90.00
R / Rfree (%)	16.5 / 20.3

The binding sites of Calcium atom in the Crystal Structure of Cel-IV Complexed with Raffinose (pdb code 3alu). 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 Complexed with Raffinose, PDB code: 3alu:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 Complexed with Raffinose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:16.1 occ:1.00 OD1 A:ASN116 2.3 16.7 1.0 OD1 A:ASN115 2.3 17.1 1.0 OE2 A:GLU113 2.3 17.3 1.0 OD1 A:ASP136 2.4 15.3 1.0 O A:ASP136 2.4 14.9 1.0 O4X A:RAF158 2.5 19.0 1.0 O3X A:RAF158 2.6 18.2 1.0 CD A:GLU113 3.3 19.1 1.0 CG A:ASN116 3.4 16.2 1.0 C4X A:RAF158 3.4 21.2 1.0 C A:ASP136 3.5 14.1 1.0 CG A:ASN115 3.5 19.6 1.0 C3X A:RAF158 3.5 22.3 1.0 CG A:ASP136 3.5 14.3 1.0 OE1 A:GLU113 3.6 18.3 1.0 N A:ASP136 3.6 13.7 1.0 CA A:ASP136 3.9 13.9 1.0 ND2 A:ASN115 4.1 25.3 1.0 CB A:ASN116 4.1 17.4 1.0 C2X A:RAF158 4.1 25.7 1.0 N A:ASN115 4.3 15.8 1.0 OD2 A:ASP136 4.3 14.4 1.0 CB A:ASP136 4.3 13.6 1.0 N A:ASN116 4.3 16.7 1.0 C2 A:EDO159 4.4 32.5 1.0 ND2 A:ASN116 4.4 19.0 1.0 N A:VAL137 4.6 13.8 1.0 C A:ALA135 4.7 14.8 1.0 CB A:ASN115 4.7 16.3 1.0 CG A:GLU113 4.7 16.6 1.0 C A:ASN115 4.7 17.7 1.0 CA A:ASN115 4.8 17.4 1.0 C5X A:RAF158 4.8 23.4 1.0 CB A:ALA135 4.9 17.0 1.0 O2X A:RAF158 4.9 25.4 1.0 CA A:ASN116 4.9 17.1 1.0 C1 A:EDO159 4.9 29.8 1.0 CA A:ALA135 5.0 14.9 1.0

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


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 Complexed with Raffinose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:13.6 occ:1.00 OD1 B:ASN116 2.2 14.5 1.0 OD1 B:ASN115 2.3 14.6 1.0 OD1 B:ASP136 2.3 13.4 1.0 OE2 B:GLU113 2.4 15.1 1.0 O4X B:RAF158 2.4 12.9 1.0 O B:ASP136 2.4 11.9 1.0 O3X B:RAF158 2.5 12.3 1.0 CG B:ASN116 3.3 14.1 1.0 CD B:GLU113 3.4 15.9 1.0 C4X B:RAF158 3.4 12.9 1.0 CG B:ASN115 3.4 17.0 1.0 CG B:ASP136 3.4 13.7 1.0 C3X B:RAF158 3.4 12.2 1.0 C B:ASP136 3.4 11.5 1.0 N B:ASP136 3.7 10.7 1.0 OE1 B:GLU113 3.7 15.1 1.0 CA B:ASP136 3.9 11.6 1.0 ND2 B:ASN115 4.0 18.0 1.0 C2X B:RAF158 4.1 15.2 1.0 CB B:ASN116 4.1 12.9 1.0 ND2 B:ASN116 4.2 13.2 1.0 OD2 B:ASP136 4.2 14.8 1.0 CB B:ASP136 4.3 12.2 1.0 N B:ASN115 4.3 14.8 1.0 N B:ASN116 4.3 13.7 1.0 N B:VAL137 4.6 12.2 1.0 CB B:ASN115 4.6 15.3 1.0 C B:ALA135 4.7 12.1 1.0 CG B:GLU113 4.7 14.7 1.0 C B:ASN115 4.7 14.6 1.0 C5X B:RAF158 4.8 13.9 1.0 CA B:ASN115 4.8 14.3 1.0 O6X B:RAF158 4.8 13.1 1.0 CB B:ALA135 4.9 12.4 1.0 O2X B:RAF158 4.9 13.6 1.0 CA B:ASN116 4.9 13.2 1.0 CA B:ALA135 4.9 11.8 1.0

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


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 Complexed with Raffinose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:12.6 occ:1.00 OD1 C:ASN116 2.3 14.9 1.0 OD1 C:ASN115 2.3 13.3 1.0 OD1 C:ASP136 2.3 12.3 1.0 OE2 C:GLU113 2.4 11.9 1.0 O C:ASP136 2.4 12.2 1.0 O3X C:RAF158 2.5 12.1 1.0 O4X C:RAF158 2.5 13.3 1.0 CD C:GLU113 3.4 14.2 1.0 C4X C:RAF158 3.4 12.6 1.0 C3X C:RAF158 3.4 14.5 1.0 C C:ASP136 3.4 12.3 1.0 CG C:ASP136 3.4 12.3 1.0 CG C:ASN116 3.4 13.1 1.0 CG C:ASN115 3.5 15.6 1.0 N C:ASP136 3.6 11.3 1.0 OE1 C:GLU113 3.6 14.4 1.0 CA C:ASP136 3.9 11.4 1.0 ND2 C:ASN115 4.0 14.9 1.0 C2X C:RAF158 4.0 13.9 1.0 CB C:ASN116 4.1 11.9 1.0 CB C:ASP136 4.3 11.5 1.0 N C:ASN115 4.3 14.4 1.0 OD2 C:ASP136 4.3 13.0 1.0 N C:ASN116 4.4 13.0 1.0 ND2 C:ASN116 4.5 11.6 1.0 C C:ALA135 4.6 12.2 1.0 N C:VAL137 4.6 12.2 1.0 CB C:ASN115 4.7 13.3 1.0 CG C:GLU113 4.7 13.1 1.0 C C:ASN115 4.7 13.0 1.0 O2X C:RAF158 4.8 15.5 1.0 CA C:ASN115 4.8 14.0 1.0 CB C:ALA135 4.8 13.2 1.0 C5X C:RAF158 4.8 14.8 1.0 CA C:ALA135 4.9 12.6 1.0 CA C:ASN116 4.9 12.7 1.0 O6X C:RAF158 4.9 14.4 1.0

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


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 Complexed with Raffinose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:15.8 occ:1.00 OD1 D:ASN116 2.3 16.8 1.0 O4X D:RAF158 2.4 16.9 1.0 OD1 D:ASN115 2.4 18.0 1.0 OD1 D:ASP136 2.4 15.7 1.0 OE2 D:GLU113 2.4 15.9 1.0 O3X D:RAF158 2.4 15.8 1.0 O D:ASP136 2.5 15.8 1.0 C4X D:RAF158 3.3 16.8 1.0 CD D:GLU113 3.4 17.2 1.0 C3X D:RAF158 3.4 17.3 1.0 CG D:ASN116 3.4 17.3 1.0 CG D:ASP136 3.4 14.9 1.0 C D:ASP136 3.5 14.5 1.0 CG D:ASN115 3.5 20.0 1.0 OE1 D:GLU113 3.6 18.5 1.0 N D:ASP136 3.6 13.8 1.0 CA D:ASP136 3.9 13.8 1.0 C2X D:RAF158 3.9 19.7 1.0 CB D:ASN116 4.1 16.1 1.0 ND2 D:ASN115 4.2 25.1 1.0 N D:ASN115 4.3 17.1 1.0 CB D:ASP136 4.3 13.8 1.0 OD2 D:ASP136 4.3 14.2 1.0 C1 D:EDO159 4.3 27.4 1.0 N D:ASN116 4.3 16.5 1.0 ND2 D:ASN116 4.5 19.7 1.0 C D:ALA135 4.7 14.9 1.0 C D:ASN115 4.7 17.4 1.0 N D:VAL137 4.7 14.6 1.0 C5X D:RAF158 4.7 18.4 1.0 CB D:ASN115 4.7 18.1 1.0 CG D:GLU113 4.7 17.9 1.0 O2X D:RAF158 4.8 21.6 1.0 CA D:ASN115 4.8 17.2 1.0 CA D:ASN116 4.9 15.8 1.0 O6X D:RAF158 4.9 16.3 1.0 CB D:ALA135 4.9 15.9 1.0 CA D:ALA135 4.9 15.2 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