Calcium in PDB 3alt: Crystal Structure of Cel-IV Complexed with Melibiose

The structure of Crystal Structure of Cel-IV Complexed with Melibiose, PDB code: 3alt 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)	38.06 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.988, 78.504, 102.898, 90.00, 98.41, 90.00
R / Rfree (%)	22.9 / 27.9

The binding sites of Calcium atom in the Crystal Structure of Cel-IV Complexed with Melibiose (pdb code 3alt). 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 Melibiose, PDB code: 3alt:
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 Melibiose


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 Melibiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:26.7 occ:1.00 OD1 A:ASP136 2.3 26.7 1.0 OD1 A:ASN116 2.3 32.3 1.0 O4 A:MLB301 2.3 32.3 1.0 OE2 A:GLU113 2.3 41.7 1.0 O3 A:MLB301 2.4 33.5 1.0 OD1 A:ASN115 2.5 35.4 1.0 O A:ASP136 2.6 27.6 1.0 C4 A:MLB301 3.2 33.8 1.0 C3 A:MLB301 3.3 34.7 1.0 CD A:GLU113 3.3 41.0 1.0 CG A:ASN116 3.4 33.2 1.0 CG A:ASP136 3.4 29.2 1.0 C A:ASP136 3.5 28.4 1.0 CG A:ASN115 3.6 35.3 1.0 N A:ASP136 3.6 28.8 1.0 OE1 A:GLU113 3.6 41.6 1.0 C2 A:MLB301 3.8 36.1 1.0 CA A:ASP136 3.9 28.7 1.0 ND2 A:ASN115 4.1 36.1 1.0 CB A:ASN116 4.1 32.8 1.0 CB A:ASP136 4.2 28.8 1.0 OD2 A:ASP136 4.3 28.3 1.0 ND2 A:ASN116 4.4 31.1 1.0 N A:ASN115 4.4 35.7 1.0 N A:ASN116 4.5 34.5 1.0 C5 A:MLB301 4.6 33.2 1.0 N A:VAL137 4.6 29.5 1.0 C A:ALA135 4.7 29.0 1.0 CG A:GLU113 4.7 39.2 1.0 O5 A:MLB301 4.8 34.9 1.0 CB A:ALA135 4.8 28.4 1.0 CB A:ASN115 4.8 35.0 1.0 O2 A:MLB301 4.8 36.2 1.0 C A:ASN115 4.8 35.0 1.0 O6 A:MLB301 4.9 32.4 1.0 C1 A:MLB301 4.9 36.8 1.0 CA A:ALA135 4.9 28.8 1.0 CA A:ASN115 4.9 35.4 1.0 CA A:ASN116 5.0 33.5 1.0

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


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 Melibiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:25.8 occ:1.00 OD1 B:ASN116 2.2 32.7 1.0 OD1 B:ASP136 2.3 27.3 1.0 OD1 B:ASN115 2.3 36.0 1.0 OE2 B:GLU113 2.4 42.3 1.0 O4 B:MLB301 2.5 32.0 1.0 O3 B:MLB301 2.6 33.2 1.0 O B:ASP136 2.6 27.6 1.0 CG B:ASN116 3.3 33.3 1.0 CG B:ASN115 3.4 35.4 1.0 CD B:GLU113 3.4 41.1 1.0 CG B:ASP136 3.5 29.3 1.0 C4 B:MLB301 3.5 33.8 1.0 C3 B:MLB301 3.5 34.8 1.0 OE1 B:GLU113 3.6 41.6 1.0 C B:ASP136 3.6 28.9 1.0 N B:ASP136 3.8 28.6 1.0 ND2 B:ASN115 3.9 36.1 1.0 CA B:ASP136 4.1 28.5 1.0 CB B:ASN116 4.1 33.1 1.0 C2 B:MLB301 4.1 36.2 1.0 ND2 B:ASN116 4.2 31.1 1.0 OD2 B:ASP136 4.3 28.4 1.0 N B:ASN115 4.4 35.5 1.0 N B:ASN116 4.4 34.5 1.0 CB B:ASP136 4.4 28.9 1.0 CB B:ASN115 4.7 35.1 1.0 C B:ASN115 4.7 35.0 1.0 CG B:GLU113 4.8 39.2 1.0 C5 B:MLB301 4.8 33.2 1.0 N B:VAL137 4.8 29.7 1.0 CA B:ASN115 4.8 35.4 1.0 CA B:ASN116 4.9 33.5 1.0 C B:ALA135 4.9 29.0 1.0 O2 B:MLB301 4.9 36.0 1.0

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


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 Melibiose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:44.1 occ:1.00 OD1 C:ASP136 2.1 27.0 1.0 OD1 C:ASN115 2.2 35.8 1.0 OD1 C:ASN116 2.3 33.2 1.0 OE2 C:GLU113 2.4 42.3 1.0 O3 C:MLB301 2.4 33.3 1.0 O4 C:MLB301 2.6 32.3 1.0 O C:ASP136 2.7 27.7 1.0 CD C:GLU113 3.3 41.3 1.0 CG C:ASN115 3.3 35.4 1.0 CG C:ASN116 3.3 33.5 1.0 CG C:ASP136 3.3 29.5 1.0 C4 C:MLB301 3.4 34.1 1.0 C3 C:MLB301 3.4 35.0 1.0 OE1 C:GLU113 3.5 42.0 1.0 C C:ASP136 3.7 28.8 1.0 N C:ASP136 3.7 29.2 1.0 ND2 C:ASN115 3.8 36.3 1.0 C2 C:MLB301 4.0 36.4 1.0 CA C:ASP136 4.0 28.8 1.0 CB C:ASN116 4.2 33.1 1.0 OD2 C:ASP136 4.2 28.5 1.0 N C:ASN115 4.2 35.8 1.0 ND2 C:ASN116 4.2 31.3 1.0 CB C:ASP136 4.3 28.7 1.0 N C:ASN116 4.4 34.5 1.0 O C:HOH175 4.5 42.9 1.0 CB C:ASN115 4.6 35.1 1.0 CG C:GLU113 4.7 39.4 1.0 C C:ASN115 4.7 35.1 1.0 CA C:ASN115 4.7 35.5 1.0 C5 C:MLB301 4.7 33.3 1.0 O2 C:MLB301 4.8 36.4 1.0 C C:ALA135 4.8 29.3 1.0 N C:VAL137 4.9 29.5 1.0 CA C:ASN116 4.9 33.7 1.0 O5 C:MLB301 5.0 35.4 1.0

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


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 Melibiose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:35.6 occ:1.00 O4 D:MLB301 2.2 31.9 1.0 OD1 D:ASN116 2.3 32.6 1.0 OD1 D:ASP136 2.3 26.9 1.0 OE2 D:GLU113 2.4 42.2 1.0 OD1 D:ASN115 2.5 35.7 1.0 O D:ASP136 2.6 28.1 1.0 O3 D:MLB301 2.7 32.8 1.0 C4 D:MLB301 3.2 34.0 1.0 CD D:GLU113 3.3 41.0 1.0 CG D:ASP136 3.4 29.2 1.0 CG D:ASN116 3.4 33.4 1.0 C3 D:MLB301 3.5 35.0 1.0 N D:ASP136 3.5 28.8 1.0 C D:ASP136 3.5 28.8 1.0 OE1 D:GLU113 3.5 41.7 1.0 CG D:ASN115 3.7 35.6 1.0 CA D:ASP136 3.9 28.7 1.0 C2 D:MLB301 4.2 36.1 1.0 ND2 D:ASN115 4.2 36.2 1.0 CB D:ASP136 4.3 28.8 1.0 CB D:ASN116 4.3 33.3 1.0 OD2 D:ASP136 4.3 28.1 1.0 ND2 D:ASN116 4.4 31.1 1.0 N D:ASN115 4.5 35.5 1.0 C5 D:MLB301 4.5 33.3 1.0 C D:ALA135 4.6 29.1 1.0 N D:ASN116 4.7 34.4 1.0 CG D:GLU113 4.7 39.2 1.0 N D:VAL137 4.7 29.5 1.0 O6 D:MLB301 4.7 32.9 1.0 CB D:ALA135 4.8 28.5 1.0 O5 D:MLB301 4.8 35.5 1.0 CA D:ALA135 4.8 28.9 1.0 CB D:ASN115 4.9 34.9 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