Magnesium in PDB 2z49: Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside

The structure of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside, PDB code: 2z49 was solved by T.Hatakeyama, H.Unno, S.Eto, H.Hidemura, T.Uchida, Y.Kouzuma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.12 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.287, 65.451, 126.993, 90.00, 97.07, 90.00
R / Rfree (%)	19.1 / 23.9

The structure of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside (pdb code 2z49). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside, PDB code: 2z49:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:28.3 occ:1.00 OD1 A:ASN32 2.3 31.2 1.0 OD1 A:ASN72 2.4 29.1 1.0 O A:ILE131 2.4 23.7 1.0 O A:VAL73 2.4 24.8 1.0 O A:ILE33 2.5 21.9 1.0 O A:HOH2007 2.5 29.6 1.0 CG A:ASN32 3.2 28.7 1.0 CG A:ASN72 3.2 29.5 1.0 C A:ILE131 3.5 23.7 1.0 ND2 A:ASN32 3.5 30.3 1.0 C A:ILE33 3.5 22.7 1.0 C A:VAL73 3.5 25.8 1.0 N A:ILE33 3.5 24.2 1.0 ND2 A:ASN72 3.6 29.6 1.0 N A:VAL73 3.6 26.9 1.0 N A:ILE131 3.7 23.1 1.0 CA A:ILE33 4.0 22.6 1.0 CA A:ILE131 4.0 23.3 1.0 CA A:VAL73 4.1 25.5 1.0 O A:HOH2293 4.3 26.9 1.0 CB A:ILE33 4.4 22.7 1.0 CB A:ILE131 4.4 22.8 1.0 CB A:ASN32 4.5 26.3 1.0 C A:ASN32 4.5 24.7 1.0 CB A:ASN72 4.5 28.7 1.0 C A:ASN72 4.6 28.4 1.0 N A:GLY132 4.6 25.2 1.0 CA A:ASN32 4.6 25.4 1.0 N A:MET74 4.7 25.8 1.0 N A:ALA34 4.7 21.8 1.0 CB A:VAL73 4.7 25.1 1.0 CA A:ASN72 4.7 28.9 1.0 C A:ASP130 4.7 24.2 1.0 CG A:MET74 4.8 31.4 1.0 CA A:ASP130 5.0 25.6 1.0 CB A:ASP130 5.0 26.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:23.6 occ:1.00 OD1 A:ASN177 2.3 23.2 1.0 O A:VAL178 2.3 23.2 1.0 OD1 A:ASN218 2.3 27.0 1.0 O A:VAL266 2.4 21.1 1.0 O A:VAL219 2.4 16.5 1.0 OD1 A:ASP265 2.6 26.4 1.0 CG A:ASN177 3.2 25.2 1.0 CG A:ASN218 3.3 27.4 1.0 C A:VAL178 3.4 23.9 1.0 C A:VAL266 3.4 20.8 1.0 ND2 A:ASN177 3.5 26.2 1.0 C A:VAL219 3.5 19.1 1.0 N A:VAL266 3.6 22.8 1.0 N A:VAL219 3.6 21.3 1.0 N A:VAL178 3.7 24.4 1.0 ND2 A:ASN218 3.7 32.9 1.0 CG A:ASP265 3.7 27.5 1.0 CA A:VAL266 3.9 21.5 1.0 CA A:VAL178 4.0 23.7 1.0 CA A:VAL219 4.0 19.5 1.0 O A:HOH2084 4.2 25.8 1.0 CB A:VAL266 4.3 20.8 1.0 OD2 A:ASP265 4.3 28.5 1.0 CB A:VAL178 4.4 23.8 1.0 O A:HOH2220 4.4 34.1 1.0 C A:ASN218 4.5 22.7 1.0 CB A:ASN177 4.5 25.0 1.0 CB A:VAL219 4.5 19.0 1.0 CB A:ASN218 4.5 24.1 1.0 N A:LEU179 4.6 24.7 1.0 C A:ASN177 4.6 24.6 1.0 N A:GLY267 4.6 20.7 1.0 C A:ASP265 4.6 24.5 1.0 N A:GLY220 4.7 19.5 1.0 CA A:ASN218 4.7 23.4 1.0 CA A:ASN177 4.7 25.8 1.0 CB A:ASP265 4.8 25.3 1.0 CA A:ASP265 4.9 25.0 1.0 CA A:LEU179 5.0 25.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:52.9 occ:1.00 O B:ILE131 2.3 42.0 1.0 O B:HOH2026 2.3 31.4 1.0 O B:ILE33 2.3 39.5 1.0 OD1 B:ASN72 2.4 49.3 1.0 O B:VAL73 2.6 45.7 1.0 OD1 B:ASN32 2.8 42.0 1.0 CG B:ASN72 3.3 48.3 1.0 C B:ILE131 3.3 42.2 1.0 C B:ILE33 3.4 39.8 1.0 N B:ILE131 3.6 42.2 1.0 CG B:ASN32 3.6 41.5 1.0 N B:VAL73 3.6 47.2 1.0 ND2 B:ASN72 3.6 49.5 1.0 C B:VAL73 3.7 46.3 1.0 N B:ILE33 3.7 40.1 1.0 ND2 B:ASN32 3.8 41.5 1.0 CA B:ILE131 3.9 41.7 1.0 CA B:ILE33 4.0 39.8 1.0 CA B:VAL73 4.1 46.4 1.0 CB B:ILE131 4.3 41.1 1.0 CB B:ILE33 4.4 40.1 1.0 N B:GLY132 4.5 42.5 1.0 C B:ASN72 4.5 48.0 1.0 CB B:ASN72 4.5 48.3 1.0 N B:ALA34 4.6 39.5 1.0 C B:ASP130 4.6 42.4 1.0 CA B:ASN72 4.6 48.5 1.0 CB B:VAL73 4.7 46.4 1.0 C B:ASN32 4.7 40.3 1.0 CB B:ASP130 4.8 43.6 1.0 CG2 B:ILE131 4.8 40.7 1.0 N B:MET74 4.8 46.1 1.0 CB B:ASN32 4.8 40.9 1.0 CA B:GLY132 4.9 43.9 1.0 CA B:ASP130 4.9 42.9 1.0 CA B:ALA34 5.0 39.7 1.0 CA B:ASN32 5.0 40.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Hemolytic Lectin Cel-III Complexed with Methyl- Alpha-D-Galactopylanoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:38.5 occ:1.00 O B:VAL178 2.2 29.4 1.0 OD1 B:ASN218 2.3 32.4 1.0 O B:VAL266 2.4 33.5 1.0 OD1 B:ASP265 2.5 32.2 1.0 O B:VAL219 2.6 30.2 1.0 OD1 B:ASN177 2.6 34.2 1.0 CG B:ASN218 3.2 32.9 1.0 CG B:ASN177 3.2 31.2 1.0 ND2 B:ASN177 3.3 31.3 1.0 C B:VAL178 3.4 29.9 1.0 C B:VAL266 3.4 34.0 1.0 N B:VAL266 3.5 34.9 1.0 ND2 B:ASN218 3.6 37.1 1.0 CG B:ASP265 3.6 36.2 1.0 C B:VAL219 3.6 30.7 1.0 N B:VAL178 3.7 29.7 1.0 N B:VAL219 3.7 31.7 1.0 CA B:VAL266 3.9 33.8 1.0 CA B:VAL178 4.0 29.4 1.0 CA B:VAL219 4.1 30.9 1.0 OD2 B:ASP265 4.1 37.8 1.0 CB B:VAL266 4.3 33.6 1.0 O B:HOH2035 4.3 30.5 1.0 CB B:VAL178 4.4 29.0 1.0 N B:LEU179 4.5 30.8 1.0 CB B:ASN218 4.5 32.9 1.0 C B:ASP265 4.5 35.9 1.0 CB B:ASN177 4.6 31.3 1.0 C B:ASN218 4.6 32.3 1.0 CB B:VAL219 4.6 31.1 1.0 N B:GLY267 4.6 33.4 1.0 C B:ASN177 4.6 30.4 1.0 CB B:ASP265 4.7 36.3 1.0 CA B:ASN218 4.8 33.2 1.0 N B:GLY220 4.8 30.4 1.0 CA B:ASN177 4.8 30.9 1.0 CA B:LEU179 4.9 31.7 1.0 CA B:ASP265 4.9 36.1 1.0

T.Hatakeyama, H.Unno, Y.Kouzuma, T.Uchida, S.Eto, H.Hidemura, N.Kato, M.Yonekura, M.Kusunoki. C-Type Lectin-Like Carbohydrate-Recognition of the Hemolytic Lectin Cel-III Containing Ricin-Type Beta-Trefoil Folds J.Biol.Chem. V. 282 37826 2007.
ISSN: ISSN 0021-9258
PubMed: 17977832
DOI: 10.1074/JBC.M705604200