Magnesium in PDB 1vcl: Crystal Structure of Hemolytic Lectin Cel-III

The structure of Crystal Structure of Hemolytic Lectin Cel-III, PDB code: 1vcl was solved by T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, T.Hatakeyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.17 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.420, 65.370, 126.020, 90.00, 98.18, 90.00
R / Rfree (%)	16.5 / 20.1

The structure of Crystal Structure of Hemolytic Lectin Cel-III also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	10 atoms

The binding sites of Magnesium atom in the Crystal Structure of Hemolytic Lectin Cel-III (pdb code 1vcl). 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, PDB code: 1vcl:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:38.3 occ:1.00 O A:HOH1390 2.3 37.1 1.0 OD1 A:ASN72 2.3 40.6 1.0 O A:ILE33 2.4 31.9 1.0 OD1 A:ASN32 2.4 36.0 1.0 O A:ILE131 2.5 34.3 1.0 O A:VAL73 2.7 32.5 1.0 CG A:ASN72 3.3 42.1 1.0 C A:ILE33 3.4 31.1 1.0 CG A:ASN32 3.5 37.6 1.0 C A:ILE131 3.5 33.8 1.0 N A:ILE33 3.6 31.3 1.0 N A:ILE131 3.6 33.9 1.0 ND2 A:ASN72 3.7 41.2 1.0 N A:VAL73 3.8 35.9 1.0 C A:VAL73 3.8 33.5 1.0 CA A:ILE33 4.0 30.3 1.0 CA A:ILE131 4.0 33.1 1.0 ND2 A:ASN32 4.1 42.3 1.0 O A:HOH1581 4.1 43.2 1.0 CA A:VAL73 4.3 33.9 1.0 CB A:ILE33 4.4 29.5 1.0 CB A:ILE131 4.5 31.6 1.0 CB A:ASN72 4.6 42.9 1.0 N A:ALA34 4.6 30.3 1.0 C A:ASN32 4.6 31.9 1.0 C A:ASP130 4.6 35.6 1.0 CB A:ASN32 4.7 34.7 1.0 C A:ASN72 4.7 38.1 1.0 N A:GLY132 4.7 33.8 1.0 CB A:ASP130 4.8 39.0 1.0 CA A:ASN72 4.8 41.3 1.0 CA A:ASP130 4.8 36.4 1.0 CA A:ASN32 4.8 33.3 1.0 CB A:VAL73 4.8 32.7 1.0 N A:MET74 4.9 33.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:25.4 occ:1.00 OD1 A:ASN177 2.3 23.9 1.0 O A:VAL178 2.3 21.6 1.0 O A:VAL266 2.4 22.5 1.0 OD1 A:ASP265 2.5 24.5 1.0 OD1 A:ASN218 2.5 23.3 1.0 O A:VAL219 2.6 21.1 1.0 CG A:ASN177 3.2 26.4 1.0 CG A:ASN218 3.4 24.6 1.0 C A:VAL178 3.4 23.6 1.0 C A:VAL266 3.5 22.4 1.0 N A:VAL266 3.5 24.6 1.0 N A:VAL178 3.5 24.6 1.0 ND2 A:ASN177 3.5 28.1 1.0 CG A:ASP265 3.6 29.3 1.0 ND2 A:ASN218 3.6 27.4 1.0 C A:VAL219 3.7 21.6 1.0 N A:VAL219 3.8 21.2 1.0 CA A:VAL266 3.9 23.1 1.0 CA A:VAL178 4.0 23.8 1.0 O A:HOH1424 4.0 32.0 1.0 OD2 A:ASP265 4.1 32.1 1.0 CA A:VAL219 4.2 20.9 1.0 O A:HOH1380 4.2 28.2 1.0 CB A:VAL266 4.3 22.6 1.0 CB A:ASN177 4.5 27.6 1.0 C A:ASN177 4.5 26.2 1.0 CB A:VAL178 4.5 22.5 1.0 C A:ASP265 4.5 25.4 1.0 N A:LEU179 4.6 24.2 1.0 CA A:ASN177 4.6 26.7 1.0 CB A:VAL219 4.6 20.1 1.0 N A:GLY267 4.7 21.6 1.0 CB A:ASP265 4.7 27.7 1.0 CB A:ASN218 4.7 23.8 1.0 C A:ASN218 4.7 22.1 1.0 CA A:ASP265 4.8 27.3 1.0 N A:GLY220 4.8 21.7 1.0 CA A:ASN218 4.9 22.9 1.0 CA A:LEU179 5.0 25.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1101 b:41.5 occ:1.00 OD1 B:ASN72 2.2 39.3 1.0 O B:HOH2607 2.2 40.9 1.0 O B:ILE33 2.4 34.0 1.0 O B:ILE131 2.4 36.8 1.0 OD1 B:ASN32 2.5 43.6 1.0 O B:VAL73 2.7 36.2 1.0 CG B:ASN72 3.1 43.3 1.0 CG B:ASN32 3.4 43.3 1.0 C B:ILE33 3.5 33.9 1.0 C B:ILE131 3.5 35.9 1.0 ND2 B:ASN72 3.5 42.6 1.0 N B:ILE33 3.6 36.2 1.0 N B:ILE131 3.6 36.1 1.0 ND2 B:ASN32 3.7 47.7 1.0 N B:VAL73 3.7 39.3 1.0 C B:VAL73 3.8 37.4 1.0 CA B:ILE131 4.0 34.8 1.0 O B:HOH2477 4.0 36.5 1.0 CA B:ILE33 4.0 34.3 1.0 CA B:VAL73 4.3 37.6 1.0 CB B:ILE33 4.4 33.2 1.0 CB B:ILE131 4.4 32.9 1.0 CB B:ASN72 4.5 45.1 1.0 C B:ASP130 4.6 37.0 1.0 N B:ALA34 4.6 33.1 1.0 C B:ASN32 4.6 37.7 1.0 N B:GLY132 4.6 36.1 1.0 CB B:ASN32 4.7 41.5 1.0 C B:ASN72 4.7 41.8 1.0 CA B:ASN72 4.7 43.7 1.0 CB B:ASP130 4.8 40.4 1.0 CA B:ASP130 4.8 38.5 1.0 CA B:ASN32 4.8 40.6 1.0 CB B:VAL73 4.8 36.0 1.0 N B:MET74 4.9 37.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Hemolytic Lectin Cel-III


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1102 b:21.8 occ:1.00 OD1 B:ASN177 2.3 22.2 1.0 OD1 B:ASN218 2.4 20.4 1.0 O B:VAL266 2.4 20.6 1.0 O B:VAL178 2.4 20.7 1.0 O B:VAL219 2.5 19.8 1.0 OD1 B:ASP265 2.5 23.1 1.0 CG B:ASN177 3.2 22.4 1.0 CG B:ASN218 3.3 21.4 1.0 C B:VAL266 3.5 19.7 1.0 C B:VAL178 3.5 21.2 1.0 ND2 B:ASN218 3.5 22.2 1.0 N B:VAL266 3.5 21.1 1.0 N B:VAL178 3.6 21.1 1.0 CG B:ASP265 3.6 26.5 1.0 C B:VAL219 3.6 20.1 1.0 ND2 B:ASN177 3.6 23.9 1.0 N B:VAL219 3.7 19.1 1.0 CA B:VAL266 3.9 20.3 1.0 O B:HOH2312 3.9 29.4 1.0 CA B:VAL178 4.0 21.3 1.0 OD2 B:ASP265 4.1 29.6 1.0 CA B:VAL219 4.1 18.9 1.0 O B:HOH2254 4.2 29.6 1.0 CB B:VAL266 4.3 20.5 1.0 CB B:VAL178 4.4 20.8 1.0 C B:ASN177 4.5 22.0 1.0 CB B:ASN177 4.5 22.6 1.0 C B:ASP265 4.6 21.6 1.0 CB B:ASN218 4.6 20.6 1.0 CB B:VAL219 4.6 17.8 1.0 N B:GLY267 4.6 19.2 1.0 C B:ASN218 4.6 19.5 1.0 CA B:ASN177 4.7 22.3 1.0 N B:LEU179 4.7 22.1 1.0 CB B:ASP265 4.7 24.2 1.0 N B:GLY220 4.7 20.2 1.0 CA B:ASN218 4.8 20.4 1.0 CA B:ASP265 4.8 24.0 1.0

T.Uchida, T.Yamasaki, S.Eto, H.Sugawara, G.Kurisu, A.Nakagawa, M.Kusunoki, T.Hatakeyama. Crystal Structure of the Hemolytic Lectin Cel-III Isolated From the Marine Invertebrate Cucumaria Echinata: Implications of Domain Structure For Its Membrane Pore-Formation Mechanism J.Biol.Chem. V. 279 37133 2004.
ISSN: ISSN 0021-9258
PubMed: 15194688
DOI: 10.1074/JBC.M404065200