Calcium in PDB 2boi: 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside

The structure of 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside, PDB code: 2boi was solved by M.Pokorna, G.Cioci, S.Perret, E.Rebuffet, J.Adam, N.Gilboa-Garber, E.P.Mitchell, A.Imberty, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.47 / 1.1
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	51.093, 89.836, 46.479, 90.00, 90.00, 90.00
R / Rfree (%)	10.1 / 11.7

The binding sites of Calcium atom in the 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside (pdb code 2boi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside, PDB code: 2boi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:7.2 occ:1.00 OD1 A:ASP98 2.4 10.4 1.0 OD1 A:ASP100 2.4 7.5 1.0 OE2 A:GLU94 2.4 8.0 1.0 OD2 A:ASP103 2.4 6.5 1.0 O3 A:MFU400 2.5 7.4 1.0 OE1 A:GLU94 2.5 7.4 1.0 O2 A:MFU400 2.5 8.1 1.0 OD1 A:ASP103 2.7 6.4 1.0 CD A:GLU94 2.8 7.1 1.0 CG A:ASP103 2.9 6.0 1.0 C2 A:MFU400 3.3 7.5 1.0 C3 A:MFU400 3.3 8.0 1.0 CG A:ASP100 3.4 7.0 1.0 CG A:ASP98 3.4 10.1 1.0 CA A:CA300 3.7 6.2 1.0 OD2 A:ASP98 3.7 10.2 1.0 OD2 A:ASP100 3.9 7.7 1.0 N A:ASP100 4.2 8.8 1.0 CG A:GLU94 4.2 7.5 1.0 OD1 A:ASP95 4.3 8.4 1.0 O A:HOH2150 4.3 16.2 1.0 CB A:ASP103 4.4 5.7 1.0 CB A:ASP100 4.5 8.7 1.0 N A:ASP95 4.5 6.8 1.0 N A:TYR101 4.5 6.8 1.0 N A:GLY96 4.6 8.9 1.0 N A:MET99 4.7 11.2 1.0 CA A:ASP100 4.7 8.2 1.0 CA A:GLU94 4.7 6.1 1.0 C4 A:MFU400 4.7 8.0 1.0 CB A:ASP98 4.7 11.5 1.0 C1 A:MFU400 4.7 8.5 1.0 N A:ASP98 4.8 12.4 1.0 OD1 A:ASN102 4.8 5.8 1.0 O4 A:MFU400 4.8 7.5 1.0 CG A:ASP95 4.9 7.3 1.0 CB A:GLU94 4.9 7.3 1.0 CA A:GLY96 5.0 10.4 1.0 C A:ASP100 5.0 7.3 1.0

Calcium binding site 2 out of 4 in the 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:6.2 occ:1.00 OD1 A:ASN102 2.3 5.8 1.0 O A:ASN21 2.4 6.1 1.0 OD1 A:ASP103 2.4 6.4 1.0 O B:GLY113 2.4 6.6 1.0 OD2 A:ASP100 2.4 7.7 1.0 O3 A:MFU400 2.5 7.4 1.0 O4 A:MFU400 2.5 7.5 1.0 OD1 A:ASP100 3.0 7.5 1.0 CG A:ASP100 3.1 7.0 1.0 C3 A:MFU400 3.4 8.0 1.0 CG A:ASN102 3.4 5.4 1.0 C B:GLY113 3.4 7.3 1.0 C4 A:MFU400 3.4 8.0 1.0 C A:ASN21 3.6 5.5 1.0 CG A:ASP103 3.6 6.0 1.0 OXT B:GLY113 3.7 9.2 1.0 CA A:CA200 3.7 7.2 1.0 ND2 A:ASN102 3.8 6.5 1.0 C2 A:MFU400 3.8 7.5 1.0 CB A:ASN21 4.0 5.5 1.0 CA A:ASP103 4.2 5.2 1.0 N A:ASP103 4.3 5.0 1.0 OD2 A:ASP103 4.4 6.5 1.0 N A:SER22 4.4 6.4 1.0 CA A:SER22 4.5 6.9 1.0 CA A:ASN21 4.5 5.2 1.0 O2 A:MFU400 4.5 8.1 1.0 CB A:ASP103 4.5 5.7 1.0 C A:ASN102 4.5 4.8 1.0 O A:HOH2152 4.5 16.0 1.0 OD2 A:ASP98 4.5 10.2 1.0 CB A:ASP100 4.6 8.7 1.0 CB A:ASN102 4.7 5.8 1.0 CA B:GLY113 4.8 8.4 1.0 CB A:SER22 4.8 6.6 1.0 C5 A:MFU400 4.8 8.8 1.0 O A:ASN102 4.8 5.3 1.0 N A:ASN102 4.9 5.6 1.0 CA A:ASN102 4.9 5.4 1.0 OD1 A:ASP98 5.0 10.4 1.0

Calcium binding site 3 out of 4 in the 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:4.5 occ:1.00 OD1 B:ASP98 2.4 7.2 1.0 OD1 B:ASP100 2.4 5.2 1.0 OE2 B:GLU94 2.4 5.3 1.0 OD2 B:ASP103 2.4 4.2 1.0 OE1 B:GLU94 2.5 5.0 1.0 O3 B:MFU700 2.5 4.8 1.0 O2 B:MFU700 2.5 5.2 1.0 OD1 B:ASP103 2.7 4.2 1.0 CD B:GLU94 2.8 4.7 1.0 CG B:ASP103 2.9 3.8 1.0 C2 B:MFU700 3.3 4.8 1.0 C3 B:MFU700 3.3 5.3 1.0 CG B:ASP100 3.4 5.0 1.0 CG B:ASP98 3.4 6.4 1.0 CA B:CA600 3.7 3.9 1.0 OD2 B:ASP98 3.7 7.2 1.0 OD2 B:ASP100 4.0 5.3 1.0 N B:ASP100 4.1 6.2 1.0 CG B:GLU94 4.3 5.5 1.0 OD1 B:ASP95 4.3 5.2 1.0 O B:HOH2166 4.4 14.2 1.0 CB B:ASP103 4.4 3.6 1.0 CB B:ASP100 4.5 5.9 1.0 N B:ASP95 4.5 4.6 1.0 N B:TYR101 4.5 5.0 1.0 N B:GLY96 4.6 6.0 1.0 N B:MET99 4.6 7.8 0.5 CA B:GLU94 4.7 4.5 1.0 CA B:ASP100 4.7 6.2 1.0 N B:MET99 4.7 7.7 0.5 C4 B:MFU700 4.7 5.2 1.0 CB B:ASP98 4.7 8.4 1.0 C1 B:MFU700 4.7 5.7 1.0 N B:ASP98 4.7 8.0 1.0 OD1 B:ASN102 4.8 4.1 1.0 O4 B:MFU700 4.8 4.8 1.0 CB B:GLU94 4.9 5.0 1.0 CG B:ASP95 4.9 4.5 1.0 CA B:GLY96 5.0 6.9 1.0 C B:ASP100 5.0 5.3 1.0 C B:ASP98 5.0 7.8 1.0

Calcium binding site 4 out of 4 in the 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with Alpha-Methyl-Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca600 b:3.9 occ:1.00 O B:ASN21 2.3 3.9 1.0 OD1 B:ASN102 2.3 4.1 1.0 OD1 B:ASP103 2.4 4.2 1.0 O A:GLY113 2.4 4.5 1.0 OD2 B:ASP100 2.4 5.3 1.0 O3 B:MFU700 2.5 4.8 1.0 O4 B:MFU700 2.5 4.8 1.0 OD1 B:ASP100 3.0 5.2 1.0 CG B:ASP100 3.1 5.0 1.0 C3 B:MFU700 3.4 5.3 1.0 C A:GLY113 3.4 4.9 1.0 CG B:ASN102 3.4 4.3 1.0 C4 B:MFU700 3.4 5.2 1.0 C B:ASN21 3.5 3.9 1.0 CG B:ASP103 3.6 3.8 1.0 OXT A:GLY113 3.7 6.0 1.0 CA B:CA500 3.7 4.5 1.0 ND2 B:ASN102 3.8 4.8 1.0 C2 B:MFU700 3.8 4.8 1.0 CB B:ASN21 4.1 3.9 1.0 CA B:ASP103 4.2 3.7 1.0 N B:ASP103 4.3 3.6 1.0 N B:SER22 4.4 4.2 1.0 OD2 B:ASP103 4.4 4.2 1.0 CA B:SER22 4.4 4.5 1.0 O2 B:MFU700 4.4 5.2 1.0 OD2 B:ASP98 4.5 7.2 1.0 CA B:ASN21 4.5 4.0 1.0 C B:ASN102 4.5 3.7 1.0 CB B:ASP103 4.5 3.6 1.0 O B:HOH2168 4.5 16.6 1.0 CB B:ASP100 4.5 5.9 1.0 CB B:ASN102 4.7 4.1 1.0 CA A:GLY113 4.7 5.6 1.0 CB B:SER22 4.7 5.2 1.0 C5 B:MFU700 4.8 5.9 1.0 O B:ASN102 4.8 4.2 1.0 N B:ASN102 4.9 4.0 1.0 CA B:ASN102 4.9 4.1 1.0 OD1 B:ASP98 5.0 7.2 1.0

M.Pokorna, G.Cioci, S.Perret, E.Rebuffet, N.Kostlanova, J.Adam, N.Gilboa-Garber, E.P.Mitchell, A.Imberty, M.Wimmerova. Unusual Entropy Driven Affinity of Chromobacter Violaceum Lectin Cv-Iil Towards Fucose and Mannose Biochemistry V. 45 7501 2006.
ISSN: ISSN 0006-2960
PubMed: 16768446
DOI: 10.1021/BI060214E