Calcium in PDB 5ava: Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan

The structure of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan, PDB code: 5ava was solved by M.Nagae, Y.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.210, 122.838, 97.664, 90.00, 90.66, 90.00
R / Rfree (%)	22.9 / 27.4

The structure of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Calcium atom in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan (pdb code 5ava). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan, PDB code: 5ava:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:34.1 occ:1.00 OD2 A:ASP155 2.3 35.9 1.0 O A:HOH2104 2.3 31.7 1.0 O A:HOH2103 2.3 31.8 1.0 OD1 A:ASN151 2.3 39.0 1.0 OD1 A:ASP147 2.3 33.3 1.0 O A:LEU149 2.3 34.4 1.0 OD2 A:ASP147 2.3 33.9 1.0 CG A:ASP147 2.6 32.2 1.0 CG A:ASP155 3.3 36.6 1.0 CG A:ASN151 3.5 40.1 1.0 C A:LEU149 3.5 33.9 1.0 OD1 A:ASP155 3.8 35.3 1.0 MN A:MN2001 4.0 33.4 1.0 CB A:ASP147 4.2 30.9 1.0 O A:HOH2101 4.2 31.1 1.0 N A:ASN151 4.2 38.8 1.0 CB A:ASN151 4.3 40.3 1.0 CA A:LEU149 4.3 32.5 1.0 N A:LEU149 4.4 30.3 1.0 ND2 A:ASN151 4.5 39.9 1.0 CB A:ASP155 4.5 37.9 1.0 CB A:LEU149 4.6 32.5 1.0 O A:GLY125 4.6 33.2 1.0 N A:TYR150 4.6 35.3 1.0 NE1 A:TRP154 4.6 51.5 1.0 O A:ASP107 4.7 33.3 1.0 CD2 A:LEU149 4.7 32.4 1.0 C A:TYR150 4.7 38.0 1.0 OD1 A:ASP107 4.7 38.9 1.0 CA A:TYR150 4.8 37.6 1.0 CE1 A:HIS160 4.8 33.0 1.0 CZ2 A:TRP154 4.8 50.6 1.0 CA A:GLY125 4.9 33.0 1.0 CA A:ASN151 4.9 41.3 1.0 NE2 A:HIS160 5.0 32.6 1.0 CE2 A:TRP154 5.0 51.3 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:35.4 occ:1.00 OD1 B:ASP147 2.3 31.8 1.0 OD2 B:ASP155 2.3 36.1 1.0 O B:HOH2102 2.3 33.5 1.0 O B:HOH2104 2.3 33.5 1.0 OD1 B:ASN151 2.3 35.9 1.0 O B:LEU149 2.3 32.8 1.0 OD2 B:ASP147 2.3 33.3 1.0 CG B:ASP147 2.6 30.9 1.0 CG B:ASP155 3.2 36.9 1.0 CG B:ASN151 3.5 35.5 1.0 C B:LEU149 3.5 31.7 1.0 OD1 B:ASP155 3.6 36.8 1.0 MN B:MN2001 3.9 34.8 1.0 CB B:ASP147 4.2 30.3 1.0 N B:ASN151 4.2 34.8 1.0 CB B:ASN151 4.3 35.5 1.0 CA B:LEU149 4.3 30.8 1.0 N B:LEU149 4.3 30.2 1.0 NE1 B:TRP154 4.4 38.2 1.0 CB B:ASP155 4.5 37.5 1.0 ND2 B:ASN151 4.5 34.6 1.0 CB B:LEU149 4.5 31.0 1.0 N B:TYR150 4.6 33.1 1.0 OD1 B:ASP107 4.6 43.8 1.0 O B:HOH2101 4.7 33.2 1.0 O B:ASP107 4.7 38.0 1.0 CA B:TYR150 4.8 34.0 1.0 CE1 B:HIS160 4.8 35.7 1.0 C B:TYR150 4.8 33.9 1.0 CZ2 B:TRP154 4.9 38.5 1.0 O B:GLY125 4.9 35.0 1.0 CA B:ASN151 4.9 36.3 1.0 CE2 B:TRP154 4.9 38.7 1.0 CD2 B:LEU149 4.9 30.3 1.0 NE2 B:HIS160 5.0 35.3 1.0 CA B:ASP147 5.0 29.2 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2002 b:42.1 occ:1.00 O C:HOH2103 2.3 38.8 1.0 O C:HOH2104 2.3 40.2 1.0 OD1 C:ASN151 2.3 44.8 1.0 OD2 C:ASP155 2.3 45.3 1.0 OD1 C:ASP147 2.3 41.4 1.0 OD2 C:ASP147 2.3 41.5 1.0 O C:LEU149 2.3 45.4 1.0 CG C:ASP147 2.6 40.6 1.0 CG C:ASP155 3.3 46.0 1.0 CG C:ASN151 3.4 44.5 1.0 C C:LEU149 3.6 44.4 1.0 OD1 C:ASP155 3.8 46.2 1.0 MN C:MN2001 4.0 41.2 1.0 N C:ASN151 4.1 45.4 1.0 CB C:ASP147 4.2 40.1 1.0 CB C:ASN151 4.2 43.6 1.0 O C:HOH2102 4.3 38.6 1.0 CB C:ASP155 4.3 45.0 1.0 ND2 C:ASN151 4.4 45.1 1.0 NE1 C:TRP154 4.4 41.7 1.0 CA C:LEU149 4.5 44.1 1.0 N C:TYR150 4.5 44.6 1.0 N C:LEU149 4.5 43.5 1.0 CA C:TYR150 4.6 45.8 1.0 C C:TYR150 4.6 46.5 1.0 O C:GLY125 4.6 41.6 1.0 CE1 C:HIS160 4.7 39.6 1.0 OD1 C:ASP107 4.7 54.7 1.0 O C:ASP107 4.8 50.3 1.0 CA C:ASN151 4.8 44.6 1.0 CZ2 C:TRP154 4.8 42.6 1.0 CA C:GLY125 4.8 42.0 1.0 CB C:LEU149 4.9 45.3 1.0 CE2 C:TRP154 4.9 42.3 1.0 CA C:ASP147 5.0 40.3 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


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 Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2002 b:44.2 occ:1.00 OD1 D:ASP147 2.3 41.7 1.0 O D:HOH2103 2.3 41.9 1.0 O D:LEU149 2.3 43.2 1.0 O D:HOH2104 2.3 42.7 1.0 OD2 D:ASP155 2.3 48.0 1.0 OD1 D:ASN151 2.3 51.8 1.0 OD2 D:ASP147 2.3 41.8 1.0 CG D:ASP147 2.6 40.1 1.0 CG D:ASP155 3.3 49.3 1.0 CG D:ASN151 3.5 53.3 1.0 C D:LEU149 3.5 43.5 1.0 OD1 D:ASP155 3.9 46.9 1.0 MN D:MN2001 4.0 40.9 1.0 CB D:ASP147 4.1 38.4 1.0 N D:ASN151 4.2 52.3 1.0 O D:HOH2101 4.3 40.0 1.0 CB D:ASN151 4.3 53.7 1.0 CB D:ASP155 4.3 50.1 1.0 CA D:LEU149 4.4 41.3 1.0 N D:LEU149 4.4 39.3 1.0 NE1 D:TRP154 4.5 63.0 1.0 N D:TYR150 4.5 47.0 1.0 O D:ASP107 4.5 41.7 1.0 ND2 D:ASN151 4.5 53.2 1.0 CA D:TYR150 4.6 50.0 1.0 C D:TYR150 4.6 50.5 1.0 O D:GLY125 4.7 40.8 1.0 CE1 D:HIS160 4.7 36.9 1.0 NE2 D:HIS160 4.8 37.3 1.0 CZ2 D:TRP154 4.9 61.1 1.0 CA D:ASN151 4.9 54.5 1.0 CB D:LEU149 4.9 40.5 1.0 CA D:ASP147 4.9 36.6 1.0 CA D:GLY125 4.9 40.0 1.0 CE2 D:TRP154 5.0 62.5 1.0 OD1 D:ASP107 5.0 41.6 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2002 b:40.2 occ:1.00 OD1 E:ASP147 2.3 38.5 1.0 OD2 E:ASP155 2.3 44.3 1.0 O E:HOH2104 2.3 38.9 1.0 O E:HOH2103 2.3 37.4 1.0 OD1 E:ASN151 2.3 42.9 1.0 O E:LEU149 2.3 41.4 1.0 OD2 E:ASP147 2.3 38.4 1.0 CG E:ASP147 2.6 37.2 1.0 CG E:ASP155 3.4 45.2 1.0 CG E:ASN151 3.4 43.7 1.0 C E:LEU149 3.5 40.8 1.0 OD1 E:ASP155 3.9 44.2 1.0 MN E:MN2001 4.0 40.6 1.0 N E:ASN151 4.1 43.4 1.0 CB E:ASP147 4.1 36.1 1.0 CB E:ASN151 4.1 43.5 1.0 ND2 E:ASN151 4.4 43.9 1.0 O E:HOH2102 4.4 38.3 1.0 CA E:LEU149 4.4 39.0 1.0 N E:LEU149 4.4 37.6 1.0 O E:GLY125 4.5 33.8 1.0 NE1 E:TRP154 4.5 43.4 1.0 N E:TYR150 4.5 42.3 1.0 CB E:ASP155 4.5 45.8 1.0 CA E:TYR150 4.7 43.4 1.0 O E:ASP107 4.7 33.8 1.0 CA E:GLY125 4.7 35.1 1.0 C E:TYR150 4.7 43.5 1.0 CZ2 E:TRP154 4.7 43.8 1.0 CB E:LEU149 4.7 38.5 1.0 CA E:ASN151 4.8 43.6 1.0 CE1 E:HIS160 4.8 38.6 1.0 CE2 E:TRP154 4.9 43.3 1.0 CA E:ASP147 5.0 34.4 1.0 NE2 E:HIS160 5.0 38.7 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca2002 b:44.8 occ:1.00 O F:HOH2103 2.3 42.7 1.0 OD1 F:ASP147 2.3 42.1 1.0 O F:HOH2104 2.3 43.5 1.0 O F:LEU149 2.3 45.1 1.0 OD2 F:ASP155 2.3 47.8 1.0 OD1 F:ASN151 2.3 47.4 1.0 OD2 F:ASP147 2.3 41.9 1.0 CG F:ASP147 2.6 40.2 1.0 CG F:ASP155 3.2 48.9 1.0 CG F:ASN151 3.5 48.5 1.0 C F:LEU149 3.5 45.6 1.0 OD1 F:ASP155 3.7 47.7 1.0 MN F:MN2001 4.0 43.8 1.0 N F:ASN151 4.1 50.5 1.0 O F:HOH2102 4.1 42.0 1.0 CB F:ASN151 4.1 49.5 1.0 CB F:ASP147 4.2 39.5 1.0 CB F:ASP155 4.3 49.7 1.0 NE1 F:TRP154 4.4 49.0 1.0 N F:TYR150 4.4 47.6 1.0 CA F:LEU149 4.5 44.8 1.0 C F:TYR150 4.5 49.8 1.0 N F:LEU149 4.5 44.1 1.0 CA F:TYR150 4.5 49.5 1.0 ND2 F:ASN151 4.6 47.8 1.0 CZ2 F:TRP154 4.7 49.5 1.0 O F:GLY125 4.7 43.1 1.0 OD1 F:ASP107 4.7 46.5 1.0 O F:ASP107 4.7 44.1 1.0 CA F:ASN151 4.8 51.1 1.0 CE1 F:HIS160 4.8 42.7 1.0 CE2 F:TRP154 4.8 49.7 1.0 CB F:LEU149 4.8 43.8 1.0 CA F:GLY125 4.9 44.7 1.0 NE2 F:HIS160 4.9 43.2 1.0 CD2 F:LEU149 5.0 43.8 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca2002 b:61.9 occ:1.00 O G:LEU149 2.3 63.0 1.0 OD2 G:ASP155 2.3 61.1 1.0 O G:HOH2104 2.3 60.2 1.0 OD1 G:ASN151 2.3 67.1 1.0 OD1 G:ASP147 2.3 61.6 1.0 O G:HOH2103 2.3 62.4 1.0 OD2 G:ASP147 2.3 59.5 1.0 CG G:ASP147 2.6 59.3 1.0 CG G:ASP155 3.2 59.4 1.0 CG G:ASN151 3.4 69.0 1.0 C G:LEU149 3.5 64.6 1.0 OD1 G:ASP155 3.7 60.2 1.0 MN G:MN2001 4.0 54.3 1.0 N G:ASN151 4.0 68.7 1.0 CB G:ASN151 4.1 68.0 1.0 CB G:ASP147 4.2 57.5 1.0 O G:HOH2102 4.2 49.3 1.0 CB G:ASP155 4.3 57.7 1.0 NE1 G:TRP154 4.4 68.8 1.0 N G:TYR150 4.5 65.2 1.0 CA G:LEU149 4.5 64.8 1.0 ND2 G:ASN151 4.5 69.5 1.0 C G:TYR150 4.5 69.2 1.0 CA G:TYR150 4.5 67.5 1.0 OD1 G:ASP107 4.5 58.7 1.0 N G:LEU149 4.6 64.1 1.0 O G:GLY125 4.7 56.0 1.0 CA G:ASN151 4.7 67.2 1.0 CE1 G:HIS160 4.7 49.0 1.0 CB G:LEU149 4.8 65.4 1.0 CZ2 G:TRP154 4.8 70.7 1.0 O G:ASP107 4.8 54.0 1.0 CE2 G:TRP154 4.9 69.2 1.0 CD2 G:LEU149 4.9 66.7 1.0 NE2 G:HIS160 4.9 49.8 1.0 CA G:GLY125 4.9 54.6 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Pha-E Lectin in Complex with Bisected Glycan within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca2002 b:72.9 occ:1.00 O H:HOH2104 2.3 69.2 1.0 O H:HOH2103 2.3 70.1 1.0 OD2 H:ASP155 2.3 73.3 1.0 O H:LEU149 2.3 72.4 1.0 OD1 H:ASP147 2.3 71.2 1.0 OD1 H:ASN151 2.3 79.2 1.0 OD2 H:ASP147 2.3 69.8 1.0 CG H:ASP147 2.6 69.0 1.0 CG H:ASP155 3.1 73.2 1.0 CG H:ASN151 3.4 80.5 1.0 C H:LEU149 3.6 75.7 1.0 OD1 H:ASP155 3.6 71.6 1.0 N H:ASN151 4.0 84.7 1.0 O H:HOH2102 4.0 61.6 1.0 MN H:MN2001 4.0 63.9 1.0 CB H:ASP147 4.1 65.5 1.0 CB H:ASP155 4.2 72.7 1.0 ND2 H:ASN151 4.3 80.7 1.0 CB H:ASN151 4.3 81.1 1.0 CA H:TYR150 4.4 83.2 1.0 N H:TYR150 4.4 79.3 1.0 C H:TYR150 4.5 85.0 1.0 CE1 H:HIS160 4.5 57.5 1.0 CA H:LEU149 4.6 74.3 1.0 N H:LEU149 4.6 70.9 1.0 NE1 H:TRP154 4.7 93.9 1.0 CA H:ASN151 4.8 84.2 1.0 OD1 H:ASP107 4.9 73.8 1.0 NE2 H:HIS160 4.9 58.2 1.0 CA H:ASP147 5.0 60.9 1.0

M.Nagae, M.Kanagawa, K.Morita-Matsumoto, S.Hanashima, Y.Kizuka, N.Taniguchi, Y.Yamaguchi. Atomic Visualization of A Flipped-Back Conformation of Bisected Glycans Bound to Specific Lectins Sci Rep V. 6 22973 2016.
ISSN: ESSN 2045-2322
PubMed: 26971576
DOI: 10.1038/SREP22973