Calcium in PDB 3uk9: Galactose-Specific Lectin From Dolichos Lablab

The structure of Galactose-Specific Lectin From Dolichos Lablab, PDB code: 3uk9 was solved by K.N.Shetty, V.L.Latha, R.N.Rao, S.K.Nadimpalli, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.17 / 3.11
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.990, 84.130, 93.159, 89.92, 76.01, 77.00
R / Rfree (%)	25.1 / 30.6

The structure of Galactose-Specific Lectin From Dolichos Lablab also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Calcium atom in the Galactose-Specific Lectin From Dolichos Lablab (pdb code 3uk9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Galactose-Specific Lectin From Dolichos Lablab, PDB code: 3uk9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:45.5 occ:1.00 O A:HOH403 2.2 2.0 1.0 OD2 A:ASP156 2.3 53.8 1.0 OD1 A:ASN152 2.4 56.7 1.0 O A:PHE150 2.6 51.3 1.0 O A:HOH402 2.7 2.0 1.0 OD2 A:ASP148 2.7 44.0 1.0 OD1 A:ASP148 3.3 43.7 1.0 CG A:ASP148 3.4 43.4 1.0 CG A:ASN152 3.4 58.9 1.0 CG A:ASP156 3.4 54.5 1.0 NE1 A:TRP155 3.7 58.4 1.0 C A:PHE150 3.8 51.8 1.0 OD1 A:ASP156 3.9 53.1 1.0 N A:ASN152 4.0 58.4 1.0 CB A:ASN152 4.1 60.5 1.0 MN A:MN307 4.3 49.9 1.0 ND2 A:ASN152 4.3 60.6 1.0 OD1 A:ASP108 4.3 47.0 1.0 O A:HOH401 4.4 2.0 1.0 CD1 A:TRP155 4.5 58.7 1.0 CA A:GLY126 4.6 49.9 1.0 O A:GLY126 4.6 49.6 1.0 N A:TYR151 4.7 53.9 1.0 CB A:ASP156 4.7 56.8 1.0 CA A:TYR151 4.7 55.5 1.0 C A:TYR151 4.7 58.1 1.0 CA A:ASN152 4.7 61.1 1.0 CE2 A:TRP155 4.7 60.8 1.0 CA A:PHE150 4.8 50.6 1.0 CB A:ASP148 4.8 41.9 1.0 CD2 A:PHE150 4.9 56.5 1.0 CB A:PHE150 5.0 51.8 1.0

Calcium binding site 2 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:48.1 occ:1.00 O B:HOH402 2.3 2.0 1.0 OD1 B:ASN152 2.6 76.2 1.0 OD1 B:ASP148 2.7 62.0 1.0 O B:PHE150 2.7 71.0 1.0 OD2 B:ASP156 2.8 72.3 1.0 O B:HOH401 3.1 2.0 1.0 OD2 B:ASP148 3.2 59.8 1.0 CG B:ASP148 3.3 60.3 1.0 CG B:ASN152 3.6 78.4 1.0 CG B:ASP156 3.8 71.1 1.0 C B:PHE150 3.9 72.2 1.0 O B:GLY126 4.0 62.4 1.0 NE1 B:TRP155 4.1 73.9 1.0 OD1 B:ASP156 4.1 69.2 1.0 CA B:GLY126 4.2 66.2 1.0 CB B:ASN152 4.2 78.8 1.0 N B:ASN152 4.2 76.9 1.0 C B:GLY126 4.6 64.3 1.0 ND2 B:ASN152 4.6 81.0 1.0 MN B:MN304 4.7 40.1 1.0 CA B:PHE150 4.8 72.0 1.0 OD1 B:ASP108 4.8 68.3 1.0 CB B:ASP148 4.8 58.4 1.0 CB B:PHE150 4.8 73.7 1.0 CA B:ASN152 4.9 79.8 1.0 N B:TYR151 4.9 73.9 1.0 CD1 B:TRP155 4.9 73.3 1.0 CD2 B:PHE150 4.9 78.2 1.0 C B:TYR151 4.9 77.5 1.0 CA B:TYR151 5.0 74.7 1.0 N B:PHE150 5.0 68.8 1.0

Calcium binding site 3 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:34.6 occ:1.00 O C:HOH402 2.2 2.0 1.0 O C:HOH403 2.3 5.5 1.0 OD2 C:ASP148 2.3 44.5 1.0 OD2 C:ASP156 2.4 52.7 1.0 OD1 C:ASN152 2.6 54.0 1.0 O C:PHE150 2.7 51.1 1.0 OD1 C:ASP148 3.0 45.3 1.0 CG C:ASP148 3.0 44.2 1.0 CG C:ASP156 3.4 52.4 1.0 CG C:ASN152 3.6 56.4 1.0 OD1 C:ASP156 3.7 50.9 1.0 C C:PHE150 3.9 52.4 1.0 CB C:ASN152 4.0 57.5 1.0 MN C:MN305 4.1 35.3 1.0 N C:ASN152 4.1 57.4 1.0 NE1 C:TRP155 4.1 54.3 1.0 O C:HOH401 4.2 2.0 1.0 O C:GLY126 4.3 43.1 1.0 CA C:GLY126 4.4 44.8 1.0 CB C:ASP148 4.4 42.7 1.0 OD1 C:ASP108 4.6 45.7 1.0 CA C:ASN152 4.7 59.3 1.0 CB C:ASP156 4.7 54.6 1.0 ND2 C:ASN152 4.7 58.8 1.0 CA C:PHE150 4.8 51.5 1.0 C C:GLY126 4.8 43.6 1.0 CB C:PHE150 4.8 51.7 1.0 N C:TYR151 4.9 55.1 1.0 N C:PHE150 4.9 48.9 1.0 CD1 C:TRP155 4.9 54.6 1.0

Calcium binding site 4 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:56.6 occ:1.00 O D:HOH403 2.2 2.0 1.0 O D:HOH402 2.2 2.0 1.0 O D:PHE150 2.3 55.2 1.0 OD2 D:ASP156 2.3 57.7 1.0 OD1 D:ASP148 2.8 49.5 1.0 OD1 D:ASN152 2.9 60.6 1.0 OD2 D:ASP148 2.9 49.3 1.0 CG D:ASP148 3.3 48.3 1.0 CG D:ASP156 3.5 58.5 1.0 C D:PHE150 3.5 55.5 1.0 CG D:ASN152 3.6 62.9 1.0 N D:ASN152 3.9 61.9 1.0 OD1 D:ASP156 4.0 57.9 1.0 CB D:ASN152 4.1 63.9 1.0 O D:HOH401 4.2 2.2 1.0 O D:GLY126 4.3 54.2 1.0 MN D:MN304 4.3 48.2 1.0 CA D:PHE150 4.4 54.2 1.0 OD1 D:ASP108 4.4 48.2 1.0 NE1 D:TRP155 4.4 60.5 1.0 CB D:PHE150 4.5 55.0 1.0 N D:TYR151 4.5 57.4 1.0 N D:PHE150 4.6 51.4 1.0 ND2 D:ASN152 4.6 65.4 1.0 CA D:ASN152 4.6 64.7 1.0 CA D:TYR151 4.7 59.3 1.0 C D:TYR151 4.7 61.8 1.0 CB D:ASP156 4.7 60.4 1.0 CD2 D:PHE150 4.7 59.9 1.0 CB D:ASP148 4.8 46.2 1.0 CA D:GLY126 4.8 56.4 1.0 O D:ASP108 4.9 40.1 1.0

Calcium binding site 5 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca303 b:47.6 occ:1.00 OD1 E:ASN152 2.4 54.4 1.0 OD2 E:ASP156 2.5 51.7 1.0 OD2 E:ASP148 2.6 46.4 1.0 O E:PHE150 2.8 49.5 1.0 OD1 E:ASP148 2.9 45.3 1.0 CG E:ASP148 3.2 45.1 1.0 CG E:ASN152 3.5 56.4 1.0 O E:HOH401 3.6 2.0 1.0 CG E:ASP156 3.6 52.0 1.0 OD1 E:ASP108 3.7 40.7 1.0 OD1 E:ASP156 3.9 51.4 1.0 O E:GLY126 4.0 42.7 1.0 C E:PHE150 4.1 49.9 1.0 NE1 E:TRP155 4.1 56.5 1.0 CA E:GLY126 4.1 43.0 1.0 ND2 E:ASN152 4.3 57.5 1.0 CB E:ASN152 4.4 58.2 1.0 C E:GLY126 4.5 43.0 1.0 N E:ASN152 4.6 56.2 1.0 CB E:ASP148 4.7 43.4 1.0 CG E:ASP108 4.7 40.2 1.0 O E:ASP108 4.8 34.8 1.0 MN E:MN304 4.9 56.5 1.0 CA E:PHE150 4.9 48.6 1.0 CB E:ASP156 4.9 53.5 1.0 CB E:PHE150 5.0 49.5 1.0 CE2 E:TRP155 5.0 59.1 1.0

Calcium binding site 6 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca303 b:86.9 occ:1.00 O F:HOH403 2.3 20.6 1.0 O F:HOH404 2.3 10.2 1.0 OD1 F:ASN152 2.3 0.8 1.0 OD2 F:ASP156 2.8 99.1 1.0 O F:PHE150 2.8 0.9 1.0 OD2 F:ASP148 2.9 88.5 1.0 OD1 F:ASP148 3.0 91.0 1.0 CG F:ASN152 3.3 0.1 1.0 CG F:ASP148 3.4 88.2 1.0 CG F:ASP156 3.8 97.5 1.0 CB F:ASN152 3.8 0.3 1.0 O F:GLY126 4.0 95.7 1.0 NE1 F:TRP155 4.0 0.4 1.0 C F:PHE150 4.0 0.7 1.0 OD1 F:ASP156 4.1 94.7 1.0 CA F:GLY126 4.1 0.2 1.0 N F:ASN152 4.2 0.2 1.0 ND2 F:ASN152 4.4 0.8 1.0 C F:GLY126 4.5 98.6 1.0 CA F:ASN152 4.6 0.7 1.0 O F:ASP108 4.8 80.6 1.0 CB F:PHE150 4.8 0.9 1.0 MN F:MN304 4.8 73.9 1.0 CD2 F:PHE150 4.8 0.3 1.0 CA F:PHE150 4.8 0.1 1.0 O F:HOH401 4.8 2.0 1.0 CE2 F:TRP155 4.8 0.7 1.0 CB F:ASP148 4.9 84.7 1.0 CD1 F:TRP155 4.9 99.4 1.0 N F:PHE150 5.0 99.5 1.0 CZ2 F:TRP155 5.0 0.9 1.0

Calcium binding site 7 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca304 b:30.7 occ:1.00 O G:HOH402 2.3 8.6 1.0 O G:HOH403 2.3 2.0 1.0 OD2 G:ASP148 2.7 44.9 1.0 OD2 G:ASP156 2.7 52.2 1.0 OD1 G:ASN152 2.8 56.1 1.0 O G:PHE150 3.0 51.0 1.0 CG G:ASP148 3.3 44.0 1.0 OD1 G:ASP148 3.3 44.7 1.0 CG G:ASP156 3.6 52.2 1.0 O G:GLY126 3.7 47.4 1.0 CG G:ASN152 3.8 58.2 1.0 OD1 G:ASP156 3.8 50.5 1.0 NE1 G:TRP155 4.0 53.3 1.0 OD1 G:ASP108 4.2 45.8 1.0 CA G:GLY126 4.2 49.7 1.0 C G:PHE150 4.2 52.3 1.0 O G:HOH401 4.3 2.0 1.0 MN G:MN305 4.3 32.6 1.0 C G:GLY126 4.4 48.3 1.0 CZ2 G:TRP155 4.6 56.9 1.0 CE2 G:TRP155 4.6 56.1 1.0 CB G:ASN152 4.6 59.4 1.0 CB G:ASP148 4.7 42.1 1.0 ND2 G:ASN152 4.7 60.5 1.0 N G:ASN152 4.7 57.9 1.0 O G:ASP108 4.8 39.4 1.0 CD2 G:PHE150 4.9 56.5 1.0 CB G:PHE150 4.9 52.2 1.0 CD1 G:TRP155 4.9 54.0 1.0 CA G:PHE150 5.0 51.5 1.0

Calcium binding site 8 out of 8 in the Galactose-Specific Lectin From Dolichos Lablab


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Galactose-Specific Lectin From Dolichos Lablab within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca301 b:30.1 occ:1.00 O H:HOH402 2.3 2.0 1.0 OD2 H:ASP156 2.5 80.6 1.0 O H:PHE150 2.5 80.4 1.0 OD1 H:ASP148 2.6 73.0 1.0 OD2 H:ASP148 2.9 71.8 1.0 CG H:ASP148 3.1 71.8 1.0 OD1 H:ASN152 3.3 84.3 1.0 OD1 H:ASP108 3.6 71.7 1.0 CG H:ASP156 3.6 80.6 1.0 C H:PHE150 3.6 81.9 1.0 CB H:ASN152 4.0 86.7 1.0 CG H:ASN152 4.0 86.7 1.0 OD1 H:ASP156 4.2 79.2 1.0 N H:ASN152 4.2 86.9 1.0 CB H:PHE150 4.2 81.3 1.0 CA H:PHE150 4.3 80.8 1.0 O H:GLY126 4.3 72.3 1.0 MN H:MN302 4.3 64.5 1.0 N H:PHE150 4.4 77.7 1.0 NE1 H:TRP155 4.4 81.3 1.0 CG H:ASP108 4.6 70.8 1.0 CB H:ASP148 4.6 70.2 1.0 CD2 H:PHE150 4.7 85.8 1.0 CB H:ASP108 4.7 67.6 1.0 O H:ASP108 4.7 65.0 1.0 N H:TYR151 4.7 84.7 1.0 O H:HOH401 4.8 2.0 1.0 CA H:ASN152 4.8 88.8 1.0 CB H:ASP156 4.8 83.1 1.0 CA H:GLY126 4.8 75.3 1.0 CG H:PHE150 5.0 84.8 1.0

K.N.Shetty, V.L.Latha, R.N.Rao, S.K.Nadimpalli, K.Suguna. Affinity of A Galactose-Specific Legume Lectin From Dolichos Lablab to Adenine Revealed By X-Ray Cystallography. Iubmb Life V. 65 633 2013.
ISSN: ISSN 1521-6543
PubMed: 23794513
DOI: 10.1002/IUB.1177