Calcium in PDB 6kbj: Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate

The structure of Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate, PDB code: 6kbj was solved by S.Vajravijayan, S.Pletnev, Z.Luo, K.Gunasekaran, N.Nandhagopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.477, 152.477, 146.162, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 21.5

The binding sites of Calcium atom in the Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate (pdb code 6kbj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate, PDB code: 6kbj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:52.0 occ:1.00 O A:PRO305 2.3 27.8 1.0 OD2 A:ASP260 2.4 30.4 1.0 OD1 A:ASN301 2.5 34.0 1.0 O7 A:MLI405 2.6 46.4 1.0 OD1 A:ASP259 2.7 34.4 1.0 O A:GLY303 2.7 36.7 1.0 C2 A:MLI405 3.3 76.4 1.0 C1 A:MLI405 3.4 48.8 1.0 CG A:ASP259 3.4 33.0 1.0 CG A:ASP260 3.4 36.1 1.0 C A:PRO305 3.5 39.0 1.0 C A:GLY303 3.5 40.2 1.0 OD2 A:ASP259 3.6 34.6 1.0 CG A:ASN301 3.6 38.6 1.0 OD1 A:ASP260 3.8 38.7 1.0 C A:GLY304 3.9 47.6 1.0 N A:PRO305 4.0 51.4 1.0 N A:GLY303 4.1 38.8 1.0 N A:GLY304 4.1 41.0 1.0 CA A:GLY304 4.1 49.2 1.0 O A:GLY304 4.2 40.7 1.0 ND2 A:ASN301 4.2 27.8 1.0 O A:ASP259 4.4 29.0 1.0 CA A:PRO305 4.4 44.6 1.0 CA A:ALA306 4.4 33.6 1.0 N A:ALA306 4.4 36.2 1.0 CA A:GLY303 4.5 40.0 1.0 N A:ASP260 4.5 28.7 1.0 C A:ASP259 4.5 26.8 1.0 CD A:PRO305 4.5 55.1 1.0 O6 A:MLI405 4.5 87.2 1.0 N A:GLY302 4.6 45.7 1.0 CB A:ALA306 4.6 34.1 1.0 CB A:ASP259 4.6 27.3 1.0 CB A:ASN301 4.7 34.6 1.0 CB A:ASP260 4.7 33.5 1.0 CA A:ASN301 4.8 32.5 1.0 C3 A:MLI405 4.8 62.7 1.0

Calcium binding site 2 out of 2 in the Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Lectin From Pleurotus Ostreatus in Complex with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:35.1 occ:1.00 OD1 A:ASN138 2.3 26.1 1.0 OD1 A:ASP97 2.4 26.5 1.0 O A:PRO144 2.5 22.4 1.0 OG A:SER143 2.6 25.6 1.0 O9 A:MLI404 2.6 44.8 1.0 OD2 A:ASP98 2.7 28.0 1.0 O8 A:MLI404 3.0 38.5 1.0 C3 A:MLI404 3.1 55.2 1.0 CG A:ASP97 3.3 26.7 1.0 CG A:ASP98 3.4 26.2 1.0 CG A:ASN138 3.4 26.3 1.0 OD1 A:ASP98 3.5 31.4 1.0 CB A:SER143 3.6 24.8 1.0 C A:PRO144 3.6 27.0 1.0 OD2 A:ASP97 3.7 27.3 1.0 C A:SER143 4.1 23.2 1.0 ND2 A:ASN138 4.1 25.3 1.0 N A:PRO144 4.2 22.7 1.0 O A:SER143 4.3 20.7 1.0 C A:ASP97 4.3 25.4 1.0 O A:ASP97 4.3 21.9 1.0 O A:VAL140 4.4 37.3 1.0 N A:ASP98 4.4 23.4 1.0 CA A:SER143 4.5 23.5 1.0 CB A:ASN138 4.5 25.8 1.0 CA A:PRO144 4.5 26.6 1.0 N A:VAL140 4.5 34.3 1.0 N A:ALA145 4.5 27.0 1.0 CA A:ALA145 4.5 25.6 1.0 CB A:ASP97 4.5 24.3 1.0 CA A:ASN138 4.6 28.9 1.0 N A:LEU139 4.6 31.3 1.0 C1 A:MLI404 4.6 44.2 1.0 CB A:VAL140 4.7 32.9 1.0 CB A:ASP98 4.7 26.0 1.0 CD A:PRO144 4.8 24.5 1.0 CA A:ASP97 4.9 24.0 1.0 CB A:ALA145 4.9 26.5 1.0 CA A:ASP98 5.0 24.7 1.0

S.Vajravijayan, S.Pletnev, Z.Luo, V.Z.Pletnev, N.Nandhagopal, K.Gunasekaran. Crystallographic and Calorimetric Analysis on Pleurotus Ostreatus Lectin and Its Sugar Complexes - Promiscuous Binding Driven By Geometry. Int.J.Biol.Macromol. V. 152 862 2020.
ISSN: ISSN 0141-8130
PubMed: 32112837
DOI: 10.1016/J.IJBIOMAC.2020.02.294