Calcium in PDB 5c9l: Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution

The structure of Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution, PDB code: 5c9l was solved by A.Kumar, P.Sykorova, G.Demo, P.Dobes, P.Hyrsl, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.15 / 1.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	71.120, 87.677, 157.691, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 15.9

The structure of Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution also contains other interesting chemical elements:

Mercury	(Hg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution (pdb code 5c9l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution, PDB code: 5c9l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution


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 Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:14.2 occ:0.80 O A:HOH704 2.2 26.5 1.0 O A:HOH778 2.3 31.1 1.0 ND1 A:HIS203 2.3 13.4 1.0 OD2 A:ASP132 2.4 10.6 1.0 O A:HIS203 2.5 15.9 1.0 O A:HOH805 2.6 27.0 1.0 CE1 A:HIS203 3.1 12.1 1.0 CG A:HIS203 3.4 13.2 1.0 C A:HIS203 3.6 14.0 1.0 CG A:ASP132 3.6 8.7 1.0 CB A:HIS203 3.7 14.0 1.0 NH2 A:ARG134 4.0 12.7 1.0 CB A:ASP132 4.1 7.7 1.0 CA A:HIS203 4.3 12.8 1.0 NE2 A:HIS203 4.3 14.2 1.0 NE A:ARG134 4.4 8.2 1.0 CD2 A:HIS203 4.4 13.1 1.0 OG1 A:THR204 4.4 17.2 1.0 OD1 A:ASP132 4.6 8.1 1.0 CZ A:ARG134 4.6 9.5 1.0 N A:THR204 4.6 13.8 1.0 O A:ALA202 4.6 12.2 1.0 CA A:THR204 4.9 14.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution


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 Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:11.5 occ:0.70 O A:HOH775 2.2 20.4 1.0 O A:HOH790 2.3 29.1 1.0 O A:HOH504 2.3 21.8 1.0 ND1 A:HIS155 2.4 9.7 1.0 OD2 A:ASP84 2.4 8.7 1.0 O A:HIS155 2.5 10.3 1.0 O A:HOH734 2.6 26.0 1.0 CE1 A:HIS155 3.3 10.2 1.0 CG A:HIS155 3.4 8.3 1.0 CG A:ASP84 3.5 8.2 1.0 C A:HIS155 3.6 8.8 1.0 CB A:HIS155 3.7 8.6 1.0 NH2 A:ARG86 4.0 11.9 1.0 CB A:ASP84 4.1 7.4 1.0 CA A:HIS155 4.2 8.3 1.0 NE A:ARG86 4.4 9.4 1.0 NE2 A:HIS155 4.4 9.8 1.0 CD2 A:HIS155 4.5 8.7 1.0 OD1 A:ASP84 4.6 8.1 1.0 O A:HOH859 4.6 28.1 1.0 CZ A:ARG86 4.6 10.2 1.0 N A:THR156 4.6 10.6 1.0 OG1 A:THR156 4.7 14.6 1.0 O A:ALA154 4.7 8.2 1.0 CA A:THR156 4.9 12.1 1.0

A.Kumar, P.Sykorova, G.Demo, P.Dobes, P.Hyrsl, M.Wimmerova. A Novel Fucose-Binding Lectin From Photorhabdus Luminescens (Pll) with An Unusual Heptabladed Beta-Propeller Tetrameric Structure. J.Biol.Chem. V. 291 25032 2016.
ISSN: ESSN 1083-351X
PubMed: 27758853
DOI: 10.1074/JBC.M115.693473