Calcium in PDB 3lp9: Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus

The structure of Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus, PDB code: 3lp9 was solved by V.Gaur, I.A.Qureshi, A.Singh, V.Chanana, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.170, 88.140, 154.530, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 26.6

The structure of Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Calcium atom in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus (pdb code 3lp9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus, PDB code: 3lp9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca310 b:15.5 occ:1.00 O A:ASP65 2.5 16.6 1.0 O A:ASN7 2.5 16.8 1.0 O A:ASP121 2.5 13.3 1.0 O A:ASP175 2.5 15.9 1.0 OD1 A:ASN7 2.6 14.7 1.0 O A:HOH232 2.9 15.0 1.0 C A:ASP121 3.5 14.2 1.0 CG A:ASN7 3.5 15.9 1.0 C A:ASN7 3.6 15.5 1.0 C A:ASP65 3.6 15.3 1.0 C A:ASP175 3.7 15.5 1.0 OG1 A:THR1 3.8 15.4 1.0 CA A:ASP121 3.8 14.2 1.0 CA A:ASN7 4.0 15.9 1.0 CB A:ASN7 4.4 16.3 1.0 CA A:ASP65 4.4 15.6 1.0 O A:ILE120 4.4 14.9 1.0 ND2 A:ASN7 4.4 15.4 1.0 CB A:ASP65 4.4 15.6 1.0 CA A:ASP175 4.5 15.2 1.0 N A:CYS66 4.6 15.4 1.0 CB A:ASP121 4.6 14.2 1.0 N A:ALA8 4.7 15.5 1.0 N A:ALA122 4.7 13.9 1.0 N A:ALA176 4.7 15.1 1.0 CA A:CYS66 4.8 14.9 1.0 CB A:CYS66 4.9 15.6 1.0 CA A:ALA176 4.9 15.4 1.0 O A:ALA174 5.0 15.0 1.0 CB A:THR1 5.0 14.9 1.0 N A:ASP121 5.0 14.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca311 b:15.6 occ:1.00 O B:ASP121 2.4 15.5 1.0 O B:ASP65 2.5 16.7 1.0 OD1 B:ASN7 2.5 12.3 1.0 O B:ASN7 2.6 16.0 1.0 O B:ASP175 2.7 16.3 1.0 O B:HOH308 2.9 14.5 1.0 C B:ASP121 3.4 15.6 1.0 CG2 B:THR1 3.5 18.0 1.0 CG B:ASN7 3.5 15.4 1.0 C B:ASP65 3.6 15.2 1.0 C B:ASN7 3.6 15.0 1.0 C B:ASP175 3.7 15.5 1.0 CA B:ASP121 3.8 15.5 1.0 CA B:ASN7 4.0 15.5 1.0 CA B:ASP65 4.2 15.6 1.0 CB B:ASP65 4.3 15.7 1.0 CB B:ASN7 4.4 14.6 1.0 CA B:ASP175 4.4 15.8 1.0 O B:ILE120 4.4 15.3 1.0 ND2 B:ASN7 4.4 15.6 1.0 N B:CYS66 4.6 15.5 1.0 CB B:ASP121 4.6 15.3 1.0 N B:ALA122 4.6 15.0 1.0 N B:ALA176 4.8 16.3 1.0 N B:ALA8 4.8 15.2 1.0 CA B:CYS66 4.8 15.1 1.0 CB B:CYS66 4.9 15.3 1.0 CB B:THR1 4.9 16.3 1.0 N B:ASP121 4.9 16.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca312 b:15.2 occ:1.00 O C:ASP175 2.5 15.9 1.0 O C:ASP121 2.5 14.1 1.0 O C:ASN7 2.5 17.2 1.0 O C:HOH317 2.6 16.0 1.0 O C:ASP65 2.6 16.4 1.0 OD1 C:ASN7 2.7 15.6 1.0 CG C:ASN7 3.5 16.1 1.0 C C:ASN7 3.6 15.5 1.0 C C:ASP121 3.6 15.2 1.0 C C:ASP175 3.7 15.5 1.0 OG1 C:THR1 3.7 15.5 1.0 C C:ASP65 3.7 15.5 1.0 CA C:ASN7 3.9 16.1 1.0 CA C:ASP121 4.1 15.1 1.0 ND2 C:ASN7 4.2 15.4 1.0 CB C:ASN7 4.3 15.3 1.0 CA C:ASP175 4.3 15.3 1.0 CA C:ASP65 4.3 15.3 1.0 CB C:ASP65 4.4 15.2 1.0 O C:HOH421 4.6 20.5 1.0 O C:ILE120 4.6 15.8 1.0 N C:CYS66 4.7 15.5 1.0 N C:ALA8 4.7 15.4 1.0 N C:ALA176 4.7 15.8 1.0 N C:ALA122 4.7 14.6 1.0 CB C:ASP121 4.8 15.5 1.0 CA C:CYS66 4.9 15.2 1.0 CB C:ASP175 4.9 15.9 1.0 CB C:CYS66 4.9 15.0 1.0 CB C:THR1 4.9 15.5 1.0 CA C:ALA176 5.0 15.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca313 b:15.6 occ:1.00 O D:ASP121 2.4 14.5 1.0 O D:ASN7 2.5 17.6 1.0 O D:ASP175 2.5 15.2 1.0 O D:ASP65 2.6 16.5 1.0 OD1 D:ASN7 2.7 16.5 1.0 O D:HOH446 2.7 16.1 1.0 CG D:ASN7 3.4 15.5 1.0 C D:ASP121 3.5 15.6 1.0 C D:ASN7 3.5 16.0 1.0 C D:ASP175 3.7 15.2 1.0 C D:ASP65 3.7 15.8 1.0 OG1 D:THR1 3.7 16.5 1.0 CA D:ASP121 3.9 15.6 1.0 CA D:ASN7 3.9 15.9 1.0 ND2 D:ASN7 4.0 16.4 1.0 CB D:ASN7 4.2 15.5 1.0 CA D:ASP65 4.3 15.5 1.0 CB D:ASP65 4.4 14.9 1.0 CA D:ASP175 4.4 15.7 1.0 O D:ILE120 4.4 16.0 1.0 CB D:ASP121 4.6 15.9 1.0 N D:ALA122 4.7 14.9 1.0 N D:CYS66 4.7 16.1 1.0 N D:ALA8 4.7 16.0 1.0 N D:ALA176 4.7 15.7 1.0 CB D:CYS66 4.9 15.9 1.0 CA D:CYS66 4.9 15.6 1.0 CB D:THR1 4.9 14.6 1.0 CA D:ALA176 5.0 15.6 1.0 OD1 D:ASP121 5.0 15.8 1.0

V.Gaur, I.A.Qureshi, A.Singh, V.Chanana, D.M.Salunke. Crystal Structure and Functional Insights of Hemopexin Fold Protein From Grass Pea Plant Physiol. V. 152 1842 2010.
ISSN: ISSN 0032-0889
PubMed: 20147493
DOI: 10.1104/PP.109.150680