Calcium in PDB 5lf2: Crystal Structure of Laminin BETA2 LE5-Lf-LE6

The structure of Crystal Structure of Laminin BETA2 LE5-Lf-LE6, PDB code: 5lf2 was solved by D.Pulido, E.Hohenester, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.88 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.320, 55.350, 111.340, 90.00, 119.38, 90.00
R / Rfree (%)	17.8 / 21

The structure of Crystal Structure of Laminin BETA2 LE5-Lf-LE6 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Laminin BETA2 LE5-Lf-LE6 (pdb code 5lf2). 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 Laminin BETA2 LE5-Lf-LE6, PDB code: 5lf2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Laminin BETA2 LE5-Lf-LE6


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 Laminin BETA2 LE5-Lf-LE6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:31.4 occ:1.00 OD1 A:ASP719 2.3 31.0 1.0 O A:GLY601 2.4 30.1 1.0 OE1 A:GLU573 2.4 34.4 1.0 O A:THR598 2.4 31.6 1.0 OE2 A:GLU575 2.5 36.1 1.0 OE1 A:GLU575 2.6 34.3 1.0 O A:ASP719 2.6 30.4 1.0 CD A:GLU575 2.9 36.4 1.0 HA A:ASP719 3.3 36.2 1.0 C A:ASP719 3.4 29.4 1.0 C A:GLY601 3.5 31.6 1.0 CG A:ASP719 3.5 31.2 1.0 CD A:GLU573 3.5 35.0 1.0 H A:GLY601 3.5 42.1 1.0 C A:THR598 3.5 34.1 1.0 H A:THR598 3.7 39.0 1.0 HB3 A:GLU573 3.7 39.2 1.0 HA3 A:GLY599 3.8 44.4 1.0 HG1 A:THR598 3.8 38.0 1.0 CA A:ASP719 3.8 30.2 1.0 HB3 A:SER720 3.8 35.5 1.0 HA A:PHE602 4.0 41.5 1.0 HA A:GLU573 4.1 38.2 1.0 H A:ALA574 4.1 36.7 1.0 N A:GLY601 4.2 35.0 1.0 CB A:ASP719 4.2 30.6 1.0 CA A:GLY601 4.2 33.2 1.0 HB2 A:TRP597 4.2 38.0 1.0 HD1 A:TRP597 4.2 41.2 1.0 OE2 A:GLU573 4.3 35.0 1.0 N A:THR598 4.3 32.5 1.0 H A:GLU575 4.3 42.1 1.0 HA2 A:GLY601 4.3 39.8 1.0 N A:GLY599 4.4 35.9 1.0 CB A:GLU573 4.4 32.6 1.0 CA A:GLY599 4.4 37.0 1.0 CG A:GLU575 4.4 37.2 1.0 OG1 A:THR598 4.4 31.7 1.0 N A:PHE602 4.4 35.0 1.0 CG A:GLU573 4.4 34.0 1.0 CA A:THR598 4.5 32.4 1.0 OD2 A:ASP719 4.5 28.8 1.0 N A:SER720 4.6 28.9 1.0 HG3 A:GLU573 4.6 40.8 1.0 CA A:GLU573 4.7 31.8 1.0 HB2 A:ASP719 4.7 36.7 1.0 CA A:PHE602 4.7 34.6 1.0 N A:ALA574 4.7 30.6 1.0 HG2 A:GLU575 4.7 44.6 1.0 CB A:SER720 4.7 29.6 1.0 C A:GLY599 4.7 37.3 1.0 HB3 A:ALA574 4.8 40.5 1.0 HG3 A:GLU575 4.8 44.6 1.0 H A:VAL600 4.9 48.1 1.0 HB3 A:GLU575 5.0 45.8 1.0 N A:VAL600 5.0 40.1 1.0 HB3 A:ASP719 5.0 36.7 1.0 HA A:SER720 5.0 34.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Laminin BETA2 LE5-Lf-LE6


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 Laminin BETA2 LE5-Lf-LE6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:30.6 occ:1.00 OE1 B:GLU573 2.3 33.7 1.0 OD1 B:ASP719 2.3 29.4 1.0 O B:GLY601 2.4 33.4 1.0 O B:THR598 2.4 31.4 1.0 OE2 B:GLU575 2.5 33.7 1.0 OE1 B:GLU575 2.5 32.5 1.0 O B:ASP719 2.6 30.6 1.0 CD B:GLU575 2.8 33.5 1.0 HA B:ASP719 3.3 35.4 1.0 C B:ASP719 3.5 30.2 1.0 H B:GLY601 3.5 45.8 1.0 CD B:GLU573 3.5 34.3 1.0 C B:GLY601 3.5 34.3 1.0 C B:THR598 3.5 32.3 1.0 CG B:ASP719 3.6 30.2 1.0 H B:THR598 3.7 39.0 1.0 HA3 B:GLY599 3.7 43.2 1.0 HB3 B:GLU573 3.7 37.8 1.0 HB3 B:SER720 3.8 34.4 1.0 CA B:ASP719 3.8 29.5 1.0 HA B:GLU573 4.0 37.6 1.0 H B:ALA574 4.1 36.1 1.0 HA B:PHE602 4.1 41.1 1.0 N B:GLY601 4.2 38.1 1.0 HB2 B:TRP597 4.2 40.7 1.0 CB B:ASP719 4.3 29.0 1.0 OE2 B:GLU573 4.3 34.6 1.0 H B:GLU575 4.3 36.5 1.0 CA B:GLY601 4.3 34.8 1.0 N B:THR598 4.3 32.5 1.0 CG B:GLU575 4.4 34.9 1.0 N B:GLY599 4.4 34.6 1.0 CB B:GLU573 4.4 31.5 1.0 CA B:GLY599 4.4 36.0 1.0 OG1 B:THR598 4.4 34.2 1.0 HD1 B:TRP597 4.4 44.1 1.0 CG B:GLU573 4.4 33.5 1.0 N B:PHE602 4.5 35.1 1.0 CA B:THR598 4.5 33.2 1.0 HA2 B:GLY601 4.5 41.7 1.0 OD2 B:ASP719 4.5 29.7 1.0 N B:SER720 4.6 28.6 1.0 HG2 B:GLU575 4.6 41.8 1.0 HG3 B:GLU573 4.6 40.1 1.0 CA B:GLU573 4.6 31.4 1.0 N B:ALA574 4.7 30.1 1.0 CB B:SER720 4.7 28.7 1.0 HB2 B:ASP719 4.7 34.8 1.0 C B:GLY599 4.7 36.9 1.0 HG3 B:GLU575 4.8 41.8 1.0 CA B:PHE602 4.8 34.2 1.0 H B:VAL600 4.8 45.0 1.0 HB3 B:ALA574 4.8 38.0 1.0 N B:VAL600 4.9 37.5 1.0 HA B:SER720 5.0 33.1 1.0

D.Pulido, D.C.Briggs, J.Hua, E.Hohenester. Crystallographic Analysis of the Laminin Beta 2 Short Arm Reveals How the Lf Domain Is Inserted Into A Regular Array of Le Domains. Matrix Biol. V.7-58 204 2017.
ISSN: ISSN 1569-1802
PubMed: 27425256
DOI: 10.1016/J.MATBIO.2016.06.006