Calcium in PDB 2d39: Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain

The structure of Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain, PDB code: 2d39 was solved by M.Tanio, S.Kondo, S.Sugio, T.Kohno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.160, 117.450, 55.190, 90.00, 99.88, 90.00
R / Rfree (%)	20.9 / 24

The binding sites of Calcium atom in the Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain (pdb code 2d39). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain, PDB code: 2d39:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1401 b:20.5 occ:1.00 OD2 A:ASP264 2.5 13.9 1.0 OD2 A:ASP262 2.5 18.7 1.0 O A:SER266 2.5 21.0 1.0 O A:HOH1402 2.6 15.0 1.0 O A:SER268 2.6 21.5 1.0 O A:HOH1403 2.7 25.3 1.0 OD1 A:ASP262 2.8 17.3 1.0 CG A:ASP262 3.0 18.9 1.0 CG A:ASP264 3.2 17.4 1.0 OD1 A:ASP264 3.3 18.9 1.0 C A:SER266 3.5 22.2 1.0 C A:SER268 3.6 23.3 1.0 N A:SER266 4.0 21.4 1.0 O A:ASP264 4.1 17.5 1.0 O A:HOH1435 4.1 21.7 1.0 CA A:SER266 4.2 21.0 1.0 CA A:ASN269 4.2 20.0 1.0 C A:SER267 4.3 22.1 1.0 N A:SER268 4.3 22.7 1.0 N A:ASN269 4.3 22.1 1.0 O A:HOH1485 4.4 28.9 1.0 C A:ASP264 4.4 16.5 1.0 CB A:ASP262 4.4 17.1 1.0 N A:SER267 4.5 22.0 1.0 CB A:SER266 4.5 22.5 1.0 O A:SER267 4.5 21.8 1.0 CB A:ASP264 4.5 16.6 1.0 CA A:SER268 4.6 24.1 1.0 CA A:SER267 4.7 21.6 1.0 N A:CYS270 4.7 18.5 1.0 N A:ASP264 4.8 15.4 1.0 CA A:ASP264 4.8 16.2 1.0 C A:VAL265 4.9 21.2 1.0 N A:VAL265 5.0 17.3 1.0

Calcium binding site 2 out of 2 in the Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Human M-Ficolin Fibrinogen-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2401 b:22.6 occ:0.50 O C:HOH2402 2.6 26.0 1.0 OD1 C:ASP262 2.7 47.1 1.0 O C:SER268 2.7 50.9 1.0 O C:SER266 2.8 47.8 1.0 OD1 C:ASP264 2.9 46.5 1.0 OD2 C:ASP262 2.9 45.5 1.0 CG C:ASP262 3.1 45.1 1.0 OD2 C:ASP264 3.3 45.0 1.0 CG C:ASP264 3.3 44.3 1.0 C C:SER266 3.6 48.5 1.0 C C:SER268 3.8 52.3 1.0 O C:ASP264 3.9 40.6 1.0 N C:SER266 4.1 46.0 1.0 N C:SER268 4.2 52.6 1.0 C C:SER267 4.2 52.1 1.0 CA C:SER266 4.3 47.3 1.0 N C:SER267 4.4 50.0 1.0 C C:ASP264 4.4 41.0 1.0 CA C:SER267 4.5 51.7 1.0 N C:ASP264 4.5 37.8 1.0 CB C:SER266 4.6 47.4 1.0 CB C:ASP262 4.6 43.6 1.0 CA C:SER268 4.6 52.5 1.0 N C:ASN269 4.6 51.6 1.0 CB C:ASP264 4.6 40.8 1.0 O C:SER267 4.7 52.2 1.0 CA C:ASN269 4.7 50.9 1.0 CA C:ASP264 4.8 39.9 1.0 OG C:SER266 4.9 48.0 1.0

M.Tanio, S.Kondo, S.Sugio, T.Kohno. Trivalent Recognition Unit of Innate Immunity System; Crystal Structure of Trimeric Human M-Ficolin Fibrinogen-Like Domain J.Biol.Chem. V. 282 3889 2007.
ISSN: ISSN 0021-9258
PubMed: 17148457
DOI: 10.1074/JBC.M608627200