Calcium in PDB 3dem: CUB1-Egf-CUB2 Domain of Human Masp-1/3

The structure of CUB1-Egf-CUB2 Domain of Human Masp-1/3, PDB code: 3dem was solved by C.Gaboriaud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.692, 110.232, 190.587, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.5

The binding sites of Calcium atom in the CUB1-Egf-CUB2 Domain of Human Masp-1/3 (pdb code 3dem). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the CUB1-Egf-CUB2 Domain of Human Masp-1/3, PDB code: 3dem:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the CUB1-Egf-CUB2 Domain of Human Masp-1/3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of CUB1-Egf-CUB2 Domain of Human Masp-1/3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:38.5 occ:1.00 OD1 A:ASN140 2.2 40.5 1.0 O A:VAL121 2.3 40.0 1.0 O A:HOH8005 2.4 39.9 1.0 O A:TYR141 2.5 40.1 1.0 O A:GLY144 2.6 40.6 1.0 OE1 A:GLU123 2.6 40.2 1.0 OD1 A:ASP120 2.7 40.0 1.0 OD2 A:ASP120 2.9 40.1 1.0 CG A:ASP120 3.1 40.3 1.0 CG A:ASN140 3.3 40.5 1.0 C A:VAL121 3.5 40.2 1.0 CD A:GLU123 3.5 40.2 1.0 C A:GLY144 3.6 40.5 1.0 C A:TYR141 3.7 40.3 1.0 OE2 A:GLU123 3.7 40.4 1.0 N A:GLY144 3.7 40.5 1.0 ND2 A:ASN140 3.7 40.3 1.0 N A:TYR141 4.0 40.4 1.0 CA A:GLY144 4.0 40.4 1.0 N A:GLY143 4.2 40.2 1.0 CA A:ASP122 4.3 40.4 1.0 N A:ASP122 4.3 40.3 1.0 N A:VAL121 4.3 40.2 1.0 N A:GLU123 4.4 40.3 1.0 CA A:VAL121 4.5 40.3 1.0 CA A:TYR141 4.5 40.4 1.0 C A:GLY143 4.5 40.4 1.0 CB A:ASN140 4.6 40.5 1.0 CB A:ASP120 4.6 40.1 1.0 O A:GLY36 4.7 40.4 1.0 N A:ILE142 4.7 40.3 1.0 N A:TYR145 4.7 40.6 1.0 CA A:ILE142 4.8 40.3 1.0 CA A:ASN140 4.8 40.6 1.0 C A:ASN140 4.8 40.6 1.0 C A:ILE142 4.8 40.3 1.0 CA A:GLY143 4.8 40.4 1.0 CB A:VAL121 4.9 40.3 1.0 CG A:GLU123 4.9 40.4 1.0 C A:ASP120 4.9 40.2 1.0 CB A:TYR145 4.9 40.5 1.0 C A:ASP122 5.0 40.3 1.0

Calcium binding site 2 out of 6 in the CUB1-Egf-CUB2 Domain of Human Masp-1/3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of CUB1-Egf-CUB2 Domain of Human Masp-1/3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5001 b:43.0 occ:1.00 OD1 A:ASP102 2.2 39.3 1.0 O A:HOH8097 2.3 41.2 1.0 OE1 A:GLU49 2.4 40.6 1.0 OD2 A:ASP57 2.5 40.0 1.0 OD1 A:ASP57 2.5 40.1 1.0 O A:SER104 2.5 42.2 1.0 O A:HOH8009 2.6 35.7 1.0 CG A:ASP57 2.8 40.3 1.0 CG A:ASP102 3.4 40.1 1.0 C A:SER104 3.4 42.4 1.0 CD A:GLU49 3.6 40.4 1.0 OD2 A:ASP102 4.0 40.3 1.0 N A:ASP102 4.0 40.4 1.0 N A:ASN105 4.2 42.6 1.0 OD1 A:ASN105 4.2 43.8 1.0 CA A:ASN105 4.3 42.8 1.0 CB A:ASP57 4.3 40.4 1.0 OE2 A:GLU49 4.3 40.5 1.0 CA A:SER104 4.3 42.3 1.0 N A:SER104 4.3 42.0 1.0 O A:ASP102 4.5 40.6 1.0 CB A:GLU49 4.5 40.3 1.0 O A:HOH8114 4.5 48.1 1.0 OG A:SER101 4.5 40.7 1.0 CB A:ASP102 4.5 40.4 1.0 CA A:ASP102 4.6 40.5 1.0 C A:ASP102 4.6 40.7 1.0 CB A:ASN105 4.6 42.8 1.0 CG A:ASN105 4.6 43.2 1.0 CG A:GLU49 4.6 40.3 1.0 CB A:SER104 4.7 42.3 1.0 OH A:TYR21 4.8 40.5 1.0 N A:ASP57 4.9 40.5 1.0 C A:SER101 4.9 40.4 1.0

Calcium binding site 3 out of 6 in the CUB1-Egf-CUB2 Domain of Human Masp-1/3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of CUB1-Egf-CUB2 Domain of Human Masp-1/3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca8001 b:32.6 occ:1.00 OE1 A:GLU216 2.3 40.5 1.0 O A:SER265 2.3 40.5 1.0 OD2 A:ASP226 2.3 40.0 1.0 O A:HOH8021 2.4 30.1 1.0 O A:HOH8002 2.4 31.5 1.0 OD1 A:ASP263 2.4 40.1 1.0 OD1 A:ASP226 2.8 39.8 1.0 CG A:ASP226 2.9 40.4 1.0 CG A:ASP263 3.4 40.4 1.0 CD A:GLU216 3.5 40.7 1.0 C A:SER265 3.5 40.4 1.0 CB A:GLU216 4.0 40.4 1.0 OD2 A:ASP263 4.0 40.4 1.0 O A:HOH8055 4.0 35.7 1.0 N A:ASP263 4.1 40.1 1.0 O A:HOH8004 4.3 32.7 1.0 OE2 A:GLU216 4.3 41.0 1.0 CG A:GLU216 4.3 40.4 1.0 O A:ASP263 4.4 40.1 1.0 N A:SER265 4.4 40.3 1.0 CA A:GLY266 4.4 40.5 1.0 OH A:TYR187 4.4 40.1 1.0 N A:GLY266 4.4 40.5 1.0 CB A:ASP226 4.4 40.3 1.0 CA A:SER265 4.5 40.4 1.0 CB A:ASP263 4.6 40.2 1.0 C A:ASP263 4.6 40.1 1.0 ND2 A:ASN268 4.6 39.5 1.0 CA A:ASP263 4.6 40.1 1.0 CE1 A:TYR187 4.6 40.3 1.0 CB A:TYR225 4.7 40.5 1.0 CZ A:TYR187 5.0 40.4 1.0

Calcium binding site 4 out of 6 in the CUB1-Egf-CUB2 Domain of Human Masp-1/3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of CUB1-Egf-CUB2 Domain of Human Masp-1/3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4001 b:37.9 occ:1.00 O B:HOH7008 2.4 34.7 1.0 OD1 B:ASN140 2.4 40.4 1.0 O B:VAL121 2.4 40.2 1.0 O B:GLY144 2.5 40.8 1.0 O B:TYR141 2.5 40.1 1.0 OE1 B:GLU123 2.5 40.4 1.0 OD1 B:ASP120 2.7 40.1 1.0 OD2 B:ASP120 3.1 40.4 1.0 CG B:ASP120 3.3 40.4 1.0 C B:GLY144 3.4 40.5 1.0 CD B:GLU123 3.4 40.2 1.0 CG B:ASN140 3.4 40.7 1.0 N B:GLY144 3.5 40.5 1.0 OE2 B:GLU123 3.5 40.5 1.0 C B:VAL121 3.6 40.2 1.0 C B:TYR141 3.7 40.3 1.0 CA B:GLY144 3.8 40.4 1.0 ND2 B:ASN140 3.9 40.5 1.0 N B:GLY143 4.0 40.2 1.0 N B:TYR141 4.1 40.4 1.0 C B:GLY143 4.3 40.5 1.0 N B:VAL121 4.4 40.2 1.0 N B:GLU123 4.5 40.3 1.0 CA B:ASP122 4.5 40.4 1.0 N B:ASP122 4.5 40.2 1.0 N B:TYR145 4.5 40.5 1.0 CA B:TYR141 4.6 40.3 1.0 CA B:VAL121 4.6 40.2 1.0 O B:GLY36 4.6 40.2 1.0 CA B:GLY143 4.7 40.4 1.0 N B:ILE142 4.7 40.4 1.0 CB B:ASN140 4.7 40.5 1.0 CB B:ASP120 4.8 40.1 1.0 C B:ILE142 4.8 40.4 1.0 CA B:ILE142 4.8 40.3 1.0 CG B:GLU123 4.8 40.4 1.0 CB B:TYR145 4.8 40.4 1.0 CA B:ASN140 4.9 40.6 1.0 CB B:VAL121 4.9 40.4 1.0 C B:ASN140 4.9 40.5 1.0

Calcium binding site 5 out of 6 in the CUB1-Egf-CUB2 Domain of Human Masp-1/3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of CUB1-Egf-CUB2 Domain of Human Masp-1/3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6001 b:52.0 occ:1.00 OD1 B:ASP102 2.4 40.7 1.0 OD2 B:ASP57 2.4 40.2 1.0 OE1 B:GLU49 2.5 40.5 1.0 O B:SER104 2.9 41.7 1.0 CG B:ASP57 3.1 40.4 1.0 OD1 B:ASP57 3.2 40.1 1.0 CG B:ASP102 3.4 40.6 1.0 CD B:GLU49 3.5 40.4 1.0 C B:SER104 3.8 41.7 1.0 OD2 B:ASP102 3.8 40.0 1.0 CB B:GLU49 4.1 40.3 1.0 CA B:ASN105 4.2 41.8 1.0 OE2 B:GLU49 4.3 40.5 1.0 CG B:GLU49 4.3 40.4 1.0 N B:ASN105 4.3 41.8 1.0 OH B:TYR21 4.3 40.5 1.0 N B:ASP102 4.5 40.5 1.0 CB B:ASP57 4.5 40.5 1.0 CB B:ASN105 4.5 41.7 1.0 ND2 B:ASN105 4.6 41.4 1.0 CB B:ASP102 4.6 40.7 1.0 N B:SER104 4.6 41.4 1.0 CE1 B:TYR21 4.7 40.5 1.0 OG B:SER101 4.7 40.7 1.0 CA B:SER104 4.8 41.6 1.0 CG B:ASN105 4.8 41.7 1.0 CA B:ASP102 4.9 40.7 1.0 C B:ASP102 4.9 40.8 1.0

Calcium binding site 6 out of 6 in the CUB1-Egf-CUB2 Domain of Human Masp-1/3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of CUB1-Egf-CUB2 Domain of Human Masp-1/3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca7001 b:30.5 occ:1.00 O B:SER265 2.2 40.6 1.0 O B:HOH7020 2.3 29.7 1.0 OD1 B:ASP263 2.3 40.1 1.0 OE1 B:GLU216 2.4 40.7 1.0 OD2 B:ASP226 2.5 40.2 1.0 O B:HOH7016 2.6 32.9 1.0 OD1 B:ASP226 2.8 39.8 1.0 CG B:ASP226 3.0 40.3 1.0 CG B:ASP263 3.4 40.3 1.0 C B:SER265 3.4 40.4 1.0 CD B:GLU216 3.6 40.7 1.0 OD2 B:ASP263 4.0 40.4 1.0 N B:ASP263 4.0 40.1 1.0 CB B:GLU216 4.1 40.5 1.0 N B:SER265 4.2 40.3 1.0 O B:ASP263 4.3 40.0 1.0 O B:HOH7074 4.3 38.7 1.0 O B:HOH7010 4.4 34.9 1.0 N B:GLY266 4.4 40.5 1.0 CA B:SER265 4.4 40.5 1.0 CA B:GLY266 4.4 40.5 1.0 OE2 B:GLU216 4.4 41.0 1.0 C B:ASP263 4.4 40.1 1.0 CB B:ASP226 4.4 40.4 1.0 CB B:ASP263 4.5 40.3 1.0 CG B:GLU216 4.5 40.4 1.0 CA B:ASP263 4.5 40.2 1.0 OH B:TYR187 4.5 40.2 1.0 CE1 B:TYR187 4.6 40.2 1.0 ND2 B:ASN268 4.7 39.5 1.0 CB B:TYR225 4.8 40.5 1.0 C B:SER262 5.0 40.3 1.0

F.Teillet, C.Gaboriaud, M.Lacroix, L.Martin, G.J.Arlaud, N.M.Thielens. Crystal Structure of the CUB1-Egf-CUB2 Domain of Human Masp-1/3 and Identification of Its Interaction Sites with Mannan-Binding Lectin and Ficolins J.Biol.Chem. V. 283 25715 2008.
ISSN: ISSN 0021-9258
PubMed: 18596036
DOI: 10.1074/JBC.M803551200