Calcium in PDB 5ckm: The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+

The structure of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+, PDB code: 5ckm was solved by R.Nan, C.M.Furze, D.W.Wright, J.Gor, R.Wallis, S.J.Perkins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.90 / 2.73
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.900, 119.390, 104.020, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.6

The binding sites of Calcium atom in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ (pdb code 5ckm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+, PDB code: 5ckm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:14.2 occ:1.00 OE2 A:GLU48 2.3 28.6 1.0 OD1 A:ASP101 2.4 28.9 1.0 OD2 A:ASP56 2.4 41.3 1.0 OD1 A:ASN104 2.4 28.4 1.0 O A:HOH479 2.4 9.8 1.0 O A:SER103 2.5 36.0 1.0 OD1 A:ASP56 2.6 44.6 1.0 CG A:ASP56 2.8 34.3 1.0 CG A:ASN104 3.3 29.3 1.0 CG A:ASP101 3.5 29.8 1.0 C A:SER103 3.5 33.9 1.0 CD A:GLU48 3.5 29.9 1.0 ND2 A:ASN104 3.8 31.1 1.0 OD2 A:ASP101 4.1 31.3 1.0 N A:ASP101 4.1 28.3 1.0 CB A:GLU48 4.2 26.8 1.0 CB A:ASP56 4.2 21.6 1.0 N A:ASN104 4.2 34.6 1.0 OE1 A:GLU48 4.3 32.1 1.0 CA A:ASN104 4.3 33.9 1.0 N A:SER103 4.3 34.5 1.0 CB A:ASN104 4.4 32.0 1.0 CG A:GLU48 4.5 29.1 1.0 CA A:SER103 4.5 35.6 1.0 OH A:TYR20 4.5 22.5 1.0 C A:ASP101 4.6 41.3 1.0 CB A:ASP101 4.7 29.5 1.0 O A:ASP101 4.7 29.6 1.0 CA A:ASP101 4.7 28.4 1.0 CB A:SER100 4.8 22.6 1.0 CB A:TYR55 4.8 28.3 1.0 N A:ASP56 4.9 23.5 1.0 O A:HOH506 4.9 20.3 1.0 OD1 A:ASN22 4.9 38.3 1.0 CE1 A:TYR20 4.9 22.5 1.0 C A:SER100 5.0 24.6 1.0

Calcium binding site 2 out of 3 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:37.4 occ:1.00 OD1 A:ASN139 2.3 20.4 1.0 O A:VAL120 2.4 24.0 1.0 O A:HOH464 2.4 20.4 1.0 O A:TYR140 2.4 34.1 1.0 O A:GLY143 2.5 19.0 1.0 OD1 A:ASP119 2.6 26.9 1.0 OE1 A:GLU122 2.8 27.4 1.0 OD2 A:ASP119 2.9 29.1 1.0 CG A:ASP119 3.1 27.1 1.0 N A:GLY143 3.3 20.4 1.0 C A:GLY143 3.4 19.5 1.0 CG A:ASN139 3.4 19.9 1.0 C A:TYR140 3.6 30.3 1.0 C A:VAL120 3.6 26.1 1.0 CD A:GLU122 3.8 24.7 1.0 CA A:GLY143 3.8 20.4 1.0 N A:TYR140 3.9 21.6 1.0 N A:GLY142 3.9 20.6 1.0 OE2 A:GLU122 4.0 24.9 1.0 ND2 A:ASN139 4.1 20.1 1.0 N A:VAL120 4.3 26.4 1.0 C A:GLY142 4.3 21.5 1.0 CA A:TYR140 4.4 17.2 1.0 N A:LEU141 4.5 23.1 1.0 CA A:VAL120 4.5 27.9 1.0 N A:ASP121 4.5 27.3 1.0 N A:TYR144 4.5 19.5 1.0 C A:LEU141 4.5 19.6 1.0 CA A:ASP121 4.6 26.1 1.0 O A:GLY35 4.6 23.5 1.0 CA A:GLY142 4.6 21.6 1.0 CB A:ASN139 4.6 19.4 1.0 CA A:LEU141 4.6 19.1 1.0 CB A:ASP119 4.6 28.2 1.0 N A:GLU122 4.7 26.0 1.0 C A:ASN139 4.7 17.3 1.0 CA A:ASN139 4.8 18.1 1.0 CB A:VAL120 5.0 29.3 1.0

Calcium binding site 3 out of 3 in the The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The CUB1-Egf-CUB2 Domains of Rat Mbl-Associated Serine Protease-2 (Masp-2) Bound to CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:25.9 occ:1.00 OD1 A:ASP262 2.2 37.6 1.0 O A:HOH463 2.5 13.5 1.0 O A:SER264 2.5 38.8 1.0 OD2 A:ASP225 2.6 48.7 1.0 OE1 A:GLU215 2.7 36.7 1.0 OD1 A:ASP225 2.7 32.9 1.0 CG A:ASP225 3.0 38.5 1.0 CG A:ASP262 3.4 40.0 1.0 C A:SER264 3.6 40.6 1.0 O A:HOH468 3.8 21.5 1.0 CD A:GLU215 3.9 38.6 1.0 N A:ASP262 4.0 43.9 1.0 OD2 A:ASP262 4.1 44.7 1.0 CE1 A:TYR186 4.2 27.8 1.0 OH A:TYR186 4.2 28.0 1.0 O A:ASP262 4.2 42.2 1.0 CA A:GLY265 4.3 38.9 1.0 N A:GLY265 4.4 40.8 1.0 N A:SER264 4.4 42.9 1.0 CB A:GLU215 4.4 34.2 1.0 C A:ASP262 4.4 40.3 1.0 CA A:ASP262 4.5 42.1 1.0 CB A:ASP262 4.5 41.0 1.0 CB A:ASP225 4.6 29.8 1.0 CZ A:TYR186 4.6 27.1 1.0 CA A:SER264 4.6 44.8 1.0 OE2 A:GLU215 4.7 41.1 1.0 CB A:THR261 4.8 31.4 1.0 CG A:GLU215 4.8 36.9 1.0 C A:THR261 4.9 35.5 1.0 ND1 A:HIS267 5.0 34.0 1.0 C A:GLY265 5.0 37.6 1.0 CB A:TYR224 5.0 38.6 1.0

R.Nan, C.M.Furze, D.W.Wright, J.Gor, R.Wallis, S.J.Perkins. Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 Provides Insight on Lectin Pathway Activation. Structure V. 25 364 2017.
ISSN: ISSN 1878-4186
PubMed: 28111019
DOI: 10.1016/J.STR.2016.12.014