Calcium in PDB 5ckq: CUB1-Egf-CUB2 Domains of Rat Masp-1

The structure of CUB1-Egf-CUB2 Domains of Rat Masp-1, PDB code: 5ckq 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)	76.36 / 3.70
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	152.710, 152.710, 152.710, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 29.4

The structure of CUB1-Egf-CUB2 Domains of Rat Masp-1 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

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

Calcium binding site 1 out of 3 in the CUB1-Egf-CUB2 Domains of Rat Masp-1


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 Domains of Rat Masp-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:0.1 occ:1.00 O A:SER265 2.4 0.5 1.0 OD2 A:ASP226 2.4 0.8 1.0 OD1 A:ASP263 2.8 0.8 1.0 OE1 A:GLU216 2.9 0.9 1.0 OH A:TYR187 3.1 0.2 1.0 C A:SER265 3.4 0.8 1.0 CG A:ASP226 3.4 0.7 1.0 CE1 A:TYR187 3.5 0.9 1.0 CA A:GLY266 3.6 0.0 1.0 CZ A:TYR187 3.7 0.9 1.0 OD1 A:ASP226 3.7 0.6 1.0 CD A:GLU216 3.8 0.9 1.0 CB A:GLU216 3.9 0.8 1.0 N A:GLY266 3.9 0.8 1.0 OD1 A:ASN268 4.0 0.2 1.0 CG A:ASP263 4.0 0.7 1.0 C A:GLY266 4.1 0.0 1.0 O A:GLY266 4.1 0.7 1.0 CG A:GLU216 4.5 0.9 1.0 N A:ASP263 4.6 0.7 1.0 CA A:SER265 4.6 0.6 1.0 O A:ASP263 4.6 0.8 1.0 OE2 A:GLU216 4.6 0.3 1.0 OD2 A:ASP263 4.7 0.5 1.0 CD1 A:TYR187 4.7 0.2 1.0 CB A:ASP226 4.8 0.4 1.0 N A:SER265 4.8 0.5 1.0 CG A:ASN268 4.8 0.7 1.0 CB A:ASN268 5.0 0.8 1.0 N A:GLU267 5.0 0.3 1.0

Calcium binding site 2 out of 3 in the CUB1-Egf-CUB2 Domains of Rat Masp-1


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 Domains of Rat Masp-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:0.7 occ:1.00 OD1 A:ASP120 2.4 0.3 1.0 OD1 A:ASN140 2.6 0.1 1.0 O A:VAL121 2.6 0.5 1.0 O A:TYR141 2.7 0.1 1.0 N A:GLY144 2.7 0.8 1.0 O A:GLY144 2.7 0.1 1.0 OE1 A:GLU123 3.0 0.9 1.0 CG A:ASP120 3.2 0.4 1.0 C A:GLY144 3.2 0.5 1.0 CA A:GLY144 3.2 0.3 1.0 OD2 A:ASP120 3.3 0.7 1.0 N A:GLY143 3.5 0.5 1.0 OE2 A:GLU123 3.6 0.1 1.0 CD A:GLU123 3.7 0.5 1.0 CG A:ASN140 3.7 0.2 1.0 C A:GLY143 3.8 0.3 1.0 C A:VAL121 3.8 0.7 1.0 C A:TYR141 3.9 1.0 1.0 CA A:GLY143 4.1 0.8 1.0 N A:VAL121 4.2 0.2 1.0 C A:ILE142 4.3 0.4 1.0 ND2 A:ASN140 4.3 0.3 1.0 N A:TYR145 4.4 0.6 1.0 CA A:ILE142 4.5 0.8 1.0 CA A:VAL121 4.5 0.9 1.0 N A:TYR141 4.5 0.0 1.0 N A:ILE142 4.6 0.4 1.0 CB A:ASP120 4.6 0.9 1.0 N A:ASP122 4.8 0.0 1.0 O A:GLY143 4.8 0.1 1.0 CB A:VAL121 4.9 0.1 1.0 C A:ASP120 4.9 0.6 1.0 CA A:TYR141 4.9 0.7 1.0 CB A:ASN140 4.9 0.3 1.0 CA A:ASP122 4.9 0.9 1.0

Calcium binding site 3 out of 3 in the CUB1-Egf-CUB2 Domains of Rat Masp-1


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 Domains of Rat Masp-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:0.1 occ:1.00 OE1 A:GLU49 2.6 0.3 1.0 OD1 A:ASP102 2.6 1.0 1.0 O A:SER104 2.6 0.2 1.0 OD1 A:ASN105 2.7 0.5 1.0 OD1 A:ASP57 2.8 0.8 1.0 C A:SER104 3.0 0.1 1.0 OD2 A:ASP57 3.0 0.5 1.0 CG A:ASP57 3.3 0.0 1.0 N A:ASN105 3.5 0.7 1.0 OG A:SER101 3.5 0.5 1.0 N A:SER104 3.5 0.4 1.0 CD A:GLU49 3.7 0.2 1.0 CA A:SER104 3.7 0.3 1.0 CG A:ASP102 3.8 0.2 1.0 CA A:ASN105 3.8 0.7 1.0 CG A:ASN105 3.8 0.5 1.0 OE2 A:GLU49 4.1 0.1 1.0 N A:PHE103 4.2 0.9 1.0 N A:ASP102 4.3 0.8 1.0 OD2 A:ASP102 4.3 0.0 1.0 C A:PHE103 4.4 0.8 1.0 CB A:ASN105 4.4 0.8 1.0 CB A:SER101 4.7 1.0 1.0 C A:SER101 4.8 0.9 1.0 CB A:ASP57 4.8 0.9 1.0 OH A:TYR22 4.8 0.3 1.0 CA A:SER101 4.8 0.9 1.0 ND2 A:ASN105 4.9 0.8 1.0 CG A:GLU49 4.9 0.6 1.0 CB A:GLU49 4.9 0.8 1.0 CA A:PHE103 4.9 0.2 1.0 CB A:ASP102 5.0 0.4 1.0 CA A:ASP102 5.0 1.0 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