Calcium in PDB 3a4u: Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53

The structure of Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53, PDB code: 3a4u was solved by M.Nishio, Y.Kamiya, T.Mizushima, S.Wakatsuki, H.Sasakawa, K.Yamamoto, S.Uchiyama, M.Noda, A.R.Mckay, K.Fukui, H.P.Hauri, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.81 / 1.84
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.410, 59.410, 198.842, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 20

The binding sites of Calcium atom in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 (pdb code 3a4u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53, PDB code: 3a4u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


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 MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca286 b:13.8 occ:1.00 OD1 A:ASP181 2.3 15.3 1.0 O A:PHE154 2.3 15.6 1.0 OD1 A:ASN156 2.3 17.2 1.0 O A:HOH4 2.4 12.2 1.0 OD1 A:ASP152 2.4 13.6 1.0 O A:HOH14 2.5 14.6 1.0 OD2 A:ASP152 2.5 14.8 1.0 CG A:ASP152 2.8 13.4 1.0 CG A:ASP181 3.3 16.7 1.0 CG A:ASN156 3.5 18.8 1.0 C A:PHE154 3.5 16.4 1.0 OD2 A:ASP181 4.0 18.3 1.0 N A:ASN156 4.1 18.4 1.0 CB A:ASN156 4.1 19.0 1.0 CB A:ASP181 4.2 16.7 1.0 CA A:PHE154 4.2 16.2 1.0 N A:PHE154 4.3 15.5 1.0 CB A:ASP152 4.3 12.0 1.0 CB A:PHE154 4.4 16.8 1.0 CA A:ASP181 4.4 16.9 1.0 O A:HIS178 4.5 20.5 1.0 ND2 A:ASN162 4.6 17.4 1.0 N A:ASP155 4.6 16.7 1.0 ND2 A:ASN156 4.6 18.6 1.0 OH A:TYR176 4.6 15.1 1.0 NE2 A:HIS178 4.7 27.7 1.0 CA A:ASN156 4.7 19.2 1.0 CZ A:PHE138 4.8 14.2 1.0 CE1 A:HIS178 4.8 27.8 1.0 CD2 A:PHE154 4.8 18.7 1.0 OD2 A:ASP121 4.8 22.8 1.0 CA A:ASP155 4.9 17.4 1.0 O A:ASP121 4.9 14.8 1.0 O A:HOH9 5.0 15.2 1.0 C A:ASP155 5.0 18.0 1.0 N A:ASP181 5.0 17.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


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 MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca287 b:18.3 occ:1.00 OD2 A:ASP181 2.4 18.3 1.0 OD1 A:ASN161 2.4 19.5 1.0 OD1 A:ASN162 2.4 16.1 1.0 OD1 A:ASP155 2.4 17.4 1.0 O A:HOH308 2.5 20.2 1.0 O A:HOH30 2.5 21.1 1.0 OD1 A:ASP157 2.5 22.9 1.0 CG A:ASN161 3.3 20.9 1.0 CG A:ASP181 3.5 16.7 1.0 CG A:ASN162 3.5 18.2 1.0 CG A:ASP157 3.5 22.5 1.0 CG A:ASP155 3.6 18.2 1.0 ND2 A:ASN161 3.8 22.1 1.0 OD2 A:ASP157 3.9 22.8 1.0 CB A:ASP181 3.9 16.7 1.0 ND2 A:ASN162 3.9 17.4 1.0 CA A:ASP155 4.0 17.4 1.0 CB A:ASP155 4.2 17.5 1.0 CB A:LYS159 4.3 25.6 1.0 O A:ASN161 4.3 19.9 1.0 O A:HOH23 4.4 20.0 1.0 C A:ASN161 4.4 20.2 1.0 N A:LYS159 4.4 24.9 1.0 C A:ASP155 4.5 18.0 1.0 OD1 A:ASP181 4.5 15.3 1.0 OD2 A:ASP155 4.5 20.1 1.0 N A:ASN161 4.6 22.2 1.0 N A:ASP157 4.6 21.0 1.0 N A:ASN156 4.6 18.4 1.0 CB A:ASN161 4.6 21.0 1.0 CA A:ASN161 4.8 21.1 1.0 CB A:ASN162 4.8 18.1 1.0 CA A:LYS159 4.8 25.4 1.0 N A:ASN162 4.8 19.1 1.0 CB A:ASP157 4.9 21.8 1.0 N A:GLY158 5.0 23.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca147 b:14.1 occ:1.00 O B:LEU87 2.3 15.7 1.0 OD1 B:ASP81 2.3 15.3 1.0 O B:HOH159 2.4 13.1 1.0 OD1 B:ASP83 2.4 14.6 1.0 OD1 B:ASN85 2.4 15.2 1.0 OE1 B:GLU92 2.5 13.6 1.0 OE2 B:GLU92 2.5 13.7 1.0 CD B:GLU92 2.8 13.2 1.0 CG B:ASP83 3.3 16.6 1.0 CG B:ASN85 3.4 15.7 1.0 C B:LEU87 3.5 16.0 1.0 CG B:ASP81 3.5 16.7 1.0 OD2 B:ASP83 3.7 16.9 1.0 ND2 B:ASN85 3.9 16.2 1.0 CA B:ASP81 4.1 16.9 1.0 N B:LEU87 4.2 16.4 1.0 CB B:ASP81 4.3 16.6 1.0 N B:ASN85 4.3 16.4 1.0 CA B:LEU87 4.3 16.1 1.0 CG B:GLU92 4.4 13.1 1.0 N B:LEU88 4.4 15.4 1.0 CA B:LEU88 4.4 14.9 1.0 OD2 B:ASP81 4.4 17.3 1.0 N B:ASP83 4.5 16.9 1.0 C B:ASP81 4.5 16.8 1.0 OD2 B:ASP89 4.5 16.2 1.0 CB B:ASN85 4.6 16.4 1.0 N B:GLY84 4.6 16.7 1.0 N B:TYR82 4.6 16.9 1.0 CB B:ASP83 4.7 16.8 1.0 CB B:LEU87 4.7 16.1 1.0 O B:HOH150 4.8 16.2 1.0 N B:ASP89 4.8 13.8 1.0 CA B:ASN85 4.8 16.5 1.0 N B:ASN86 4.9 16.9 1.0 CA B:ASP83 4.9 16.9 1.0 C B:LEU88 5.0 14.6 1.0 C B:ASP83 5.0 17.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of MCFD2 in Complex with Carbohydrate Recognition Domain of Ergic-53 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca148 b:22.0 occ:1.00 OD1 B:ASP129 2.4 20.8 1.0 O B:HOH152 2.4 20.7 1.0 OD1 B:ASP133 2.4 18.8 1.0 OD1 B:ASN131 2.4 26.2 1.0 O B:TYR135 2.4 17.6 1.0 O B:HOH154 2.5 22.6 1.0 O B:HOH163 2.7 24.1 1.0 CG B:ASP133 3.3 20.4 1.0 CG B:ASP129 3.4 22.6 1.0 CG B:ASN131 3.5 26.1 1.0 C B:TYR135 3.5 17.8 1.0 OD2 B:ASP133 3.6 21.5 1.0 OE1 B:GLU140 4.1 22.7 1.0 OD2 B:ASP129 4.1 21.6 1.0 ND2 B:ASN131 4.2 26.9 1.0 N B:TYR135 4.2 17.4 1.0 N B:ASN131 4.2 25.5 1.0 N B:ASP133 4.2 22.0 1.0 CA B:TYR135 4.3 17.4 1.0 OE2 B:GLU140 4.3 22.6 1.0 CA B:ASP129 4.4 24.3 1.0 CB B:ASP129 4.4 23.9 1.0 CB B:ASP133 4.4 20.7 1.0 CB B:TYR135 4.5 17.6 1.0 N B:ILE136 4.5 18.1 1.0 N B:LYS130 4.5 25.3 1.0 O B:HOH174 4.5 30.9 1.0 CB B:ASN131 4.6 25.5 1.0 C B:ASP129 4.6 24.8 1.0 N B:ASN132 4.6 24.6 1.0 CD B:GLU140 4.6 22.4 1.0 CA B:ILE136 4.7 18.7 1.0 CA B:ASN131 4.7 25.4 1.0 CA B:ASP133 4.8 20.8 1.0 C B:ASN131 4.8 25.1 1.0 N B:GLY134 4.9 18.8 1.0

M.Nishio, Y.Kamiya, T.Mizushima, S.Wakatsuki, H.Sasakawa, K.Yamamoto, S.Uchiyama, M.Noda, A.R.Mckay, K.Fukui, H.P.Hauri, K.Kato. Structural Basis For the Cooperative Interplay Between the Two Causative Gene Products of Combined Factor V and Factor VIII Deficiency. Proc.Natl.Acad.Sci.Usa V. 107 4034 2010.
ISSN: ISSN 0027-8424
PubMed: 20142513
DOI: 10.1073/PNAS.0908526107