Chlorine in PDB 4ygd: Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2, PDB code: 4ygd was solved by T.Satoh, M.Nishio, M.Yagi-Utsumi, K.Suzuki, T.Anzai, T.Mizushima, Y.Kamiya, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.063, 58.765, 119.386, 90.00, 109.01, 90.00
R / Rfree (%)	19.3 / 23.2

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2 also contains other interesting chemical elements:

Calcium

(Ca)

16 atoms

The binding sites of Chlorine atom in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2 (pdb code 4ygd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2, PDB code: 4ygd:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:65.8 occ:1.00 O A:HOH641 3.1 43.8 1.0 N A:GLY252 3.8 30.6 1.0 N A:LEU253 3.8 28.9 1.0 CB A:ALA120 4.1 25.0 1.0 CE2 A:PHE154 4.2 37.7 1.0 CZ A:PHE154 4.2 35.6 1.0 CA A:GLY251 4.3 30.1 1.0 CD2 A:PHE154 4.4 39.0 1.0 CE1 A:PHE154 4.4 37.6 1.0 CB A:LEU253 4.4 31.6 1.0 C A:GLY251 4.5 30.5 1.0 O A:LEU253 4.5 34.7 1.0 CD1 A:PHE154 4.5 38.0 1.0 CG A:PHE154 4.5 35.2 1.0 CA A:GLY252 4.6 27.0 1.0 CG A:LEU253 4.6 37.4 1.0 CA A:LEU253 4.6 29.4 1.0 C A:GLY252 4.7 26.8 1.0 N A:GLY251 4.8 30.1 1.0 OD2 A:ASP121 4.8 38.5 1.0 CD1 A:LEU253 4.9 37.8 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:61.8 occ:1.00 O A:HOH645 3.2 32.7 1.0 O A:LYS53 3.3 22.2 1.0 C A:GLY54 3.6 17.8 1.0 N A:HIS56 3.6 19.1 1.0 O A:GLY54 3.6 17.4 1.0 O A:HIS56 3.8 22.9 1.0 N A:PRO55 3.8 17.8 1.0 C A:HIS56 3.9 21.9 1.0 CG2 B:THR95 3.9 27.8 1.0 CD A:PRO55 4.1 17.0 1.0 CA A:HIS56 4.1 21.0 1.0 C A:LYS53 4.1 21.8 1.0 CB A:HIS56 4.2 20.9 1.0 CA A:GLY54 4.2 17.6 1.0 N A:LEU57 4.4 23.3 1.0 N A:GLY54 4.6 20.1 1.0 CG A:LYS53 4.6 23.6 1.0 C A:PRO55 4.7 17.9 1.0 CA A:LEU57 4.8 26.0 1.0 CA A:PRO55 4.8 18.9 1.0 CD2 B:TYR82 4.9 28.5 1.0 CD2 A:HIS56 4.9 27.5 1.0 O B:LEU91 4.9 15.3 1.0 CG A:HIS56 4.9 25.7 1.0 O B:HOH606 5.0 17.3 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl503 b:55.6 occ:1.00 O G:LYS53 3.2 17.3 1.0 O G:GLY54 3.4 18.7 1.0 C G:GLY54 3.5 19.4 1.0 N G:HIS56 3.5 19.6 1.0 O G:HIS56 3.7 21.7 1.0 N G:PRO55 3.8 19.9 1.0 C G:HIS56 3.8 20.2 1.0 C G:LYS53 4.0 20.1 1.0 CA G:HIS56 4.1 19.7 1.0 CD G:PRO55 4.1 19.3 1.0 CA G:GLY54 4.1 19.9 1.0 CG2 H:THR95 4.1 26.8 1.0 CB G:HIS56 4.2 19.4 1.0 N G:LEU57 4.3 22.4 1.0 N G:GLY54 4.4 20.1 1.0 CG G:LYS53 4.5 21.4 1.0 C G:PRO55 4.6 18.8 1.0 CA G:LEU57 4.7 24.4 1.0 CA G:PRO55 4.7 19.8 1.0 CD2 G:HIS56 4.9 22.4 1.0 CG G:HIS56 4.9 20.9 1.0 CD2 H:TYR82 5.0 26.2 1.0

T.Satoh, M.Nishio, M.Yagi-Utsumi, K.Suzuki, T.Anzai, T.Mizushima, Y.Kamiya, K.Kato. Interaction Mode of Coagulation Factors V and VIII with the Cargo Receptor MCFD2/Ergic-53 Complex To Be Published.