Chlorine in PDB 4ygc: Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1, PDB code: 4ygc 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 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.616, 168.892, 73.955, 90.00, 119.86, 90.00
R / Rfree (%)	20.5 / 24.6

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

Chlorine binding site 1 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:49.6 occ:1.00 O A:HOH653 2.5 29.6 1.0 O A:HOH614 3.1 27.0 1.0 N A:HIS56 3.2 31.9 1.0 O A:LYS53 3.3 26.6 1.0 O A:HIS56 3.6 31.3 1.0 C A:HIS56 3.6 27.4 1.0 C A:GLY54 3.6 34.0 1.0 CA A:HIS56 3.6 31.0 1.0 CB A:HIS56 3.7 32.7 1.0 O A:GLY54 3.7 36.0 1.0 N A:PRO55 3.8 32.2 1.0 CD A:PRO55 4.1 32.9 1.0 CA A:GLY54 4.2 30.4 1.0 N A:LEU57 4.2 26.2 1.0 C A:LYS53 4.2 25.0 1.0 CG2 B:THR95 4.3 35.6 1.0 C A:PRO55 4.3 31.2 1.0 CG A:HIS56 4.5 39.7 1.0 CD2 B:TYR82 4.5 31.8 1.0 CD2 A:HIS56 4.5 44.8 1.0 CA A:PRO55 4.6 29.8 1.0 N A:GLY54 4.7 28.4 1.0 CE2 B:TYR82 4.7 31.6 1.0 CA A:LEU57 4.7 27.4 1.0 CG A:LYS53 4.9 27.6 1.0 O B:LEU91 4.9 29.3 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl503 b:53.1 occ:1.00 O C:HOH628 2.4 29.6 1.0 O C:GLY54 3.3 25.9 1.0 O D:HOH608 3.3 29.8 1.0 CD2 D:TYR82 3.6 28.3 1.0 CE C:LYS53 3.8 34.5 1.0 CG D:GLU92 3.9 29.9 1.0 CG C:LYS53 3.9 33.1 1.0 C C:GLY54 4.0 24.5 1.0 CD C:LYS53 4.1 32.2 1.0 CD C:PRO55 4.2 25.2 1.0 O C:LYS53 4.2 26.0 1.0 NZ C:LYS53 4.2 38.7 1.0 CE2 D:TYR82 4.3 25.6 1.0 N C:PRO55 4.4 24.3 1.0 CB D:LEU91 4.5 26.6 1.0 N D:GLU92 4.5 31.3 1.0 O C:HOH650 4.6 33.9 1.0 CG D:TYR82 4.6 29.9 1.0 C D:LEU91 4.6 28.2 1.0 CA D:GLU92 4.6 29.7 1.0 CB D:TYR82 4.7 30.6 1.0 C C:LYS53 4.7 25.1 1.0 O D:LEU91 4.8 27.2 1.0 CD D:GLU92 4.9 29.0 1.0 CB D:GLU92 4.9 31.6 1.0 OE2 D:GLU92 4.9 31.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl503 b:82.3 occ:1.00 O E:LYS53 3.5 25.6 1.0 O E:GLY54 3.7 39.1 1.0 C E:GLY54 3.9 40.5 1.0 CG2 F:THR95 4.0 53.6 1.0 N E:HIS56 4.2 35.4 1.0 O F:LEU91 4.2 39.4 1.0 O E:HIS56 4.3 39.1 1.0 C E:LYS53 4.3 31.1 1.0 CD2 F:TYR82 4.3 46.7 1.0 N E:PRO55 4.3 44.8 1.0 CG E:LYS53 4.4 42.2 1.0 CD E:PRO55 4.4 50.2 1.0 C E:HIS56 4.4 35.4 1.0 CB F:LEU91 4.5 39.7 1.0 C F:LEU91 4.5 37.8 1.0 CE2 F:TYR82 4.6 44.0 1.0 CB E:HIS56 4.6 40.5 1.0 CA E:GLY54 4.6 34.9 1.0 CA E:HIS56 4.7 38.5 1.0 CE E:LYS53 4.8 47.0 1.0 N F:GLU92 4.9 38.5 1.0 N E:GLY54 4.9 32.3 1.0 CA F:GLU92 5.0 46.1 1.0 CD E:LYS53 5.0 41.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl503 b:72.5 occ:1.00 O G:LYS53 3.6 33.0 1.0 O G:GLY54 3.6 31.7 1.0 C G:GLY54 3.8 36.5 1.0 N G:HIS56 3.9 43.4 1.0 N G:PRO55 4.1 37.7 1.0 CG2 H:THR95 4.1 53.4 1.0 CD G:PRO55 4.2 40.3 1.0 O G:HIS56 4.3 47.0 1.0 CD2 H:TYR82 4.3 52.9 1.0 C G:HIS56 4.4 43.8 1.0 CB G:HIS56 4.4 45.3 1.0 C G:LYS53 4.4 34.5 1.0 O H:LEU91 4.5 32.6 1.0 O H:HOH610 4.5 38.3 1.0 CA G:HIS56 4.5 42.7 1.0 CA G:GLY54 4.5 31.8 1.0 CG G:LYS53 4.6 41.4 1.0 CB H:LEU91 4.6 34.0 1.0 CE2 H:TYR82 4.7 51.9 1.0 C H:LEU91 4.7 31.0 1.0 N G:GLY54 4.9 34.2 1.0 CD2 G:HIS56 4.9 48.1 1.0 C G:PRO55 4.9 47.4 1.0 N G:LEU57 4.9 48.9 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.