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

The structure of Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2, PDB code: 4yge 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 / 3.05
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.128, 113.128, 157.602, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.1

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

Calcium

(Ca)

9 atoms

The binding sites of Chlorine atom in the Crystal Structure of Ergic-53/MCFD2, Trigonal Calcium-Bound Form 2 (pdb code 4yge). 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, Trigonal Calcium-Bound Form 2, PDB code: 4yge:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Ergic-53/MCFD2, Trigonal 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, Trigonal Calcium-Bound Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:58.6 occ:1.00 O A:LYS53 3.3 30.8 1.0 O A:GLY54 3.4 42.8 1.0 O A:HIS56 3.5 43.7 1.0 N A:HIS56 3.8 43.6 1.0 C A:HIS56 3.8 46.7 1.0 C A:GLY54 3.9 42.5 1.0 CG2 B:THR95 4.0 50.1 1.0 CA A:HIS56 4.2 45.2 1.0 C A:LYS53 4.2 32.2 1.0 O B:LEU91 4.4 37.1 1.0 CB A:HIS56 4.4 46.9 1.0 CB B:LEU91 4.4 38.6 1.0 N A:PRO55 4.4 47.2 1.0 CG A:LYS53 4.5 29.8 1.0 N A:LEU57 4.6 50.4 1.0 C B:LEU91 4.6 38.9 1.0 CA A:GLY54 4.7 39.4 1.0 N A:GLY54 4.9 36.2 1.0 CD A:PRO55 4.9 47.1 1.0 CA A:LEU57 4.9 46.3 1.0 C A:PRO55 4.9 44.9 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Ergic-53/MCFD2, Trigonal 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, Trigonal Calcium-Bound Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl502 b:51.8 occ:1.00 O C:HIS56 3.5 40.8 1.0 O C:LYS53 3.6 26.2 1.0 O C:GLY54 3.7 32.8 1.0 C C:HIS56 3.9 35.7 1.0 CG2 D:THR95 4.0 49.0 1.0 N C:HIS56 4.0 33.0 1.0 O D:LEU91 4.3 29.5 1.0 CA C:HIS56 4.3 36.3 1.0 C C:GLY54 4.3 33.2 1.0 CB C:HIS56 4.4 38.9 1.0 CB D:LEU91 4.4 26.6 1.0 C C:LYS53 4.5 25.5 1.0 C D:LEU91 4.5 28.8 1.0 N C:LEU57 4.6 34.3 1.0 CG C:LYS53 4.7 23.4 1.0 N C:PRO55 4.8 35.2 1.0 N D:GLU92 5.0 27.7 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Ergic-53/MCFD2, Trigonal 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, Trigonal Calcium-Bound Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl501 b:38.8 occ:1.00 O E:GLY54 3.2 39.3 1.0 O E:LYS53 3.3 29.0 1.0 O E:HIS56 3.6 38.4 1.0 N E:HIS56 3.7 35.9 1.0 C E:GLY54 3.8 34.1 1.0 C E:HIS56 3.9 39.0 1.0 C E:LYS53 4.2 26.0 1.0 CA E:HIS56 4.2 39.3 1.0 CG2 F:THR95 4.2 32.3 1.0 N E:PRO55 4.3 34.4 1.0 CB E:HIS56 4.4 42.8 1.0 CG E:LYS53 4.4 23.2 1.0 N E:LEU57 4.6 36.7 1.0 CB F:LEU91 4.6 24.9 1.0 O F:LEU91 4.6 24.4 1.0 CA E:GLY54 4.6 32.5 1.0 CD E:PRO55 4.7 33.9 1.0 N E:GLY54 4.8 28.6 1.0 C F:LEU91 4.8 25.5 1.0 C E:PRO55 4.9 35.4 1.0 CA E:LEU57 5.0 32.9 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.