Calcium in PDB 5gl8: The Crystal Structure of Nattokinase Fragments

All present enzymatic activity of The Crystal Structure of Nattokinase Fragments:
3.4.21.62;

The structure of The Crystal Structure of Nattokinase Fragments, PDB code: 5gl8 was solved by W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.284, 73.959, 67.811, 90.00, 97.47, 90.00
R / Rfree (%)	23.1 / 29.1

The binding sites of Calcium atom in the The Crystal Structure of Nattokinase Fragments (pdb code 5gl8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of Nattokinase Fragments, PDB code: 5gl8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Crystal Structure of Nattokinase Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Nattokinase Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:22.7 occ:1.00 O B:HOH435 2.2 4.6 1.0 O B:TYR171 2.2 9.0 1.0 O B:THR174 2.3 6.7 1.0 O B:ALA169 2.4 7.8 1.0 OG1 B:THR174 2.6 8.0 1.0 C B:THR174 3.2 7.2 1.0 C B:TYR171 3.4 9.2 1.0 C B:ALA169 3.5 8.7 1.0 CB B:THR174 3.6 8.0 1.0 O B:HOH662 3.7 21.7 1.0 CA B:THR174 3.7 7.7 1.0 N B:THR174 3.7 7.4 1.0 N B:TYR171 3.9 9.1 1.0 OD2 B:ASP197 4.0 7.2 1.0 CB B:ALA176 4.0 5.4 1.0 C B:LYS170 4.1 10.0 1.0 N B:ALA176 4.1 5.2 1.0 O B:PRO172 4.1 8.2 1.0 C B:PRO172 4.2 8.3 1.0 N B:ILE175 4.2 6.6 1.0 CA B:ALA169 4.3 8.5 1.0 CA B:TYR171 4.3 9.4 1.0 O B:LYS170 4.3 9.4 1.0 N B:PRO172 4.4 8.2 1.0 O B:PRO168 4.4 7.1 1.0 CA B:PRO172 4.4 8.1 1.0 O B:HOH702 4.4 7.8 1.0 O B:GLU195 4.4 8.6 1.0 C B:ILE175 4.4 5.8 1.0 NH2 B:ARG247 4.5 6.9 1.0 N B:LYS170 4.5 9.3 1.0 CA B:ALA176 4.5 5.3 1.0 CA B:ILE175 4.6 6.1 1.0 CA B:LYS170 4.6 10.2 1.0 N B:SER173 4.7 7.5 1.0 C B:SER173 4.8 7.7 1.0 CG2 B:THR174 4.8 8.0 1.0 O B:HOH583 4.9 13.4 1.0

Calcium binding site 2 out of 2 in the The Crystal Structure of Nattokinase Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Nattokinase Fragments within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:6.0 occ:1.00 O B:LEU75 2.4 7.7 1.0 OD1 B:ASN77 2.4 9.0 1.0 O B:VAL81 2.4 8.9 1.0 O B:ILE79 2.4 9.4 1.0 OE1 B:GLN2 2.4 9.3 1.0 OD1 B:ASP41 2.4 9.3 1.0 OD2 B:ASP41 2.5 8.3 1.0 CG B:ASP41 2.8 8.5 1.0 CG B:ASN77 3.4 8.9 1.0 CD B:GLN2 3.4 9.8 1.0 C B:VAL81 3.5 7.7 1.0 C B:LEU75 3.6 7.8 1.0 C B:ILE79 3.6 9.4 1.0 N B:VAL81 3.7 8.0 1.0 CG B:GLN2 3.9 10.1 1.0 ND2 B:ASN77 3.9 9.8 1.0 N B:ASN77 4.1 9.2 1.0 C B:GLY80 4.2 8.4 1.0 CA B:VAL81 4.2 7.6 1.0 CG1 B:ILE79 4.3 10.0 1.0 N B:LEU75 4.4 6.4 1.0 CB B:ASP41 4.4 8.1 1.0 N B:ILE79 4.4 9.4 1.0 CA B:GLY80 4.4 8.6 1.0 N B:GLY80 4.5 8.9 1.0 CA B:LEU75 4.5 6.7 1.0 CB B:GLN2 4.5 11.2 1.0 N B:ASN76 4.5 8.4 1.0 O B:ASN77 4.5 8.7 1.0 CA B:ASN76 4.6 9.4 1.0 CA B:ILE79 4.6 9.9 1.0 N B:LEU82 4.6 7.4 1.0 NE2 B:GLN2 4.6 10.0 1.0 CB B:ASN77 4.6 8.9 1.0 C B:ASN77 4.6 8.9 1.0 CA B:ASN77 4.7 8.6 1.0 C B:ASN76 4.7 9.3 1.0 CA B:LEU82 4.8 7.2 1.0 C B:ALA74 4.8 5.9 1.0 CB B:LEU75 4.8 6.7 1.0 O B:GLY80 4.9 8.6 1.0

Y.Ren, X.Pan, Q.Lyu, W.Liu. Unpublished To Be Published.