Calcium in PDB 4dww: Crystal Structure of Nattokinase From Bacillus Subtilis Natto

All present enzymatic activity of Crystal Structure of Nattokinase From Bacillus Subtilis Natto:
3.4.21.62;

The structure of Crystal Structure of Nattokinase From Bacillus Subtilis Natto, PDB code: 4dww was solved by T.Chatake, Y.Yanagisawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.37 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.293, 49.899, 56.338, 90.00, 95.24, 90.00
R / Rfree (%)	13.3 / 19.9

The binding sites of Calcium atom in the Crystal Structure of Nattokinase From Bacillus Subtilis Natto (pdb code 4dww). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Nattokinase From Bacillus Subtilis Natto, PDB code: 4dww:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Nattokinase From Bacillus Subtilis Natto


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 Nattokinase From Bacillus Subtilis Natto within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:24.9 occ:1.00 O A:ALA169 2.3 10.3 1.0 O A:THR174 2.4 8.7 1.0 O A:TYR171 2.5 12.5 1.0 OG1 A:THR174 2.6 9.7 1.0 O A:HOH416 2.6 12.2 1.0 C A:THR174 3.2 10.3 1.0 C A:ALA169 3.4 12.2 1.0 C A:TYR171 3.5 12.5 1.0 OD2 A:ASP197 3.6 12.3 1.0 CB A:THR174 3.7 8.3 1.0 CA A:THR174 3.7 9.6 1.0 N A:THR174 3.8 7.4 1.0 N A:ALA176 3.8 7.7 1.0 CB A:ALA176 3.8 8.3 1.0 CA A:ALA169 4.1 9.8 1.0 N A:TYR171 4.1 8.1 1.0 N A:ILE175 4.2 7.7 1.0 C A:LYS170 4.2 11.7 1.0 CA A:ALA176 4.3 9.4 1.0 C A:PRO172 4.3 11.4 1.0 C A:ILE175 4.3 10.9 1.0 CA A:PRO172 4.3 10.7 1.0 N A:PRO172 4.3 13.8 1.0 O A:PRO172 4.4 11.8 1.0 N A:LYS170 4.4 9.4 1.0 O A:GLU195 4.4 11.1 1.0 O A:PRO168 4.4 8.3 1.0 CA A:TYR171 4.4 7.1 1.0 CA A:ILE175 4.4 8.9 1.0 O A:LYS170 4.5 13.1 1.0 CA A:LYS170 4.6 10.9 1.0 N A:SER173 4.7 11.2 1.0 CG2 A:THR174 4.8 7.1 1.0 O A:HOH731 4.8 26.2 1.0 CG A:ASP197 4.8 13.0 1.0 C A:SER173 4.9 8.9 1.0 NH2 A:ARG247 4.9 11.7 1.0 CB A:ALA169 4.9 8.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Nattokinase From Bacillus Subtilis Natto


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 Nattokinase From Bacillus Subtilis Natto within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:9.2 occ:1.00 OD1 A:ASP41 2.4 6.7 1.0 O A:VAL81 2.4 8.1 1.0 O A:ILE79 2.4 6.9 1.0 O A:LEU75 2.4 6.6 1.0 OE1 A:GLN2 2.5 9.5 1.0 OD1 A:ASN77 2.5 7.4 1.0 OD2 A:ASP41 2.6 8.4 1.0 CG A:ASP41 2.9 7.3 1.0 CG A:ASN77 3.4 10.2 1.0 CD A:GLN2 3.5 10.8 1.0 C A:ILE79 3.6 9.1 1.0 C A:VAL81 3.6 8.3 1.0 C A:LEU75 3.6 8.4 1.0 N A:VAL81 3.7 10.5 1.0 CG A:GLN2 3.8 9.2 1.0 ND2 A:ASN77 3.9 9.8 1.0 N A:ASN77 4.0 11.3 1.0 C A:GLY80 4.2 10.1 1.0 CG1 A:ILE79 4.3 11.7 1.0 CA A:VAL81 4.3 9.2 1.0 CB A:ASP41 4.4 7.8 1.0 N A:LEU75 4.4 6.2 1.0 N A:ILE79 4.4 10.2 1.0 CA A:GLY80 4.4 9.3 1.0 N A:GLY80 4.4 8.9 1.0 CA A:LEU75 4.5 5.4 1.0 CA A:ILE79 4.5 8.8 1.0 CB A:GLN2 4.5 10.5 1.0 N A:ASN76 4.5 8.1 1.0 CA A:ASN76 4.6 9.8 1.0 O A:ASN77 4.6 8.9 1.0 CB A:ASN77 4.6 11.8 1.0 N A:LEU82 4.6 9.7 1.0 CA A:ASN77 4.7 10.7 1.0 NE2 A:GLN2 4.7 9.7 1.0 C A:ASN76 4.7 11.5 1.0 C A:ASN77 4.7 10.8 1.0 C A:ALA74 4.8 7.8 1.0 CA A:LEU82 4.8 8.3 1.0 O A:GLY80 4.9 9.5 1.0 CB A:LEU75 4.9 5.7 1.0

Y.Yanagisawa, T.Chatake, K.Chiba-Kamoshida, S.Naito, T.Ohsugi, H.Sumi, I.Yasuda, Y.Morimoto. Purification, Crystallization and Preliminary X-Ray Diffraction Experiment of Nattokinase From Bacillus Subtilis Natto Acta Crystallogr.,Sect.F V. 66 1670 2010.
ISSN: ESSN 1744-3091
PubMed: 21139221
DOI: 10.1107/S1744309110043137