Calcium in PDB 1cvm: Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens

All present enzymatic activity of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens:
3.1.3.8;

The structure of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens, PDB code: 1cvm was solved by S.Shin, N.-C.Ha, B.-H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.090, 65.010, 105.540, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 27.4

The structure of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens also contains other interesting chemical elements:

Cadmium

(Cd)

5 atoms

The binding sites of Calcium atom in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens (pdb code 1cvm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens, PDB code: 1cvm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:9.8 occ:1.00 OD2 A:ASP308 2.4 10.9 1.0 OE2 A:GLU43 2.7 12.4 1.0 OD1 A:ASP341 2.7 31.2 1.0 OE1 A:GLU43 2.7 14.3 1.0 OD1 A:ASN339 2.7 24.6 1.0 O A:ILE340 2.9 28.1 1.0 CD A:GLU43 3.0 9.9 1.0 O A:HOH529 3.1 31.8 1.0 CG A:ASP308 3.3 10.3 1.0 CG A:ASP341 3.4 25.8 1.0 C A:ILE340 3.5 24.6 1.0 CG A:ASN339 3.7 24.6 1.0 OD1 A:ASP308 3.9 8.3 1.0 OD2 A:ASP341 3.9 25.7 1.0 CA A:ASP341 3.9 27.9 1.0 N A:ASP341 4.0 27.3 1.0 N A:ILE340 4.0 21.4 1.0 NZ A:LYS351 4.1 5.0 1.0 ND2 A:ASN339 4.2 24.5 1.0 CB A:ASP341 4.2 26.2 1.0 CB A:ASP308 4.3 9.5 1.0 CA A:ILE340 4.4 23.5 1.0 N A:ASP308 4.5 5.1 1.0 O A:HOH555 4.5 59.0 1.0 CG A:GLU43 4.5 12.8 1.0 OD1 A:ASN349 4.6 13.7 1.0 CE A:LYS351 4.7 5.7 1.0 C A:ASN339 4.8 21.1 1.0 CG2 A:THR307 4.9 14.0 1.0 CB A:ASN339 5.0 21.5 1.0

Calcium binding site 2 out of 3 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:35.4 occ:1.00 O A:GLU338 2.3 21.3 1.0 O A:GLY309 2.5 11.3 1.0 OD1 A:ASP308 2.6 8.3 1.0 OD1 A:ASN336 2.7 11.7 1.0 O A:HOH507 3.0 46.3 1.0 O A:HOH554 3.1 46.4 1.0 ND2 A:ASN336 3.2 4.3 1.0 CG A:ASN336 3.3 5.3 1.0 C A:GLY309 3.4 10.8 1.0 C A:GLU338 3.5 22.3 1.0 CG A:ASP308 3.6 10.3 1.0 CA A:THR310 4.0 9.1 1.0 N A:THR310 4.1 9.9 1.0 CB A:ASP308 4.2 9.5 1.0 N A:GLY309 4.2 8.4 1.0 CA A:ASN339 4.2 22.4 1.0 N A:ASN339 4.3 22.5 1.0 CA A:GLY309 4.4 8.9 1.0 OG A:SER311 4.4 9.0 1.0 CA A:GLU338 4.5 22.8 1.0 N A:ILE340 4.5 21.4 1.0 C A:ASP308 4.5 7.2 1.0 C A:THR310 4.5 5.8 1.0 OD2 A:ASP308 4.5 10.9 1.0 CB A:GLU338 4.5 29.1 1.0 NZ A:LYS351 4.6 5.0 1.0 N A:SER311 4.7 8.4 1.0 CD1 A:ILE340 4.7 24.9 1.0 CB A:ASN336 4.8 6.8 1.0 C A:ASN339 4.8 21.1 1.0 N A:GLU338 4.8 19.0 1.0 O A:ASP308 4.9 12.3 1.0 CE A:LYS351 5.0 5.7 1.0

Calcium binding site 3 out of 3 in the Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cadmium Inhibited Crystal Structure of Phytase From Bacillus Amyloliquefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:18.6 occ:1.00 O A:VAL101 2.5 17.6 1.0 O A:HOH526 2.6 6.5 1.0 OD2 A:ASP56 2.6 7.7 1.0 O A:HOH515 2.6 12.0 1.0 O A:HOH533 2.8 48.1 1.0 O A:PRO57 2.9 9.1 1.0 OD1 A:ASP56 3.0 11.8 1.0 CG A:ASP56 3.1 7.2 1.0 C A:VAL101 3.7 12.0 1.0 C A:PRO57 4.0 9.5 1.0 O A:HOH534 4.2 12.1 1.0 CA A:ASP102 4.3 9.6 1.0 O A:HOH504 4.4 14.2 1.0 CB A:ASP56 4.5 4.8 1.0 N A:ASP102 4.5 11.2 1.0 CB A:ASP102 4.5 5.2 1.0 N A:PRO57 4.6 6.2 1.0 O A:HOH535 4.6 30.1 1.0 O A:ILE316 4.6 7.0 1.0 N A:VAL101 4.6 9.1 1.0 OD2 A:ASP317 4.7 11.8 1.0 CA A:ALA58 4.7 8.6 1.0 CB A:ALA58 4.7 2.4 1.0 CG A:ASP317 4.7 6.0 1.0 OD1 A:ASP102 4.8 15.0 1.0 CG A:ASP102 4.8 6.7 1.0 N A:ALA58 4.8 7.3 1.0 CA A:VAL101 4.8 8.9 1.0 CD A:PRO57 4.9 8.2 1.0 C A:ASP56 5.0 7.5 1.0 CG1 A:VAL101 5.0 11.2 1.0 CA A:PRO57 5.0 7.6 1.0

N.C.Ha, B.C.Oh, S.Shin, H.J.Kim, T.K.Oh, Y.O.Kim, K.Y.Choi, B.H.Oh. Crystal Structures of A Novel, Thermostable Phytase in Partially and Fully Calcium-Loaded States. Nat.Struct.Biol. V. 7 147 2000.
ISSN: ISSN 1072-8368
PubMed: 10655618
DOI: 10.1038/72421