Calcium in PDB 5ca3: Crystal Structure of the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose

The structure of Crystal Structure of the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose, PDB code: 5ca3 was solved by T.Miyazaki, T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.12 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.423, 136.911, 81.518, 90.00, 100.72, 90.00
R / Rfree (%)	14.9 / 18.7

The structure of Crystal Structure of the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose (pdb code 5ca3). 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 the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose, PDB code: 5ca3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose


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 the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:11.1 occ:1.00 O A:VAL437 2.2 10.4 1.0 OE2 A:GLU439 2.3 11.4 1.0 OD1 A:ASN433 2.3 12.1 1.0 OD1 A:ASP431 2.3 11.3 1.0 OE2 A:GLU549 2.4 10.9 1.0 OD1 A:ASN435 2.4 8.2 1.0 C A:VAL437 3.4 9.9 1.0 CG A:ASN433 3.4 12.7 1.0 CD A:GLU549 3.4 11.0 1.0 CG A:ASN435 3.4 10.8 1.0 CD A:GLU439 3.5 11.9 1.0 CG A:ASP431 3.5 13.3 1.0 CG A:GLU549 3.8 10.0 1.0 ND2 A:ASN433 3.8 11.1 1.0 ND2 A:ASN435 3.9 10.6 1.0 N A:VAL437 4.0 10.2 1.0 CA A:VAL437 4.1 9.9 1.0 CA A:ASP431 4.1 12.1 1.0 CB A:VAL437 4.2 10.3 1.0 OE1 A:GLU439 4.3 10.4 1.0 CB A:ASP431 4.3 12.4 1.0 N A:ASN435 4.4 13.6 1.0 CG A:GLU439 4.4 10.8 1.0 OD2 A:ASP431 4.4 12.5 1.0 N A:PRO438 4.4 10.5 1.0 C A:ASP431 4.4 12.2 1.0 N A:ASN433 4.4 13.5 1.0 OE1 A:GLU549 4.5 10.6 1.0 CD1 A:ILE608 4.5 10.2 1.0 CA A:PRO438 4.5 10.7 1.0 N A:HIS432 4.6 12.8 1.0 C A:PRO438 4.6 11.1 1.0 CB A:ASN435 4.7 12.8 1.0 N A:GLY434 4.7 14.4 1.0 CB A:ASN433 4.7 13.6 1.0 N A:GLY436 4.8 12.0 1.0 N A:GLU439 4.9 10.7 1.0 CA A:ASN435 4.9 13.1 1.0 CA A:ASN433 4.9 13.9 1.0 C A:ASN433 4.9 13.8 1.0 O A:ASP431 5.0 10.7 1.0 C A:ASN435 5.0 13.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose


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 the Glycosynthase Mutant D324N of Escherichia Coli GH63 Glycosidase in Complex with Glucose and Lactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:9.2 occ:1.00 OD1 B:ASP431 2.2 11.3 1.0 OE2 B:GLU439 2.3 11.3 1.0 O B:VAL437 2.3 10.1 1.0 OD1 B:ASN433 2.3 11.8 1.0 OD1 B:ASN435 2.3 12.8 1.0 OE2 B:GLU549 2.4 10.3 1.0 CG B:ASN435 3.3 12.3 1.0 CG B:ASN433 3.4 11.0 1.0 CG B:ASP431 3.4 10.2 1.0 CD B:GLU549 3.4 9.9 1.0 C B:VAL437 3.4 9.9 1.0 CD B:GLU439 3.5 12.3 1.0 ND2 B:ASN435 3.7 10.6 1.0 ND2 B:ASN433 3.8 12.2 1.0 CG B:GLU549 3.8 8.7 1.0 N B:VAL437 4.0 10.6 1.0 CA B:VAL437 4.1 9.5 1.0 CB B:VAL437 4.1 9.6 1.0 CA B:ASP431 4.2 9.6 1.0 OD2 B:ASP431 4.2 14.2 1.0 CB B:ASP431 4.3 10.5 1.0 OE1 B:GLU439 4.3 11.2 1.0 N B:ASN435 4.4 12.4 1.0 CG B:GLU439 4.4 11.1 1.0 N B:ASN433 4.5 11.8 1.0 OE1 B:GLU549 4.5 12.6 1.0 C B:ASP431 4.5 10.3 1.0 N B:PRO438 4.5 10.8 1.0 CB B:ASN435 4.6 12.4 1.0 CD1 B:ILE608 4.6 13.9 1.0 N B:GLY434 4.6 12.3 1.0 N B:HIS432 4.6 11.2 1.0 CB B:ASN433 4.7 12.1 1.0 CA B:PRO438 4.7 11.1 1.0 C B:PRO438 4.8 11.4 1.0 N B:GLY436 4.9 11.3 1.0 CA B:ASN433 4.9 12.0 1.0 CA B:ASN435 4.9 12.2 1.0 C B:ASN433 4.9 12.4 1.0 CG1 B:VAL437 5.0 7.5 1.0

T.Miyazaki, A.Nishikawa, T.Tonozuka. Crystal Structure of the Enzyme-Product Complex Reveals Sugar Ring Distortion During Catalysis By Family 63 Inverting Alpha-Glycosidase. J.Struct.Biol. 2016.
ISSN: ESSN 1095-8657
PubMed: 27688023
DOI: 10.1016/J.JSB.2016.09.015