Calcium in PDB 3d3i: Crystal Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63

The structure of Crystal Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63, PDB code: 3d3i was solved by Y.Kurakata, A.Uechi, H.Yoshida, S.Kamitori, Y.Sakano, A.Nishikawa, T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.687, 138.549, 87.543, 90.00, 96.60, 90.00
R / Rfree (%)	16.9 / 20.1

The binding sites of Calcium atom in the Crystal Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63 (pdb code 3d3i). 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 Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63, PDB code: 3d3i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:9.2 occ:1.00 OE2 A:GLU439 2.4 12.6 1.0 O A:VAL437 2.4 8.9 1.0 OD1 A:ASN433 2.4 9.2 1.0 OD1 A:ASP431 2.5 8.5 1.0 OE2 A:GLU549 2.5 8.5 1.0 OD1 A:ASN435 2.6 9.7 1.0 C A:VAL437 3.4 10.0 1.0 CD A:GLU549 3.5 7.8 1.0 CG A:ASN433 3.5 11.9 1.0 CG A:ASN435 3.5 8.7 1.0 CD A:GLU439 3.6 10.1 1.0 CG A:ASP431 3.7 10.0 1.0 CG A:GLU549 3.8 7.2 1.0 ND2 A:ASN435 3.9 6.8 1.0 ND2 A:ASN433 3.9 10.9 1.0 N A:VAL437 4.1 10.4 1.0 CA A:VAL437 4.1 10.2 1.0 CB A:VAL437 4.2 9.8 1.0 CA A:ASP431 4.2 8.5 1.0 N A:ASN435 4.4 10.3 1.0 CG A:GLU439 4.4 8.6 1.0 N A:PRO438 4.4 12.5 1.0 N A:ASN433 4.4 9.9 1.0 OE1 A:GLU439 4.5 9.9 1.0 CB A:ASP431 4.5 8.1 1.0 C A:ASP431 4.5 9.8 1.0 OD2 A:ASP431 4.5 9.9 1.0 OE1 A:GLU549 4.6 9.8 1.0 CA A:PRO438 4.6 11.4 1.0 N A:HIS432 4.6 9.5 1.0 CB A:ASN435 4.7 10.0 1.0 C A:PRO438 4.7 12.5 1.0 N A:GLY434 4.7 10.4 1.0 CB A:ASN433 4.8 9.8 1.0 O A:PRO438 4.9 13.9 1.0 N A:GLY436 4.9 10.2 1.0 CA A:ASN435 5.0 9.2 1.0 CA A:ASN433 5.0 11.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structural of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to Glycoside Hydrolase Family 63 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:11.9 occ:1.00 O B:VAL437 2.4 10.8 1.0 OE2 B:GLU439 2.4 11.7 1.0 OD1 B:ASN433 2.5 13.5 1.0 OE2 B:GLU549 2.5 11.6 1.0 OD1 B:ASP431 2.5 11.8 1.0 OD1 B:ASN435 2.5 12.7 1.0 CG B:ASN435 3.4 14.1 1.0 C B:VAL437 3.5 11.7 1.0 CD B:GLU549 3.5 10.7 1.0 CG B:ASN433 3.6 15.3 1.0 CD B:GLU439 3.6 10.9 1.0 CG B:ASP431 3.7 11.9 1.0 ND2 B:ASN435 3.8 10.7 1.0 CG B:GLU549 3.9 11.1 1.0 ND2 B:ASN433 4.0 15.2 1.0 N B:VAL437 4.0 12.5 1.0 CA B:VAL437 4.1 10.6 1.0 CB B:VAL437 4.2 12.0 1.0 CA B:ASP431 4.2 9.7 1.0 N B:ASN435 4.3 12.0 1.0 CG B:GLU439 4.4 10.3 1.0 N B:ASN433 4.5 13.0 1.0 OE1 B:GLU439 4.5 10.0 1.0 C B:ASP431 4.5 10.3 1.0 N B:PRO438 4.5 12.8 1.0 CB B:ASP431 4.5 10.0 1.0 CD1 B:ILE608 4.5 14.2 1.0 OD2 B:ASP431 4.6 13.6 1.0 OE1 B:GLU549 4.6 10.8 1.0 N B:HIS432 4.6 10.5 1.0 CB B:ASN435 4.6 12.3 1.0 CA B:PRO438 4.7 13.7 1.0 C B:PRO438 4.8 12.5 1.0 N B:GLY434 4.8 12.5 1.0 CB B:ASN433 4.8 13.9 1.0 N B:GLY436 4.9 12.2 1.0 CA B:ASN435 4.9 13.0 1.0 O B:PRO438 4.9 13.6 1.0

Y.Kurakata, A.Uechi, H.Yoshida, S.Kamitori, Y.Sakano, A.Nishikawa, T.Tonozuka. Structural Insights Into the Substrate Specificity and Function of Escherichia Coli K12 Ygjk, A Glucosidase Belonging to the Glycoside Hydrolase Family 63. J.Mol.Biol. V. 381 116 2008.
ISSN: ISSN 0022-2836
PubMed: 18586271
DOI: 10.1016/J.JMB.2008.05.061