Calcium in PDB 3w7u: Escherichia Coli K12 Ygjk Complexed with Galactose

The structure of Escherichia Coli K12 Ygjk Complexed with Galactose, PDB code: 3w7u was solved by T.Miyazaki, 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)	36.25 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.070, 140.020, 86.260, 90.00, 97.66, 90.00
R / Rfree (%)	19.1 / 23.6

The binding sites of Calcium atom in the Escherichia Coli K12 Ygjk Complexed with Galactose (pdb code 3w7u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Escherichia Coli K12 Ygjk Complexed with Galactose, PDB code: 3w7u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Escherichia Coli K12 Ygjk Complexed with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Escherichia Coli K12 Ygjk Complexed with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:28.7 occ:1.00 O A:VAL437 2.2 28.2 1.0 OE2 A:GLU439 2.3 28.0 1.0 OD1 A:ASN433 2.3 31.1 1.0 OE2 A:GLU549 2.4 29.7 1.0 OD1 A:ASN435 2.4 31.6 1.0 OD1 A:ASP431 2.5 25.2 1.0 CD A:GLU549 3.4 29.2 1.0 C A:VAL437 3.4 28.4 1.0 CG A:ASN435 3.4 31.4 1.0 CD A:GLU439 3.5 28.2 1.0 CG A:ASN433 3.5 30.3 1.0 CG A:ASP431 3.6 27.1 1.0 CG A:GLU549 3.8 27.8 1.0 ND2 A:ASN435 3.9 31.6 1.0 ND2 A:ASN433 4.0 28.8 1.0 N A:VAL437 4.1 29.4 1.0 CA A:VAL437 4.1 29.1 1.0 CA A:ASP431 4.2 27.9 1.0 CB A:VAL437 4.2 29.0 1.0 OE1 A:GLU439 4.3 27.6 1.0 N A:ASN435 4.4 31.6 1.0 CG A:GLU439 4.4 27.5 1.0 CB A:ASP431 4.4 27.6 1.0 OD2 A:ASP431 4.4 27.3 1.0 C A:ASP431 4.4 28.1 1.0 OE1 A:GLU549 4.5 29.1 1.0 N A:PRO438 4.5 28.5 1.0 N A:ASN433 4.5 29.6 1.0 CD1 A:ILE608 4.5 28.7 1.0 N A:HIS432 4.6 28.5 1.0 CA A:PRO438 4.6 28.1 1.0 CB A:ASN435 4.6 31.4 1.0 C A:PRO438 4.7 27.8 1.0 N A:GLY434 4.7 31.3 1.0 CB A:ASN433 4.8 30.3 1.0 N A:GLY436 4.9 30.9 1.0 O A:PRO438 4.9 27.5 1.0 CA A:ASN435 4.9 31.3 1.0 CA A:ASN433 5.0 30.2 1.0 O A:ASP431 5.0 27.6 1.0

Calcium binding site 2 out of 2 in the Escherichia Coli K12 Ygjk Complexed with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Escherichia Coli K12 Ygjk Complexed with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:37.3 occ:1.00 OE2 B:GLU439 2.1 35.4 1.0 OD1 B:ASP431 2.4 37.7 1.0 OD1 B:ASN435 2.4 39.5 1.0 OD1 B:ASN433 2.4 40.3 1.0 OE2 B:GLU549 2.4 39.3 1.0 O B:VAL437 2.4 37.9 1.0 CG B:ASN435 3.2 38.4 1.0 CD B:GLU439 3.3 34.7 1.0 C B:VAL437 3.5 37.4 1.0 CG B:ASP431 3.5 37.9 1.0 CD B:GLU549 3.5 39.2 1.0 CG B:ASN433 3.5 40.6 1.0 ND2 B:ASN435 3.5 35.6 1.0 ND2 B:ASN433 4.0 39.8 1.0 CG B:GLU549 4.0 38.1 1.0 CA B:ASP431 4.1 38.1 1.0 OE1 B:GLU439 4.1 35.7 1.0 N B:VAL437 4.1 37.9 1.0 CA B:VAL437 4.2 37.8 1.0 CB B:VAL437 4.3 37.4 1.0 N B:ASN435 4.3 39.1 1.0 OD2 B:ASP431 4.3 36.2 1.0 CG B:GLU439 4.3 34.7 1.0 CB B:ASP431 4.3 38.0 1.0 CD1 B:ILE608 4.4 44.6 1.0 C B:ASP431 4.4 38.5 1.0 N B:ASN433 4.4 40.1 1.0 N B:HIS432 4.4 39.1 1.0 N B:PRO438 4.5 37.1 1.0 CB B:ASN435 4.5 38.8 1.0 OE1 B:GLU549 4.5 39.4 1.0 CA B:PRO438 4.6 36.5 1.0 C B:PRO438 4.7 35.7 1.0 N B:GLY434 4.7 39.9 1.0 CB B:ASN433 4.8 40.2 1.0 CA B:ASN435 4.8 38.8 1.0 N B:GLY436 4.9 38.4 1.0 O B:PRO438 4.9 36.1 1.0 CG1 B:VAL437 4.9 37.0 1.0 CA B:ASN433 5.0 40.2 1.0 C B:ASN433 5.0 40.2 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