Calcium in PDB 3w7w: Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose

The structure of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose, PDB code: 3w7w was solved by T.Miyazaki, M.Ichikawa, G.Yokoi, M.Kitaoka, H.Mori, Y.Kitano, A.Nishikawa, T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.88 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.884, 138.136, 82.547, 90.00, 99.03, 90.00
R / Rfree (%)	17.4 / 22.6

The structure of Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Calcium atom in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose (pdb code 3w7w). 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 E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose, PDB code: 3w7w:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


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 E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:16.8 occ:1.00 O A:VAL437 2.1 16.7 1.0 OE2 A:GLU439 2.2 19.1 1.0 OE2 A:GLU549 2.4 18.8 1.0 OD1 A:ASP431 2.4 19.2 1.0 OD1 A:ASN433 2.4 22.1 1.0 OD1 A:ASN435 2.4 15.5 1.0 CD A:GLU549 3.3 17.3 1.0 C A:VAL437 3.3 16.9 1.0 CG A:ASN435 3.4 17.8 1.0 CD A:GLU439 3.4 18.6 1.0 CG A:ASN433 3.4 21.8 1.0 CG A:ASP431 3.5 19.5 1.0 CG A:GLU549 3.6 17.1 1.0 ND2 A:ASN433 3.9 19.1 1.0 ND2 A:ASN435 3.9 15.9 1.0 N A:VAL437 4.0 17.4 1.0 CA A:VAL437 4.1 16.7 1.0 CA A:ASP431 4.1 19.6 1.0 CB A:VAL437 4.2 17.1 1.0 OE1 A:GLU439 4.3 17.4 1.0 CB A:ASP431 4.3 19.5 1.0 CG A:GLU439 4.3 17.0 1.0 N A:PRO438 4.4 17.1 1.0 OE1 A:GLU549 4.4 17.7 1.0 N A:ASN435 4.4 18.5 1.0 C A:ASP431 4.4 19.8 1.0 CD1 A:ILE608 4.4 19.3 1.0 OD2 A:ASP431 4.5 18.7 1.0 CA A:PRO438 4.5 16.9 1.0 N A:HIS432 4.5 20.4 1.0 N A:ASN433 4.5 20.9 1.0 C A:PRO438 4.6 16.9 1.0 CB A:ASN435 4.6 18.4 1.0 N A:GLY434 4.7 21.0 1.0 CB A:ASN433 4.8 21.2 1.0 N A:GLU439 4.8 16.6 1.0 N A:GLY436 4.9 17.9 1.0 CA A:ASN435 4.9 18.3 1.0 O A:PRO438 5.0 16.1 1.0 O A:ARG430 5.0 18.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose


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 E. Coli Ygjk E727A Complexed with 2-O-Alpha-D- Glucopyranosyl-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:28.6 occ:1.00 OD1 B:ASP431 1.9 25.7 1.0 OE2 B:GLU439 2.2 27.2 1.0 OE2 B:GLU549 2.2 27.3 1.0 O B:VAL437 2.3 29.2 1.0 OD1 B:ASN433 2.3 35.3 1.0 OD1 B:ASN435 2.5 29.0 1.0 CG B:ASP431 3.2 27.9 1.0 CG B:ASN433 3.3 33.3 1.0 CD B:GLU549 3.3 26.8 1.0 C B:VAL437 3.4 29.3 1.0 CD B:GLU439 3.4 26.1 1.0 CG B:ASN435 3.5 31.5 1.0 ND2 B:ASN433 3.7 33.0 1.0 CG B:GLU549 3.8 26.1 1.0 ND2 B:ASN435 4.0 31.0 1.0 OD2 B:ASP431 4.0 27.0 1.0 N B:VAL437 4.0 30.4 1.0 CA B:VAL437 4.1 29.9 1.0 CB B:ASP431 4.2 29.0 1.0 CB B:VAL437 4.2 29.9 1.0 CA B:ASP431 4.2 29.4 1.0 OE1 B:GLU439 4.2 25.5 1.0 CG B:GLU439 4.4 25.2 1.0 OE1 B:GLU549 4.4 25.3 1.0 CD1 B:ILE608 4.4 29.2 1.0 N B:ASN435 4.4 32.6 1.0 N B:PRO438 4.5 28.2 1.0 N B:ASN433 4.5 32.8 1.0 C B:ASP431 4.6 30.3 1.0 CA B:PRO438 4.6 27.4 1.0 N B:HIS432 4.6 31.5 1.0 CB B:ASN433 4.7 33.1 1.0 C B:PRO438 4.7 26.6 1.0 CB B:ASN435 4.7 32.2 1.0 N B:GLY436 4.8 31.9 1.0 N B:GLY434 4.9 33.2 1.0 CA B:ASN435 4.9 32.4 1.0 N B:GLU439 4.9 25.9 1.0 CA B:ASN433 4.9 33.0 1.0 C B:ASN433 5.0 32.9 1.0

T.Miyazaki, M.Ichikawa, G.Yokoi, M.Kitaoka, H.Mori, Y.Kitano, A.Nishikawa, T.Tonozuka. Structure of A Bacterial Glycoside Hydrolase Family 63 Enzyme in Complex with Its Glycosynthase Product, and Insights Into the Substrate Specificity. Febs J. V. 280 4560 2013.
ISSN: ISSN 1742-464X
PubMed: 23826932
DOI: 10.1111/FEBS.12424