Calcium in PDB 3w7x: Crystal Structure of E. Coli Ygjk D324N Complexed with Melibiose

The structure of Crystal Structure of E. Coli Ygjk D324N Complexed with Melibiose, PDB code: 3w7x 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)	40.52 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.140, 138.160, 86.200, 90.00, 98.37, 90.00
R / Rfree (%)	18.9 / 24.9

The binding sites of Calcium atom in the Crystal Structure of E. Coli Ygjk D324N Complexed with Melibiose (pdb code 3w7x). 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 D324N Complexed with Melibiose, PDB code: 3w7x:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of E. Coli Ygjk D324N Complexed with Melibiose


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 D324N Complexed with Melibiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:13.8 occ:1.00 OD1 A:ASN435 2.2 15.9 1.0 OE2 A:GLU549 2.2 15.9 1.0 OE2 A:GLU439 2.2 19.2 1.0 O A:VAL437 2.3 18.1 1.0 OD1 A:ASN433 2.3 17.9 1.0 OD1 A:ASP431 2.8 17.9 1.0 CG A:ASN435 3.1 16.7 1.0 CD A:GLU549 3.2 15.8 1.0 CG A:ASN433 3.4 17.0 1.0 CD A:GLU439 3.4 18.7 1.0 C A:VAL437 3.5 17.3 1.0 ND2 A:ASN435 3.6 16.8 1.0 CG A:GLU549 3.7 15.9 1.0 CG A:ASP431 3.8 18.3 1.0 ND2 A:ASN433 3.9 16.9 1.0 CG A:GLU439 4.1 18.4 1.0 OE1 A:GLU549 4.2 15.6 1.0 CA A:ASP431 4.3 17.6 1.0 N A:VAL437 4.3 16.7 1.0 CD1 A:ILE608 4.3 20.1 1.0 CA A:VAL437 4.3 17.0 1.0 CB A:ASN435 4.3 16.9 1.0 N A:ASN433 4.4 16.1 1.0 OE1 A:GLU439 4.4 18.0 1.0 CB A:VAL437 4.4 17.1 1.0 N A:PRO438 4.5 17.5 1.0 C A:ASP431 4.5 17.7 1.0 C A:PRO438 4.5 17.7 1.0 CB A:ASP431 4.6 17.8 1.0 CA A:PRO438 4.6 17.8 1.0 OD2 A:ASP431 4.7 18.6 1.0 CB A:ASN433 4.7 16.7 1.0 N A:ASN435 4.7 17.6 1.0 N A:HIS432 4.7 16.7 1.0 O A:PRO438 4.8 18.2 1.0 N A:GLU439 4.9 17.6 1.0 CA A:ASN433 4.9 16.8 1.0 CG1 A:VAL437 4.9 17.1 1.0 CA A:ASN435 5.0 17.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of E. Coli Ygjk D324N Complexed with Melibiose


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 D324N Complexed with Melibiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:25.4 occ:1.00 OD1 B:ASN433 2.1 26.3 1.0 O B:VAL437 2.2 30.1 1.0 OE2 B:GLU439 2.2 27.2 1.0 OE2 B:GLU549 2.4 24.2 1.0 OD1 B:ASP431 2.5 22.1 1.0 OD1 B:ASN435 2.9 26.8 1.0 CG B:ASN433 3.2 24.9 1.0 CD B:GLU439 3.3 26.9 1.0 C B:VAL437 3.4 29.2 1.0 CD B:GLU549 3.4 23.9 1.0 ND2 B:ASN433 3.6 24.6 1.0 CG B:ASN435 3.6 26.1 1.0 CG B:ASP431 3.7 22.6 1.0 CG B:GLU549 3.8 23.3 1.0 ND2 B:ASN435 4.0 25.4 1.0 OE1 B:GLU439 4.1 26.5 1.0 CA B:ASP431 4.2 22.3 1.0 CG B:GLU439 4.3 26.9 1.0 N B:ASN433 4.3 23.1 1.0 CA B:VAL437 4.3 28.9 1.0 N B:VAL437 4.3 28.9 1.0 N B:PRO438 4.3 28.1 1.0 CA B:PRO438 4.4 27.9 1.0 N B:HIS432 4.4 23.2 1.0 N B:ASN435 4.5 26.5 1.0 CD1 B:ILE608 4.5 31.2 1.0 CB B:ASP431 4.5 22.4 1.0 CB B:ASN433 4.5 23.9 1.0 C B:ASP431 4.5 23.1 1.0 CB B:VAL437 4.5 27.9 1.0 OD2 B:ASP431 4.6 21.7 1.0 C B:PRO438 4.6 27.7 1.0 OE1 B:GLU549 4.6 23.1 1.0 CB B:ASN435 4.6 26.4 1.0 N B:GLY434 4.7 24.5 1.0 O B:PRO438 4.7 29.1 1.0 CA B:ASN433 4.8 23.3 1.0 C B:ASN433 5.0 23.9 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