Calcium in PDB 3w7t: Escherichia Coli K12 Ygjk Complexed with Mannose

The structure of Escherichia Coli K12 Ygjk Complexed with Mannose, PDB code: 3w7t 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)	46.03 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.467, 137.844, 86.524, 90.00, 98.07, 90.00
R / Rfree (%)	15.4 / 18

The structure of Escherichia Coli K12 Ygjk Complexed with Mannose also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Escherichia Coli K12 Ygjk Complexed with Mannose (pdb code 3w7t). 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 Mannose, PDB code: 3w7t:
Jump to Calcium binding site number: 1; 2;

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


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 Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:9.2 occ:1.00 OE2 A:GLU439 2.2 10.3 1.0 O A:VAL437 2.2 10.9 1.0 OD1 A:ASN433 2.3 11.4 1.0 OD1 A:ASP431 2.4 11.4 1.0 OE2 A:GLU549 2.4 9.9 1.0 OD1 A:ASN435 2.4 10.5 1.0 CG A:ASN435 3.4 11.2 1.0 CD A:GLU549 3.4 10.2 1.0 C A:VAL437 3.4 10.7 1.0 CG A:ASN433 3.4 11.9 1.0 CD A:GLU439 3.5 10.3 1.0 CG A:ASP431 3.5 11.1 1.0 CG A:GLU549 3.8 10.0 1.0 ND2 A:ASN435 3.8 10.7 1.0 ND2 A:ASN433 3.9 11.9 1.0 N A:VAL437 4.0 10.9 1.0 CA A:VAL437 4.1 10.5 1.0 CA A:ASP431 4.1 11.1 1.0 CB A:VAL437 4.2 10.4 1.0 OE1 A:GLU439 4.3 10.7 1.0 CB A:ASP431 4.4 11.2 1.0 OD2 A:ASP431 4.4 11.0 1.0 N A:ASN435 4.4 11.5 1.0 CG A:GLU439 4.4 10.2 1.0 N A:ASN433 4.4 12.2 1.0 C A:ASP431 4.4 11.4 1.0 N A:PRO438 4.5 11.2 1.0 N A:HIS432 4.5 11.4 1.0 OE1 A:GLU549 4.5 10.4 1.0 CD1 A:ILE608 4.6 11.7 1.0 CB A:ASN435 4.6 11.4 1.0 CA A:PRO438 4.6 11.2 1.0 C A:PRO438 4.6 11.2 1.0 CB A:ASN433 4.7 11.7 1.0 N A:GLY434 4.7 12.2 1.0 O A:PRO438 4.8 11.2 1.0 CA A:ASN435 4.9 11.9 1.0 CA A:ASN433 4.9 12.1 1.0 N A:GLY436 4.9 11.6 1.0

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


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 Mannose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:9.9 occ:1.00 O B:VAL437 2.2 11.7 1.0 OE2 B:GLU439 2.3 11.2 1.0 OD1 B:ASN433 2.3 11.4 1.0 OD1 B:ASP431 2.3 12.0 1.0 OE2 B:GLU549 2.4 11.0 1.0 OD1 B:ASN435 2.4 12.0 1.0 C B:VAL437 3.4 12.8 1.0 CG B:ASN433 3.4 12.2 1.0 CD B:GLU549 3.4 10.8 1.0 CG B:ASN435 3.4 12.0 1.0 CD B:GLU439 3.5 11.1 1.0 CG B:ASP431 3.5 11.8 1.0 CG B:GLU549 3.8 10.9 1.0 ND2 B:ASN433 3.8 12.8 1.0 ND2 B:ASN435 3.9 11.9 1.0 N B:VAL437 4.0 12.7 1.0 CA B:VAL437 4.1 12.8 1.0 CB B:VAL437 4.1 12.5 1.0 CA B:ASP431 4.2 11.4 1.0 OE1 B:GLU439 4.3 10.7 1.0 N B:ASN435 4.4 13.5 1.0 N B:PRO438 4.4 14.7 1.0 CB B:ASP431 4.4 11.6 1.0 N B:ASN433 4.4 12.6 1.0 OD2 B:ASP431 4.4 11.7 1.0 CG B:GLU439 4.4 11.0 1.0 OE1 B:GLU549 4.4 11.5 1.0 C B:ASP431 4.5 11.7 1.0 CA B:PRO438 4.5 14.3 1.0 CD1 B:ILE608 4.5 12.4 1.0 N B:HIS432 4.5 12.5 1.0 CB B:ASN435 4.6 12.6 1.0 C B:PRO438 4.6 13.9 1.0 CB B:ASN433 4.7 12.6 1.0 N B:GLY434 4.7 13.1 1.0 CA B:ASN435 4.9 13.3 1.0 CA B:ASN433 4.9 12.9 1.0 O B:PRO438 4.9 16.1 1.0 N B:GLY436 4.9 13.3 1.0 CG1 B:VAL437 4.9 12.6 1.0 C B:ASN433 5.0 13.3 1.0 N B:GLU439 5.0 11.9 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