Calcium in PDB 7fe1: Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside

The structure of Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside, PDB code: 7fe1 was solved by T.Miyazaki, S.Alonso-Gil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.62 / 1.72
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.162, 169.601, 258.659, 90, 90, 90
R / Rfree (%)	14.9 / 17.1

The structure of Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside (pdb code 7fe1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside, PDB code: 7fe1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside


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 GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:21.3 occ:1.00 O3 A:MAN802 2.4 19.1 1.0 O A:HOH1191 2.4 16.4 1.0 OD1 A:ASN562 2.5 16.6 1.0 OD2 A:ASP604 2.5 16.2 1.0 OE1 A:GLN563 2.5 16.6 1.0 O A:HOH1078 2.5 15.6 1.0 O2 A:MAN802 2.6 31.4 1.0 O A:HOH997 2.7 19.6 1.0 CD A:GLN563 3.5 17.6 1.0 CG A:ASP604 3.5 16.6 1.0 C3 A:MAN802 3.5 27.8 1.0 C2 A:MAN802 3.6 34.1 1.0 CG A:ASN562 3.6 17.3 1.0 NE2 A:GLN563 3.8 17.8 1.0 OD1 A:ASP604 3.9 16.3 1.0 CB A:ASP602 4.1 15.4 1.0 OD1 A:ASP313 4.2 19.9 1.0 C1 A:MAN802 4.3 29.4 1.0 CZ3 A:TRP312 4.5 25.3 1.0 ND2 A:ASN562 4.5 16.6 1.0 CA A:ASN562 4.5 16.4 1.0 O A:HOH910 4.5 35.6 1.0 N A:GLN563 4.5 15.7 1.0 C4 A:MAN802 4.5 26.4 1.0 CB A:ASN562 4.5 16.2 1.0 O A:ASP602 4.6 15.3 1.0 O A:HOH980 4.6 14.1 1.0 OD2 A:ASP602 4.7 17.1 1.0 OE1 A:GLU546 4.7 17.7 1.0 CB A:ASP604 4.8 16.1 1.0 O A:SER561 4.8 16.2 1.0 CG A:ASP602 4.8 17.0 1.0 CG A:GLN563 4.8 17.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside


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 GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:20.7 occ:1.00 O3 B:MAN802 2.4 21.9 1.0 OD2 B:ASP604 2.4 15.9 1.0 OE1 B:GLN563 2.4 17.1 1.0 O B:HOH1208 2.5 15.7 1.0 O B:HOH1176 2.5 17.2 1.0 OD1 B:ASN562 2.6 17.9 1.0 O B:HOH1011 2.6 19.2 1.0 O2 B:MAN802 2.6 29.2 1.0 CG B:ASP604 3.4 17.7 1.0 CD B:GLN563 3.4 17.6 1.0 C3 B:MAN802 3.5 27.7 1.0 C2 B:MAN802 3.5 33.6 1.0 CG B:ASN562 3.7 17.9 1.0 NE2 B:GLN563 3.8 18.1 1.0 OD1 B:ASP604 3.9 17.5 1.0 CB B:ASP602 4.1 16.7 1.0 OD1 B:ASP313 4.2 20.2 1.0 C1 B:MAN802 4.4 30.2 1.0 C4 B:MAN802 4.5 26.5 1.0 CZ3 B:TRP312 4.5 27.0 1.0 N B:GLN563 4.5 16.2 1.0 CA B:ASN562 4.6 16.3 1.0 ND2 B:ASN562 4.6 18.4 1.0 O B:HOH931 4.6 31.0 1.0 CB B:ASN562 4.6 17.4 1.0 O B:HOH1045 4.6 16.0 1.0 O B:ASP602 4.6 14.8 1.0 CB B:ASP604 4.7 16.1 1.0 OD2 B:ASP602 4.7 17.8 1.0 OE1 B:GLU546 4.8 16.6 1.0 CG B:GLN563 4.8 19.3 1.0 O B:SER561 4.9 16.8 1.0 CG B:ASP602 4.9 17.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca803 b:21.1 occ:1.00 O C:HOH1216 2.5 15.7 1.0 OE1 C:GLN563 2.5 18.6 1.0 O3 C:MAN802 2.5 21.4 1.0 OD2 C:ASP604 2.5 19.1 1.0 OD1 C:ASN562 2.5 17.9 1.0 O2 C:MAN802 2.5 26.2 1.0 O C:HOH1054 2.5 15.8 1.0 O C:HOH1126 2.5 18.9 1.0 CD C:GLN563 3.5 19.3 1.0 C2 C:MAN802 3.5 27.8 1.0 C3 C:MAN802 3.5 26.8 1.0 CG C:ASP604 3.5 17.0 1.0 CG C:ASN562 3.7 17.5 1.0 NE2 C:GLN563 3.8 20.6 1.0 OD1 C:ASP604 4.0 18.1 1.0 CB C:ASP602 4.1 16.7 1.0 OD1 C:ASP313 4.3 19.5 1.0 C1 C:MAN802 4.4 26.1 1.0 C4 C:MAN802 4.5 25.0 1.0 CZ3 C:TRP312 4.5 24.1 1.0 ND2 C:ASN562 4.5 18.5 1.0 CA C:ASN562 4.5 16.5 1.0 N C:GLN563 4.5 16.6 1.0 CB C:ASN562 4.6 18.8 1.0 O C:ASP602 4.6 17.4 1.0 O C:HOH1029 4.6 16.8 1.0 O C:HOH957 4.6 30.7 1.0 OD2 C:ASP602 4.7 18.9 1.0 OE1 C:GLU546 4.8 20.7 1.0 CB C:ASP604 4.8 17.1 1.0 CG C:GLN563 4.8 19.9 1.0 CG C:ASP602 4.8 19.6 1.0 O C:SER561 4.9 16.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Methyl Alpha-1,2-C-Mannobioside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca803 b:21.7 occ:1.00 OD2 D:ASP604 2.4 20.8 1.0 OD1 D:ASN562 2.4 18.6 1.0 OE1 D:GLN563 2.4 18.0 1.0 O3 D:MAN802 2.5 24.9 1.0 O D:HOH1065 2.5 19.3 1.0 O D:HOH1133 2.5 18.2 1.0 O D:HOH1071 2.6 22.4 1.0 O2 D:MAN802 2.7 31.7 1.0 CD D:GLN563 3.5 20.4 1.0 CG D:ASP604 3.5 18.5 1.0 C3 D:MAN802 3.6 33.8 1.0 CG D:ASN562 3.6 16.9 1.0 C2 D:MAN802 3.6 36.3 1.0 NE2 D:GLN563 3.8 19.8 1.0 OD1 D:ASP604 4.0 20.4 1.0 CB D:ASP602 4.0 16.3 1.0 OD1 D:ASP313 4.3 23.0 1.0 C1 D:MAN802 4.3 34.0 1.0 ND2 D:ASN562 4.4 17.9 1.0 O D:HOH903 4.5 37.1 1.0 CB D:ASN562 4.5 17.4 1.0 CA D:ASN562 4.5 15.8 1.0 N D:GLN563 4.5 18.8 1.0 CZ3 D:TRP312 4.6 28.0 1.0 O D:HOH1023 4.6 18.8 1.0 O D:ASP602 4.6 18.9 1.0 C4 D:MAN802 4.6 34.8 1.0 OD2 D:ASP602 4.7 19.4 1.0 OE1 D:GLU546 4.7 22.0 1.0 CB D:ASP604 4.7 17.4 1.0 CG D:ASP602 4.8 19.8 1.0 O D:SER561 4.8 18.4 1.0 CG D:GLN563 4.8 18.8 1.0

S.Alonso-Gil, K.Parkan, J.Kaminsky, R.Pohl, T.Miyazaki. Unlocking the Hydrolytic Mechanism of GH92 Alpha-1,2-Mannosidases: Computation Inspires the Use of C-Glycosides As Michaelis Complex Mimics. Chemistry V. 28 00148 2022.
ISSN: ISSN 0947-6539
PubMed: 35049087
DOI: 10.1002/CHEM.202200148