Calcium in PDB 7fe2: Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose

The structure of Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose, PDB code: 7fe2 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)	48.57 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	162.626, 168.61, 260.282, 90, 90, 90
R / Rfree (%)	16.9 / 19.8

The structure of Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose (pdb code 7fe2). 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 the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose, PDB code: 7fe2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:29.7 occ:1.00 O3 E:MAN2 2.4 27.4 1.0 O2 E:MAN2 2.4 44.7 1.0 OD2 A:ASP604 2.4 17.5 1.0 O A:HOH1137 2.4 16.8 1.0 OD1 A:ASN562 2.5 20.0 1.0 OE1 A:GLN563 2.6 18.9 1.0 O A:HOH1064 2.6 16.5 1.0 O A:HOH925 2.9 22.7 1.0 CG A:ASP604 3.5 18.3 1.0 CD A:GLN563 3.5 18.4 1.0 C2 E:MAN2 3.6 40.1 1.0 C3 E:MAN2 3.6 38.0 1.0 CG A:ASN562 3.7 20.0 1.0 NE2 A:GLN563 3.8 18.5 1.0 OD1 A:ASP604 3.9 18.1 1.0 CB A:ASP602 4.0 18.2 1.0 OD1 A:ASP313 4.1 25.4 1.0 CZ3 A:TRP312 4.4 38.6 1.0 CA A:ASN562 4.5 17.1 1.0 OE1 A:GLN494 4.5 29.3 1.0 N A:GLN563 4.5 17.6 1.0 O A:HOH1027 4.5 17.3 1.0 O A:ASP602 4.6 17.0 1.0 ND2 A:ASN562 4.6 21.0 1.0 C1 E:MAN2 4.6 39.1 1.0 CB A:ASN562 4.6 17.3 1.0 OD2 A:ASP602 4.7 18.7 1.0 C4 E:MAN2 4.7 35.9 1.0 CB A:ASP604 4.7 17.7 1.0 OE1 A:GLU546 4.8 23.2 1.0 O A:SER561 4.8 18.0 1.0 CG A:ASP602 4.8 18.2 1.0 CG A:GLN563 4.9 20.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:32.1 occ:1.00 O3 F:MAN2 2.3 32.8 1.0 OD2 B:ASP604 2.3 20.0 1.0 OE1 B:GLN563 2.4 21.5 1.0 O2 F:MAN2 2.4 45.0 1.0 O B:HOH1061 2.5 18.7 1.0 OD1 B:ASN562 2.5 22.1 1.0 O B:HOH1091 2.5 21.1 1.0 O B:HOH975 3.1 29.5 1.0 CD B:GLN563 3.4 19.9 1.0 CG B:ASP604 3.4 20.5 1.0 C3 F:MAN2 3.6 40.5 1.0 C2 F:MAN2 3.6 44.5 1.0 NE2 B:GLN563 3.7 20.5 1.0 CG B:ASN562 3.7 20.2 1.0 OD1 B:ASP604 3.9 22.3 1.0 CB B:ASP602 4.0 18.7 1.0 OD1 B:ASP313 4.2 30.1 1.0 CZ3 B:TRP312 4.4 48.6 1.0 CA B:ASN562 4.5 18.3 1.0 N B:GLN563 4.5 19.7 1.0 O B:HOH1009 4.5 20.1 1.0 CB B:ASN562 4.6 20.1 1.0 O B:ASP602 4.6 17.9 1.0 ND2 B:ASN562 4.6 20.8 1.0 C4 F:MAN2 4.6 38.2 1.0 CB B:ASP604 4.7 18.7 1.0 OE1 B:GLN494 4.7 35.5 1.0 C1 F:MAN2 4.7 42.5 1.0 O B:SER561 4.7 22.3 1.0 OD2 B:ASP602 4.8 22.8 1.0 CG B:GLN563 4.8 20.9 1.0 OE1 B:GLU546 4.8 26.3 1.0 CG B:ASP602 4.8 19.4 1.0 CA B:ASP602 5.0 17.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:32.5 occ:1.00 O2 G:MAN2 2.4 44.5 1.0 O3 G:MAN2 2.4 38.1 1.0 OD1 C:ASN562 2.5 20.2 1.0 O C:HOH1099 2.5 16.8 1.0 OE1 C:GLN563 2.5 21.4 1.0 OD2 C:ASP604 2.5 21.4 1.0 O C:HOH984 2.6 20.1 1.0 O C:HOH958 2.9 26.9 1.0 CD C:GLN563 3.4 22.6 1.0 CG C:ASP604 3.6 21.3 1.0 C2 G:MAN2 3.6 43.4 1.0 CG C:ASN562 3.6 21.0 1.0 C3 G:MAN2 3.6 40.4 1.0 NE2 C:GLN563 3.7 24.4 1.0 OD1 C:ASP604 4.0 21.4 1.0 CB C:ASP602 4.1 19.7 1.0 OD1 C:ASP313 4.2 27.4 1.0 CA C:ASN562 4.4 18.9 1.0 CZ3 C:TRP312 4.4 48.7 1.0 N C:GLN563 4.5 18.5 1.0 ND2 C:ASN562 4.5 22.8 1.0 CB C:ASN562 4.5 19.0 1.0 O C:HOH1006 4.5 21.1 1.0 C1 G:MAN2 4.5 41.6 1.0 O C:ASP602 4.6 20.1 1.0 OE1 C:GLN494 4.6 39.0 1.0 C4 G:MAN2 4.7 39.1 1.0 O C:SER561 4.7 18.2 1.0 OE1 C:GLU546 4.8 28.0 1.0 CB C:ASP604 4.8 19.2 1.0 OD2 C:ASP602 4.8 22.0 1.0 CG C:GLN563 4.8 23.7 1.0 CG C:ASP602 4.8 22.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose


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 the Mutant E494Q of GH92 Alpha-1,2-Mannosidase From Enterococcus Faecalis Atcc 10100 in Complex with Alpha-1,2- Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:35.2 occ:1.00 OD2 D:ASP604 2.4 21.3 1.0 O3 H:MAN2 2.4 37.4 1.0 O2 H:MAN2 2.4 52.0 1.0 OE1 D:GLN563 2.5 20.0 1.0 O D:HOH1058 2.5 18.9 1.0 OD1 D:ASN562 2.6 19.6 1.0 O D:HOH1126 2.6 18.9 1.0 O D:HOH980 3.1 29.0 1.0 CD D:GLN563 3.4 22.4 1.0 CG D:ASP604 3.5 21.5 1.0 NE2 D:GLN563 3.6 22.2 1.0 CG D:ASN562 3.7 20.9 1.0 C3 H:MAN2 3.7 49.5 1.0 C2 H:MAN2 3.7 53.1 1.0 CB D:ASP602 4.0 19.2 1.0 OD1 D:ASP604 4.1 22.8 1.0 OD1 D:ASP313 4.2 32.2 1.0 CZ3 D:TRP312 4.4 52.5 1.0 CA D:ASN562 4.4 18.3 1.0 N D:GLN563 4.4 19.9 1.0 O D:HOH1020 4.4 20.0 1.0 O D:ASP602 4.5 20.7 1.0 CB D:ASN562 4.5 18.5 1.0 ND2 D:ASN562 4.6 22.2 1.0 NE2 D:GLN494 4.7 38.1 1.0 CB D:ASP604 4.7 18.4 1.0 O D:SER561 4.7 18.9 1.0 C1 H:MAN2 4.7 53.3 1.0 C4 H:MAN2 4.8 49.1 1.0 CG D:GLN563 4.8 22.1 1.0 CG D:ASP602 4.8 21.2 1.0 OD2 D:ASP602 4.9 21.4 1.0 OE1 D:GLU546 4.9 28.8 1.0 CA D:ASP602 5.0 18.8 1.0 C D:ASN562 5.0 17.8 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