Calcium in PDB 2ww3: Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside

The structure of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside, PDB code: 2ww3 was solved by M.D.L.Suits, Y.Zhu, A.J.Thompson, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	203.33 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	161.260, 68.590, 204.009, 90.00, 94.66, 90.00
R / Rfree (%)	18.989 / 24.366

The binding sites of Calcium atom in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside (pdb code 2ww3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside, PDB code: 2ww3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca800 b:25.9 occ:1.00 OD2 A:ASP644 2.0 28.1 1.0 O A:HOH2163 2.1 31.6 1.0 O13 A:SMD801 2.1 29.5 1.0 OE1 A:GLN602 2.2 25.7 1.0 O A:HOH2161 2.3 24.7 1.0 O12 A:SMD801 2.7 29.7 1.0 CG A:ASP644 3.0 26.8 1.0 CD A:GLN602 3.2 24.1 1.0 C12 A:SMD801 3.2 28.7 1.0 C13 A:SMD801 3.2 27.4 1.0 OD1 A:ASP644 3.3 26.1 1.0 NE2 A:GLN602 3.5 25.9 1.0 OD2 A:ASP348 3.8 21.7 1.0 O A:GLY600 4.1 26.1 1.0 CB A:ASP642 4.1 23.9 1.0 C14 A:SMD801 4.2 26.8 1.0 CB A:ASP644 4.3 25.0 1.0 OE2 A:GLU533 4.4 25.5 1.0 CZ3 A:TRP347 4.5 23.2 1.0 CG A:GLN602 4.5 24.5 1.0 O A:ASP642 4.6 24.9 1.0 C11 A:SMD801 4.7 28.7 1.0 CG A:ASP348 4.7 21.7 1.0 O14 A:SMD801 4.9 23.7 1.0 OD2 A:ASP642 5.0 25.4 1.0

Calcium binding site 2 out of 6 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca800 b:36.4 occ:1.00 OD2 B:ASP644 1.8 35.2 1.0 OE1 B:GLN602 2.0 32.1 1.0 O B:HOH2134 2.2 38.3 1.0 O13 B:SMD801 2.5 39.0 1.0 O B:HOH2123 2.5 36.7 1.0 O12 B:SMD801 2.7 40.0 1.0 CG B:ASP644 2.9 34.1 1.0 CD B:GLN602 3.0 30.8 1.0 NE2 B:GLN602 3.3 30.9 1.0 C12 B:SMD801 3.4 39.5 1.0 OD1 B:ASP644 3.4 34.5 1.0 C13 B:SMD801 3.5 39.3 1.0 O B:GLY600 3.9 33.2 1.0 OD2 B:ASP348 4.0 31.6 1.0 CB B:ASP644 4.1 32.4 1.0 CB B:ASP642 4.1 28.5 1.0 OE2 B:GLU533 4.3 35.7 1.0 CG B:GLN602 4.4 31.7 1.0 CZ3 B:TRP347 4.5 29.3 1.0 O B:ASP642 4.5 28.6 1.0 C14 B:SMD801 4.6 38.3 1.0 C11 B:SMD801 4.9 39.9 1.0 CB B:GLN602 4.9 31.2 1.0 N B:GLN602 4.9 32.1 1.0 O B:HOH2129 4.9 25.2 1.0 C B:GLY600 5.0 32.8 1.0

Calcium binding site 3 out of 6 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca800 b:26.3 occ:1.00 O C:HOH2260 2.1 27.4 1.0 O13 C:SMD801 2.1 27.0 1.0 OD2 C:ASP644 2.2 25.7 1.0 OE1 C:GLN602 2.3 26.0 1.0 O C:HOH2257 2.4 24.2 1.0 O12 C:SMD801 2.5 25.2 1.0 CG C:ASP644 3.0 22.2 1.0 C12 C:SMD801 3.1 25.4 1.0 C13 C:SMD801 3.2 26.3 1.0 CD C:GLN602 3.2 24.2 1.0 OD1 C:ASP644 3.3 22.9 1.0 NE2 C:GLN602 3.5 24.8 1.0 OD2 C:ASP348 3.7 22.0 1.0 CB C:ASP642 3.9 20.5 1.0 O C:GLY600 4.1 27.2 1.0 C14 C:SMD801 4.2 24.7 1.0 CB C:ASP644 4.3 21.3 1.0 O C:HOH2258 4.4 25.1 1.0 OE2 C:GLU533 4.4 28.0 1.0 CZ3 C:TRP347 4.5 17.8 1.0 O C:ASP642 4.5 21.1 1.0 C11 C:SMD801 4.6 24.8 1.0 CG C:GLN602 4.6 22.7 1.0 OD2 C:ASP642 4.7 21.0 1.0 CG C:ASP348 4.8 19.8 1.0 CG C:ASP642 4.8 21.0 1.0 O C:HOH2248 4.9 19.7 1.0 CA C:ASP642 4.9 20.7 1.0 O14 C:SMD801 4.9 24.7 1.0 C C:ASP642 4.9 20.7 1.0

Calcium binding site 4 out of 6 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca800 b:29.5 occ:1.00 OD2 D:ASP644 1.9 28.8 1.0 O D:HOH2117 2.2 37.1 1.0 O13 D:SMD801 2.3 30.6 1.0 O12 D:SMD801 2.3 30.7 1.0 OE1 D:GLN602 2.3 30.9 1.0 CG D:ASP644 2.9 29.1 1.0 C12 D:SMD801 3.0 30.5 1.0 C13 D:SMD801 3.2 31.5 1.0 CD D:GLN602 3.2 29.4 1.0 OD1 D:ASP644 3.3 30.6 1.0 NE2 D:GLN602 3.4 30.8 1.0 OD2 D:ASP348 3.8 26.4 1.0 CB D:ASP642 4.0 21.1 1.0 O D:GLY600 4.1 30.3 1.0 CB D:ASP644 4.2 28.5 1.0 C14 D:SMD801 4.3 32.0 1.0 C11 D:SMD801 4.4 31.2 1.0 OE2 D:GLU533 4.4 30.7 1.0 CZ3 D:TRP347 4.5 20.6 1.0 CG D:GLN602 4.5 29.1 1.0 O D:ASP642 4.7 21.7 1.0 CG D:ASP348 4.8 26.1 1.0 OD2 D:ASP642 4.9 22.8 1.0 CG D:ASP642 4.9 22.6 1.0 CA D:ASP642 5.0 21.8 1.0

Calcium binding site 5 out of 6 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca800 b:24.6 occ:1.00 OD2 E:ASP644 2.0 29.3 1.0 O E:HOH2149 2.1 36.6 1.0 OE1 E:GLN602 2.2 22.9 1.0 O13 E:SMD801 2.3 22.1 1.0 O E:HOH2148 2.3 22.9 1.0 O12 E:SMD801 2.6 28.3 1.0 CG E:ASP644 2.9 26.8 1.0 CD E:GLN602 3.0 23.5 1.0 OD1 E:ASP644 3.2 26.5 1.0 NE2 E:GLN602 3.2 22.2 1.0 C12 E:SMD801 3.3 27.7 1.0 C13 E:SMD801 3.3 26.1 1.0 OD2 E:ASP348 3.7 21.0 1.0 CB E:ASP642 4.1 23.5 1.0 O E:GLY600 4.1 26.3 1.0 CB E:ASP644 4.2 25.0 1.0 C14 E:SMD801 4.3 26.3 1.0 O E:ASP642 4.4 23.9 1.0 CG E:GLN602 4.4 23.0 1.0 CZ3 E:TRP347 4.5 20.1 1.0 OE2 E:GLU533 4.6 25.1 1.0 CG E:ASP348 4.7 22.3 1.0 C11 E:SMD801 4.7 27.4 1.0 OD2 E:ASP642 5.0 27.4 1.0 C E:ASP642 5.0 23.6 1.0 CB E:GLN602 5.0 23.7 1.0 O14 E:SMD801 5.0 25.3 1.0 CA E:ASP642 5.0 23.7 1.0

Calcium binding site 6 out of 6 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 in Complex with Thiomannobioside within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca800 b:31.2 occ:1.00 OD2 F:ASP644 1.8 34.2 1.0 O F:HOH2150 2.1 26.7 1.0 OE1 F:GLN602 2.3 28.4 1.0 O13 F:SMD801 2.3 31.2 1.0 O12 F:SMD801 2.3 33.0 1.0 CG F:ASP644 2.9 32.9 1.0 C12 F:SMD801 3.0 33.7 1.0 C13 F:SMD801 3.2 32.3 1.0 CD F:GLN602 3.2 29.8 1.0 OD1 F:ASP644 3.3 34.9 1.0 NE2 F:GLN602 3.6 29.8 1.0 OD2 F:ASP348 3.8 27.4 1.0 CB F:ASP642 4.0 28.5 1.0 O F:GLY600 4.1 32.2 1.0 CB F:ASP644 4.1 32.0 1.0 C14 F:SMD801 4.3 33.9 1.0 CZ3 F:TRP347 4.4 25.9 1.0 O F:HOH2148 4.4 29.4 1.0 OE2 F:GLU533 4.4 34.8 1.0 C11 F:SMD801 4.5 34.6 1.0 CG F:GLN602 4.6 28.7 1.0 O F:ASP642 4.6 28.9 1.0 CG F:ASP348 4.8 26.3 1.0 CA F:ASP642 4.9 29.0 1.0 CG F:ASP642 4.9 30.0 1.0

Y.Zhu, M.D.L.Suits, A.J.Thompson, S.Chavan, Z.Dinev, C.Dumon, N.Smith, K.W.Moremen, Y.Xiang, A.Siriwardena, S.J.Williams, H.J.Gilbert, G.J.Davies. Mechanistic Insights Into A Ca(2+)-Dependent Family of Alpha-Mannosidases in A Human Gut Symbiont. Nat.Chem.Biol. V. 6 125 2010.
ISSN: ISSN 1552-4450
PubMed: 20081828
DOI: 10.1038/NCHEMBIO.278