Calcium in PDB 2ww0: Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482

The structure of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 2ww0 was solved by M.D.L.Suits, A.Thompson, Y.Zhu, 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)	218.23 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.810, 151.960, 218.619, 90.00, 93.43, 90.00
R / Rfree (%)	18.439 / 21.156

The binding sites of Calcium atom in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 (pdb code 2ww0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482, PDB code: 2ww0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca800 b:28.4 occ:1.00 O13 A:SWA801 2.2 41.0 1.0 OD2 A:ASP644 2.3 18.9 1.0 O11 A:SWA801 2.5 39.2 1.0 OD1 A:ASN601 2.6 20.9 1.0 OE1 A:GLN602 2.6 17.4 1.0 O A:HOH2097 2.7 2.0 1.0 C8 A:SWA801 3.1 40.0 1.0 CG A:ASP644 3.3 15.7 1.0 C7 A:SWA801 3.3 39.8 1.0 C9 A:SWA801 3.4 40.7 1.0 OD1 A:ASP644 3.5 16.7 1.0 CD A:GLN602 3.6 15.8 1.0 CG A:ASN601 3.8 18.7 1.0 NE2 A:GLN602 3.9 17.0 1.0 CB A:ASP642 4.1 12.6 1.0 OD2 A:ASP348 4.4 13.5 1.0 OE2 A:GLU585 4.5 18.4 1.0 ND2 A:ASN601 4.5 19.6 1.0 C3 A:SWA801 4.5 40.1 1.0 OD2 A:ASP642 4.5 15.4 1.0 OE2 A:GLU533 4.6 24.6 1.0 N4 A:SWA801 4.6 40.8 1.0 CB A:ASP644 4.6 14.1 1.0 CZ3 A:TRP347 4.6 9.4 1.0 O A:GLY600 4.8 16.3 1.0 CG A:ASP642 4.8 13.2 1.0 C1 A:SWA801 4.8 38.9 1.0 O A:ASP642 4.8 13.1 1.0 CA A:ASN601 4.9 16.6 1.0 CB A:ASN601 4.9 17.0 1.0 CG A:GLN602 4.9 14.5 1.0 N A:GLN602 4.9 15.7 1.0

Calcium binding site 2 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca800 b:11.4 occ:1.00 OD2 B:ASP644 2.3 18.8 1.0 O13 B:SWA801 2.4 17.4 1.0 OD1 B:ASN601 2.4 20.8 1.0 O B:HOH2096 2.5 8.1 1.0 OE1 B:GLN602 2.6 17.5 1.0 O11 B:SWA801 2.8 9.5 1.0 C8 B:SWA801 3.4 13.5 1.0 CG B:ASP644 3.4 15.7 1.0 C9 B:SWA801 3.4 15.0 1.0 CD B:GLN602 3.5 15.9 1.0 CG B:ASN601 3.6 18.6 1.0 C7 B:SWA801 3.7 13.4 1.0 NE2 B:GLN602 3.8 17.1 1.0 OD1 B:ASP644 3.8 16.8 1.0 O B:HOH2095 3.9 11.6 1.0 CB B:ASP642 4.1 12.5 1.0 OE2 B:GLU585 4.3 18.1 1.0 ND2 B:ASN601 4.4 19.1 1.0 OD2 B:ASP348 4.5 13.7 1.0 O B:GLY600 4.5 16.5 1.0 OD2 B:ASP642 4.6 15.2 1.0 N4 B:SWA801 4.6 15.2 1.0 CA B:ASN601 4.6 16.5 1.0 C3 B:SWA801 4.7 14.3 1.0 CB B:ASN601 4.7 17.0 1.0 OE2 B:GLU533 4.7 24.8 1.0 CZ3 B:TRP347 4.7 9.5 1.0 CB B:ASP644 4.7 14.0 1.0 N B:GLN602 4.8 15.7 1.0 O B:ASP642 4.8 12.9 1.0 CG B:ASP642 4.8 13.2 1.0 C1 B:SWA801 4.9 14.4 1.0 CG B:GLN602 4.9 14.4 1.0

Calcium binding site 3 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca800 b:23.8 occ:1.00 O13 C:SWA801 2.1 24.2 1.0 OD2 C:ASP644 2.4 18.9 1.0 OD1 C:ASN601 2.4 21.0 1.0 OE1 C:GLN602 2.8 17.4 1.0 O C:HOH2061 2.8 3.2 1.0 O11 C:SWA801 3.1 21.8 1.0 C8 C:SWA801 3.4 22.6 1.0 CG C:ASP644 3.5 15.7 1.0 CG C:ASN601 3.6 18.8 1.0 CD C:GLN602 3.7 16.0 1.0 C9 C:SWA801 3.8 21.8 1.0 OD1 C:ASP644 3.8 16.9 1.0 CB C:ASP642 3.8 12.5 1.0 C7 C:SWA801 3.9 21.5 1.0 NE2 C:GLN602 3.9 16.9 1.0 O C:HOH2055 4.1 17.4 1.0 OE2 C:GLU585 4.2 18.4 1.0 O C:GLY600 4.3 16.7 1.0 OD2 C:ASP642 4.4 15.4 1.0 ND2 C:ASN601 4.4 19.6 1.0 CG C:ASP642 4.5 13.4 1.0 CA C:ASN601 4.6 16.4 1.0 O C:ASP642 4.6 12.8 1.0 CB C:ASN601 4.7 16.9 1.0 OE2 C:GLU533 4.7 24.4 1.0 OD2 C:ASP348 4.7 13.6 1.0 CA C:ASP642 4.8 12.5 1.0 CB C:ASP644 4.8 14.0 1.0 N4 C:SWA801 4.8 21.8 1.0 N C:ASP642 4.8 12.2 1.0 C3 C:SWA801 4.9 21.4 1.0 N C:GLN602 4.9 15.7 1.0

Calcium binding site 4 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca800 b:30.5 occ:1.00 OD2 D:ASP644 2.1 18.7 1.0 O13 D:SWA801 2.2 20.3 1.0 OE1 D:GLN602 2.4 17.5 1.0 OD1 D:ASN601 2.5 20.8 1.0 O D:HOH2094 2.7 2.0 1.0 O11 D:SWA801 2.8 21.6 1.0 CG D:ASP644 3.2 15.6 1.0 CD D:GLN602 3.2 15.9 1.0 NE2 D:GLN602 3.4 17.1 1.0 C8 D:SWA801 3.5 20.0 1.0 OD1 D:ASP644 3.7 16.6 1.0 C7 D:SWA801 3.7 20.4 1.0 CG D:ASN601 3.7 18.6 1.0 CB D:ASP642 4.0 12.4 1.0 C9 D:SWA801 4.3 18.4 1.0 O D:GLY600 4.3 16.3 1.0 OD2 D:ASP348 4.4 13.7 1.0 CB D:ASP644 4.5 13.9 1.0 O D:ASP642 4.5 12.6 1.0 CA D:ASN601 4.5 16.6 1.0 ND2 D:ASN601 4.6 19.3 1.0 N D:GLN602 4.6 15.6 1.0 OE2 D:GLU585 4.7 18.0 1.0 OD2 D:ASP642 4.7 15.2 1.0 CB D:ASN601 4.7 17.0 1.0 CG D:GLN602 4.7 14.5 1.0 CG D:ASP642 4.8 13.4 1.0 C3 D:SWA801 4.8 19.1 1.0 CA D:ASP642 4.9 12.4 1.0 CZ3 D:TRP347 4.9 9.5 1.0 N D:ASP642 4.9 12.3 1.0 N4 D:SWA801 4.9 18.1 1.0 OE2 D:GLU533 5.0 24.3 1.0 C D:ASP642 5.0 12.7 1.0

Calcium binding site 5 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca800 b:33.9 occ:1.00 OD2 E:ASP644 1.9 18.8 1.0 OE1 E:GLN602 2.5 17.5 1.0 O13 E:SWA801 2.5 12.7 1.0 OD1 E:ASN601 2.5 20.8 1.0 CG E:ASP644 3.1 15.8 1.0 O11 E:SWA801 3.2 13.4 1.0 CD E:GLN602 3.3 15.9 1.0 NE2 E:GLN602 3.5 17.0 1.0 OD1 E:ASP644 3.5 17.0 1.0 C8 E:SWA801 3.5 14.0 1.0 C9 E:SWA801 3.7 13.4 1.0 CG E:ASN601 3.8 18.6 1.0 CB E:ASP642 3.8 12.4 1.0 C7 E:SWA801 4.0 13.3 1.0 O E:GLY600 4.2 16.4 1.0 O E:ASP642 4.3 12.9 1.0 CB E:ASP644 4.4 14.1 1.0 CA E:ASN601 4.5 16.5 1.0 OD2 E:ASP348 4.5 13.8 1.0 OD2 E:ASP642 4.6 15.6 1.0 CA E:ASP642 4.7 12.4 1.0 CG E:ASP642 4.7 13.4 1.0 ND2 E:ASN601 4.7 19.3 1.0 CB E:ASN601 4.7 16.9 1.0 N E:GLN602 4.7 15.6 1.0 OE2 E:GLU585 4.7 18.3 1.0 N E:ASP642 4.7 12.2 1.0 CG E:GLN602 4.8 14.6 1.0 C E:ASP642 4.8 12.8 1.0

Calcium binding site 6 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


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 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca800 b:22.5 occ:1.00 OD2 F:ASP644 2.0 18.8 1.0 OE1 F:GLN602 2.3 17.5 1.0 OD1 F:ASN601 2.4 20.9 1.0 O11 F:SWA801 2.5 24.8 1.0 O13 F:SWA801 2.5 22.3 1.0 CD F:GLN602 3.1 16.0 1.0 CG F:ASP644 3.1 15.8 1.0 NE2 F:GLN602 3.4 17.1 1.0 C7 F:SWA801 3.5 24.2 1.0 C8 F:SWA801 3.5 23.7 1.0 CG F:ASN601 3.6 18.6 1.0 OD1 F:ASP644 3.6 16.8 1.0 CB F:ASP642 4.0 12.4 1.0 O F:GLY600 4.2 16.6 1.0 CA F:ASN601 4.3 16.5 1.0 OD2 F:ASP348 4.3 13.7 1.0 O F:ASP642 4.3 12.9 1.0 CB F:ASP644 4.4 14.1 1.0 N F:GLN602 4.5 15.6 1.0 N4 F:SWA801 4.5 24.9 1.0 C9 F:SWA801 4.5 23.9 1.0 CB F:ASN601 4.5 16.9 1.0 ND2 F:ASN601 4.6 19.5 1.0 CG F:GLN602 4.6 14.6 1.0 C3 F:SWA801 4.6 24.5 1.0 OE2 F:GLU585 4.8 18.3 1.0 CA F:ASP642 4.8 12.5 1.0 OD2 F:ASP642 4.8 15.2 1.0 N F:ASP642 4.9 12.4 1.0 CG F:ASP642 4.9 13.2 1.0 CZ3 F:TRP347 4.9 9.3 1.0 C F:ASP642 4.9 12.8 1.0 C F:ASN601 4.9 16.2 1.0

Calcium binding site 7 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca800 b:39.1 occ:1.00 OD2 G:ASP644 2.1 18.7 1.0 O13 G:SWA801 2.2 40.5 1.0 OE1 G:GLN602 2.3 17.5 1.0 C8 G:SWA801 2.4 41.5 1.0 OD1 G:ASN601 2.4 20.7 1.0 O11 G:SWA801 2.8 45.1 1.0 C7 G:SWA801 2.9 42.5 1.0 CD G:GLN602 3.1 16.0 1.0 CG G:ASP644 3.2 15.7 1.0 NE2 G:GLN602 3.2 16.9 1.0 CG G:ASN601 3.6 18.5 1.0 OD1 G:ASP644 3.8 16.9 1.0 O G:GLY600 3.8 16.4 1.0 CB G:ASP642 3.9 12.5 1.0 C9 G:SWA801 3.9 40.5 1.0 O G:ASP642 4.1 12.9 1.0 CA G:ASN601 4.1 16.5 1.0 C5 G:SWA801 4.4 40.1 1.0 C3 G:SWA801 4.4 41.0 1.0 N G:GLN602 4.4 15.6 1.0 CB G:ASP644 4.4 14.0 1.0 CB G:ASN601 4.4 16.9 1.0 N4 G:SWA801 4.6 40.5 1.0 CG G:GLN602 4.6 14.6 1.0 CA G:ASP642 4.6 12.5 1.0 N G:ASP642 4.6 12.3 1.0 OD2 G:ASP348 4.6 13.6 1.0 ND2 G:ASN601 4.6 19.4 1.0 C G:ASP642 4.7 12.8 1.0 CG G:ASP642 4.8 13.3 1.0 OD2 G:ASP642 4.8 15.2 1.0 C G:GLY600 4.8 16.0 1.0 C G:ASN601 4.8 16.3 1.0 OE2 G:GLU585 4.9 18.3 1.0

Calcium binding site 8 out of 8 in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca800 b:43.2 occ:1.00 O13 H:SWA801 1.9 26.1 1.0 OD2 H:ASP644 2.1 18.7 1.0 O11 H:SWA801 2.2 29.3 1.0 OE1 H:GLN602 2.4 17.4 1.0 OD1 H:ASN601 2.5 20.9 1.0 C8 H:SWA801 3.0 27.5 1.0 C7 H:SWA801 3.2 28.2 1.0 CD H:GLN602 3.2 16.0 1.0 CG H:ASP644 3.2 15.6 1.0 NE2 H:GLN602 3.3 17.0 1.0 C9 H:SWA801 3.6 28.0 1.0 CG H:ASN601 3.7 18.5 1.0 OD1 H:ASP644 3.7 16.7 1.0 CB H:ASP642 3.8 12.6 1.0 O H:GLY600 3.9 16.5 1.0 O H:ASP642 4.1 12.9 1.0 CA H:ASN601 4.3 16.5 1.0 C3 H:SWA801 4.3 28.6 1.0 C1 H:SWA801 4.4 30.4 1.0 CB H:ASP644 4.5 14.0 1.0 CB H:ASN601 4.5 16.9 1.0 N H:GLN602 4.5 15.6 1.0 CA H:ASP642 4.6 12.5 1.0 N H:ASP642 4.6 12.2 1.0 OD2 H:ASP348 4.6 13.6 1.0 ND2 H:ASN601 4.6 19.2 1.0 CG H:GLN602 4.7 14.6 1.0 N4 H:SWA801 4.7 27.0 1.0 C H:ASP642 4.7 12.7 1.0 CG H:ASP642 4.7 13.3 1.0 OD2 H:ASP642 4.7 15.1 1.0 OE2 H:GLU585 4.7 18.1 1.0 O1 H:SWA801 4.8 33.5 1.0 C H:GLY600 4.9 15.9 1.0 C H:ASN601 5.0 16.3 1.0

Y.Zhu, M.D.L.Suits, A.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 CA2+-Dependent Family of A-Mannosidases in A Human Gut Symbiont. Nat.Chem.Biol. V. 6 125 2010.
ISSN: ISSN 1552-4450
PubMed: 20081828
DOI: 10.1038/NCHEMBIO.278