Calcium in PDB 2wvz: 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: 2wvz was solved by M.D.L.Suits, Y.Zhu, A.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)	191.14 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.900, 150.190, 382.290, 90.00, 90.00, 90.00
R / Rfree (%)	20.112 / 25.718

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

Calcium binding site 1 out of 4 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:32.9 occ:1.00 OD1 A:ASN601 2.2 35.0 1.0 O2 A:KIF801 2.4 25.5 1.0 O3 A:KIF801 2.5 28.4 1.0 O A:HOH2209 2.6 18.7 1.0 O A:HOH2188 2.6 50.4 1.0 OD2 A:ASP644 2.6 24.6 1.0 OE1 A:GLN602 2.7 26.5 1.0 C2 A:KIF801 3.4 26.8 1.0 CG A:ASN601 3.4 32.1 1.0 C3 A:KIF801 3.5 27.7 1.0 CD A:GLN602 3.6 26.9 1.0 CG A:ASP644 3.6 24.1 1.0 NE2 A:GLN602 3.9 29.8 1.0 OD1 A:ASP644 3.9 23.6 1.0 C1 A:KIF801 4.0 27.1 1.0 ND2 A:ASN601 4.1 32.5 1.0 CB A:ASP642 4.2 23.9 1.0 OD2 A:ASP348 4.4 17.9 1.0 OE2 A:GLU533 4.4 40.8 1.0 O A:GLY600 4.4 30.2 1.0 CZ3 A:TRP347 4.5 22.8 1.0 CB A:ASN601 4.6 30.2 1.0 N9 A:KIF801 4.6 29.5 1.0 C4 A:KIF801 4.6 26.4 1.0 CA A:ASN601 4.6 29.6 1.0 OE2 A:GLU585 4.7 31.5 1.0 OD2 A:ASP642 4.8 26.5 1.0 N A:GLN602 4.8 28.2 1.0 CG A:ASP642 4.8 24.7 1.0 CB A:ASP644 4.9 22.8 1.0 CG A:GLN602 5.0 26.0 1.0

Calcium binding site 2 out of 4 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:30.6 occ:1.00 OD1 B:ASN601 2.3 34.5 1.0 O3 B:KIF801 2.4 34.9 1.0 O2 B:KIF801 2.4 31.5 1.0 OD2 B:ASP644 2.5 27.3 1.0 O B:HOH2136 2.6 19.3 1.0 OE1 B:GLN602 2.6 30.0 1.0 C2 B:KIF801 3.3 35.7 1.0 C3 B:KIF801 3.3 35.7 1.0 CG B:ASN601 3.5 31.6 1.0 CD B:GLN602 3.6 29.2 1.0 CG B:ASP644 3.6 28.0 1.0 NE2 B:GLN602 3.8 29.4 1.0 C1 B:KIF801 4.0 36.5 1.0 OD1 B:ASP644 4.0 31.0 1.0 OD2 B:ASP348 4.1 19.7 1.0 OE2 B:GLU533 4.1 38.1 1.0 CB B:ASP642 4.3 22.1 1.0 ND2 B:ASN601 4.3 32.5 1.0 O B:HOH2133 4.4 26.2 1.0 CA B:ASN601 4.4 30.3 1.0 CZ3 B:TRP347 4.5 25.6 1.0 O B:GLY600 4.5 31.2 1.0 CB B:ASN601 4.5 30.8 1.0 OE2 B:GLU585 4.5 32.9 1.0 C4 B:KIF801 4.6 36.0 1.0 N B:GLN602 4.6 29.7 1.0 N9 B:KIF801 4.7 37.6 1.0 O B:ASP642 4.8 22.8 1.0 CB B:ASP644 4.8 26.2 1.0 OD2 B:ASP642 5.0 22.9 1.0 CG B:GLN602 5.0 28.7 1.0

Calcium binding site 3 out of 4 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:26.7 occ:1.00 O2 C:KIF801 2.2 33.7 1.0 OD1 C:ASN601 2.4 27.5 1.0 OD2 C:ASP644 2.5 26.9 1.0 O3 C:KIF801 2.5 35.8 1.0 OE1 C:GLN602 2.6 33.4 1.0 O C:HOH2156 2.6 10.8 1.0 C2 C:KIF801 3.2 34.8 1.0 CG C:ASP644 3.3 27.4 1.0 C3 C:KIF801 3.4 34.6 1.0 CG C:ASN601 3.6 25.9 1.0 CD C:GLN602 3.6 30.8 1.0 OD1 C:ASP644 3.6 28.9 1.0 C1 C:KIF801 3.7 35.6 1.0 NE2 C:GLN602 3.9 30.4 1.0 OD2 C:ASP348 4.0 23.7 1.0 CB C:ASP642 4.2 23.7 1.0 ND2 C:ASN601 4.2 27.9 1.0 N9 C:KIF801 4.2 36.8 1.0 O C:HOH2139 4.3 27.3 1.0 CZ3 C:TRP347 4.4 21.6 1.0 OE2 C:GLU533 4.5 35.8 1.0 C4 C:KIF801 4.5 35.1 1.0 CB C:ASP644 4.6 25.6 1.0 OE2 C:GLU585 4.6 27.2 1.0 CA C:ASN601 4.7 25.5 1.0 CB C:ASN601 4.7 25.8 1.0 O C:GLY600 4.8 24.4 1.0 OD2 C:ASP642 4.8 27.0 1.0 N C:GLN602 4.8 25.6 1.0 CG C:ASP642 4.9 25.7 1.0 CG C:GLN602 4.9 27.2 1.0 CG C:ASP348 5.0 21.4 1.0 O C:ASP642 5.0 25.0 1.0

Calcium binding site 4 out of 4 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:45.0 occ:1.00 O3 D:KIF801 2.2 40.7 1.0 O2 D:KIF801 2.2 38.4 1.0 OE1 D:GLN602 2.5 40.0 1.0 OD2 D:ASP644 2.5 31.4 1.0 O D:HOH2166 2.6 26.1 1.0 O D:HOH2155 2.6 27.8 1.0 OD1 D:ASN601 2.8 48.0 1.0 C2 D:KIF801 3.2 38.6 1.0 C3 D:KIF801 3.2 38.9 1.0 CG D:ASP644 3.4 30.5 1.0 CD D:GLN602 3.5 41.4 1.0 OD1 D:ASP644 3.7 31.3 1.0 CG D:ASN601 3.8 47.2 1.0 C1 D:KIF801 3.9 38.2 1.0 NE2 D:GLN602 3.9 41.2 1.0 CB D:ASP642 4.2 28.6 1.0 OD2 D:ASP348 4.2 22.9 1.0 OE2 D:GLU533 4.3 47.3 1.0 CZ3 D:TRP347 4.3 39.3 1.0 C4 D:KIF801 4.4 37.9 1.0 ND2 D:ASN601 4.5 49.2 1.0 N9 D:KIF801 4.5 37.8 1.0 CA D:ASN601 4.6 45.5 1.0 N D:GLN602 4.6 44.8 1.0 O D:GLY600 4.6 44.5 1.0 CB D:ASP644 4.7 29.1 1.0 CG D:GLN602 4.8 43.5 1.0 CB D:ASN601 4.8 46.1 1.0 CH2 D:TRP347 4.9 40.1 1.0 CG D:ASP642 5.0 29.5 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