Calcium in PDB 2wvx: 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: 2wvx 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)	133.63 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.230, 190.950, 135.100, 90.00, 96.97, 90.00
R / Rfree (%)	15.502 / 18.647

The binding sites of Calcium atom in the Structure of the Family GH92 Inverting Mannosidase BT3990 From Bacteroides Thetaiotaomicron Vpi-5482 (pdb code 2wvx). 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: 2wvx:
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:Ca801 b:23.2 occ:1.00 O A:HOH2369 2.3 16.1 1.0 O A:GLY600 2.4 9.2 1.0 O A:HOH2448 2.4 17.2 1.0 OE1 A:GLN602 2.4 9.9 1.0 OD2 A:ASP644 2.7 20.1 1.0 O A:HOH2453 2.7 24.5 1.0 OE2 A:GLU533 2.8 16.1 1.0 O A:HOH2421 2.9 26.7 1.0 CD A:GLN602 3.4 10.0 1.0 C A:GLY600 3.5 8.7 1.0 CD A:GLU533 3.6 17.1 1.0 OE1 A:GLU533 3.6 20.6 1.0 NE2 A:GLN602 3.8 12.0 1.0 O A:HOH2454 3.8 25.2 1.0 CG A:ASP644 4.0 18.2 1.0 N A:GLN602 4.1 6.7 1.0 CA A:ASN601 4.3 7.8 1.0 N A:ASN601 4.3 8.0 1.0 CA A:GLY600 4.4 7.8 1.0 O A:ASP642 4.4 7.3 1.0 O A:HOH2405 4.5 24.4 1.0 CB A:ASP642 4.6 6.9 1.0 O A:HOH2449 4.7 16.1 1.0 C A:ASN601 4.7 7.6 1.0 O A:HOH2408 4.7 18.0 1.0 CG A:GLN602 4.7 10.3 1.0 O A:HOH2450 4.8 18.3 1.0 OD1 A:ASP644 4.8 19.6 1.0 CB A:ASP644 4.9 13.4 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:Ca801 b:26.3 occ:1.00 O B:HOH2312 2.2 30.3 1.0 OE1 B:GLN602 2.5 11.7 1.0 O B:HOH2311 2.5 19.7 1.0 O B:GLY600 2.5 13.0 1.0 OE2 B:GLU533 2.5 19.1 1.0 OD2 B:ASP644 2.5 20.5 1.0 CD B:GLU533 3.5 18.4 1.0 CD B:GLN602 3.5 11.9 1.0 C B:GLY600 3.6 11.3 1.0 CG B:ASP644 3.8 20.1 1.0 NE2 B:GLN602 3.9 14.0 1.0 OE1 B:GLU533 3.9 21.1 1.0 N B:GLN602 4.2 9.5 1.0 CA B:ASN601 4.3 10.3 1.0 N B:ASN601 4.4 10.9 1.0 O B:HOH2344 4.4 10.5 1.0 OD1 B:ASP644 4.4 21.7 1.0 CA B:GLY600 4.5 11.1 1.0 O B:ASP642 4.6 10.2 1.0 CB B:ASP642 4.6 10.9 1.0 CG B:GLU533 4.6 16.9 1.0 C B:ASN601 4.7 10.3 1.0 CG B:GLN602 4.8 11.6 1.0 O B:HOH2343 4.8 16.7 1.0 CB B:ASP644 4.9 15.9 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:Ca801 b:19.8 occ:1.00 O C:GLY600 2.3 9.0 1.0 OD2 C:ASP644 2.4 11.9 0.5 O C:HOH2386 2.4 24.3 1.0 OE2 C:GLU533 2.5 15.5 1.0 NE2 C:GLN602 2.5 9.3 1.0 OD2 C:ASP644 2.7 11.2 0.5 O C:HOH2431 2.8 18.9 1.0 OD1 C:ASP644 3.0 15.0 0.5 CG C:ASP644 3.2 12.1 0.5 CD C:GLU533 3.4 17.5 1.0 C C:GLY600 3.4 8.8 1.0 CD C:GLN602 3.5 11.7 1.0 CG C:ASP644 3.6 12.5 0.5 OE1 C:GLU533 3.7 19.9 1.0 OE1 C:GLN602 3.8 14.1 1.0 N C:GLN602 4.1 7.2 1.0 CA C:ASN601 4.3 8.1 1.0 N C:ASN601 4.3 7.8 1.0 CA C:GLY600 4.3 8.9 1.0 O C:HOH2419 4.3 5.1 1.0 OD1 C:ASP644 4.4 11.6 0.5 O C:ASP642 4.5 9.0 1.0 CB C:ASP644 4.6 11.0 0.5 C C:ASN601 4.7 8.0 1.0 O C:HOH2417 4.7 15.7 1.0 CG C:GLU533 4.7 15.5 1.0 CB C:ASP644 4.7 10.9 0.5 CB C:ASP642 4.7 7.7 1.0 CG C:GLN602 4.8 10.4 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:Ca801 b:25.2 occ:1.00 OE2 D:GLU533 2.4 15.6 1.0 O D:GLY600 2.4 12.0 1.0 NE2 D:GLN602 2.5 10.8 1.0 OD2 D:ASP644 2.8 18.1 1.0 O D:HOH2401 2.8 22.4 1.0 CD D:GLU533 3.3 17.8 1.0 CD D:GLN602 3.5 12.8 1.0 C D:GLY600 3.6 11.3 1.0 OE1 D:GLU533 3.7 19.9 1.0 OE1 D:GLN602 3.8 15.5 1.0 CG D:ASP644 4.0 17.3 1.0 N D:GLN602 4.2 9.1 1.0 CA D:ASN601 4.3 9.7 1.0 O D:HOH2389 4.4 11.1 1.0 N D:ASN601 4.4 9.9 1.0 CA D:GLY600 4.5 10.8 1.0 CB D:ASP642 4.6 8.4 1.0 CG D:GLU533 4.6 15.7 1.0 O D:ASP642 4.6 8.0 1.0 OD1 D:ASP644 4.6 20.8 1.0 O D:HOH2430 4.7 20.0 1.0 C D:ASN601 4.7 9.5 1.0 O D:HOH2390 4.8 22.9 1.0 CG D:GLN602 4.9 12.3 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