Calcium in PDB 6f92: Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani), PDB code: 6f92 was solved by A.J.Thompson, R.J.Spears, Y.Zhu, M.D.L.Suits, S.J.Williams, 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)	46.73 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.507, 186.904, 95.050, 90.00, 91.74, 90.00
R / Rfree (%)	17.7 / 20.8

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Calcium atom in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) (pdb code 6f92). 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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani), PDB code: 6f92:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:15.7 occ:1.00 O A:HOH1106 2.3 15.9 1.0 O3 A:MVL804 2.3 14.3 1.0 O2 A:MVL804 2.3 18.4 1.0 OD1 A:ASN590 2.4 16.3 1.0 O A:HOH1117 2.4 15.8 1.0 O A:HOH1080 2.4 15.1 1.0 OD2 A:ASP633 2.4 13.2 1.0 OE1 A:GLU591 2.4 14.1 1.0 CG A:ASP633 3.4 12.4 1.0 C2 A:MVL804 3.4 16.0 1.0 C3 A:MVL804 3.4 15.5 1.0 CD A:GLU591 3.4 15.7 1.0 CG A:ASN590 3.6 15.2 1.0 OD1 A:ASP633 3.7 12.6 1.0 OE2 A:GLU591 3.8 16.7 1.0 OD1 A:ASP344 4.0 10.4 1.0 C1 A:MVL804 4.3 16.6 1.0 CA A:ASN590 4.4 15.6 1.0 C4 A:MVL804 4.4 14.4 1.0 CZ3 A:TRP343 4.5 12.7 1.0 ND2 A:ASN590 4.5 14.1 1.0 CB A:ASN590 4.5 15.5 1.0 CB A:ASN631 4.5 12.3 1.0 O A:HOH1168 4.6 17.2 1.0 O A:GLY589 4.6 18.8 1.0 OE1 A:GLU531 4.6 21.9 1.0 OD1 A:ASN631 4.7 13.3 1.0 N A:GLU591 4.7 15.1 1.0 O A:HOH1297 4.7 18.3 1.0 CB A:ASP633 4.8 11.9 1.0 N1 A:MVL804 4.8 17.9 1.0 CG A:GLU591 4.8 15.2 1.0 O A:ASN631 4.9 12.7 1.0 CG A:ASP344 4.9 10.5 1.0

Calcium binding site 2 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:20.4 occ:1.00 O B:HOH1079 2.3 23.4 1.0 O3 B:MVL804 2.3 21.5 1.0 O2 B:MVL804 2.3 20.9 1.0 O B:HOH1030 2.3 21.6 1.0 OD1 B:ASN590 2.4 21.1 1.0 OD2 B:ASP633 2.4 20.1 1.0 O B:HOH1203 2.4 17.6 1.0 OE1 B:GLU591 2.4 22.5 1.0 C2 B:MVL804 3.4 22.0 1.0 C3 B:MVL804 3.4 20.4 1.0 CG B:ASP633 3.4 19.2 1.0 CD B:GLU591 3.5 21.6 1.0 CG B:ASN590 3.6 22.4 1.0 OD1 B:ASP633 3.7 20.8 1.0 OE2 B:GLU591 3.9 22.5 1.0 OD1 B:ASP344 4.0 18.3 1.0 C1 B:MVL804 4.2 22.2 1.0 C4 B:MVL804 4.4 21.2 1.0 CA B:ASN590 4.4 22.7 1.0 CB B:ASN631 4.5 21.7 1.0 ND2 B:ASN590 4.5 22.1 1.0 CZ3 B:TRP343 4.5 19.4 1.0 OD1 B:ASN631 4.5 22.9 1.0 CB B:ASN590 4.5 23.2 1.0 OE1 B:GLU531 4.6 24.9 1.0 O B:GLY589 4.6 20.5 1.0 O B:HOH1192 4.7 20.7 1.0 O B:HOH1032 4.7 18.6 1.0 N B:GLU591 4.7 21.6 1.0 N1 B:MVL804 4.7 22.5 1.0 CB B:ASP633 4.8 19.5 1.0 O B:ASN631 4.8 18.5 1.0 CG B:GLU591 4.9 21.8 1.0 CG B:ASP344 4.9 17.3 1.0 CG B:ASN631 4.9 23.0 1.0

Calcium binding site 3 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:27.9 occ:1.00 O3 C:MVL804 2.3 27.4 1.0 O C:HOH1131 2.3 34.4 1.0 OD1 C:ASN590 2.3 29.9 1.0 O C:HOH961 2.3 28.6 1.0 O2 C:MVL804 2.4 30.7 1.0 O C:HOH958 2.4 26.4 1.0 OE1 C:GLU591 2.4 28.6 1.0 OD2 C:ASP633 2.4 27.7 1.0 C2 C:MVL804 3.4 28.6 1.0 CG C:ASP633 3.4 28.0 1.0 CD C:GLU591 3.5 32.8 1.0 C3 C:MVL804 3.5 28.2 1.0 CG C:ASN590 3.5 32.3 1.0 OD1 C:ASP633 3.7 26.8 1.0 OE2 C:GLU591 3.8 31.8 1.0 OD1 C:ASP344 4.1 29.9 1.0 CA C:ASN590 4.3 31.2 1.0 C1 C:MVL804 4.3 29.7 1.0 CB C:ASN590 4.4 32.0 1.0 ND2 C:ASN590 4.5 29.1 1.0 CB C:ASN631 4.5 25.4 1.0 C4 C:MVL804 4.5 28.1 1.0 O C:GLY589 4.5 37.8 1.0 CZ3 C:TRP343 4.5 26.1 1.0 O C:HOH1003 4.6 32.3 1.0 OD1 C:ASN631 4.6 25.1 1.0 OE1 C:GLU531 4.6 33.5 1.0 N C:GLU591 4.6 28.4 1.0 O C:HOH1169 4.7 31.9 1.0 O C:ASN631 4.8 24.6 1.0 N1 C:MVL804 4.8 29.6 1.0 CB C:ASP633 4.8 25.6 1.0 CG C:GLU591 4.9 31.6 1.0 CG C:ASN631 5.0 25.2 1.0 CG C:ASP344 5.0 31.3 1.0

Calcium binding site 4 out of 4 in the Structure of the Family GH92 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)


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 Alpha-Mannosidase BT3965 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca802 b:16.1 occ:1.00 O D:HOH983 2.3 15.4 1.0 O3 D:MVL804 2.3 16.2 1.0 OD1 D:ASN590 2.3 17.0 1.0 O2 D:MVL804 2.3 18.2 1.0 O D:HOH1049 2.4 16.5 1.0 O D:HOH1080 2.4 14.7 1.0 OD2 D:ASP633 2.4 14.6 1.0 OE1 D:GLU591 2.4 17.1 1.0 C3 D:MVL804 3.4 15.9 1.0 C2 D:MVL804 3.4 16.1 1.0 CG D:ASP633 3.4 14.9 1.0 CD D:GLU591 3.4 16.6 1.0 CG D:ASN590 3.6 18.5 1.0 OD1 D:ASP633 3.7 14.6 1.0 OE2 D:GLU591 3.8 16.7 1.0 OD1 D:ASP344 4.0 13.2 1.0 C1 D:MVL804 4.3 15.9 1.0 C4 D:MVL804 4.4 14.3 1.0 CA D:ASN590 4.4 19.6 1.0 CZ3 D:TRP343 4.4 14.4 1.0 ND2 D:ASN590 4.5 17.6 1.0 CB D:ASN590 4.5 18.5 1.0 CB D:ASN631 4.5 15.4 1.0 O D:GLY589 4.6 17.4 1.0 OE1 D:GLU531 4.6 21.0 1.0 OD1 D:ASN631 4.6 17.5 1.0 N D:GLU591 4.7 18.6 1.0 O D:HOH1317 4.8 22.4 1.0 O D:HOH944 4.8 20.4 1.0 CB D:ASP633 4.8 14.4 1.0 CG D:GLU591 4.8 17.5 1.0 N1 D:MVL804 4.9 15.1 1.0 O D:ASN631 4.9 13.5 1.0 CG D:ASP344 4.9 13.1 1.0

A.J.Thompson, R.J.Spears, Y.Zhu, M.D.L.Suits, S.J.Williams, H.J.Gilbert, G.J.Davies. Bacteroides Thetaiotaomicron Generates Diverse Alpha-Mannosidase Activities Through Subtle Evolution of A Distal Substrate-Binding Motif. Acta Crystallogr D Struct V. 74 394 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29717710
DOI: 10.1107/S2059798318002942