Calcium in PDB 6f90: Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani)

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani), PDB code: 6f90 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)	49.38 / 2.40
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	273.666, 273.666, 189.759, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.2

The binding sites of Calcium atom in the Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) (pdb code 6f90). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani), PDB code: 6f90:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Family GH92 Alpha-Mannosidase BT3130 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 BT3130 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:33.9 occ:1.00 O3 A:MVL802 2.3 34.1 1.0 O A:HOH1136 2.3 28.5 1.0 OE2 A:GLU595 2.3 38.0 1.0 O2 A:MVL802 2.3 33.1 1.0 OD1 A:ASN594 2.3 41.0 1.0 O A:HOH967 2.3 34.1 1.0 O A:HOH970 2.3 33.0 1.0 OD2 A:ASP637 2.3 36.3 1.0 CG A:ASP637 3.4 36.9 1.0 C2 A:MVL802 3.4 34.8 1.0 C3 A:MVL802 3.4 33.1 1.0 CD A:GLU595 3.4 39.0 1.0 CG A:ASN594 3.6 39.9 1.0 OD1 A:ASP637 3.7 38.8 1.0 OE1 A:GLU595 4.0 36.4 1.0 OD1 A:ASP353 4.1 32.8 1.0 C1 A:MVL802 4.2 34.5 1.0 C4 A:MVL802 4.4 32.5 1.0 CB A:ASN635 4.4 32.2 1.0 ND2 A:ASN594 4.4 38.4 1.0 CA A:ASN594 4.5 37.0 1.0 O A:GLY593 4.5 36.4 1.0 OD1 A:ASN582 4.5 55.5 1.0 CB A:ASN594 4.5 39.7 1.0 OE1 A:GLU535 4.6 38.1 1.0 CG A:GLU595 4.6 40.9 1.0 CZ3 A:TRP352 4.6 25.2 1.0 CB A:ASP637 4.7 35.2 1.0 ND2 A:ASN635 4.7 32.9 1.0 N1 A:MVL802 4.7 35.1 1.0 O A:ASN635 4.8 30.6 1.0 O A:HOH1342 4.8 44.5 1.0 N A:GLU595 4.9 36.2 1.0

Calcium binding site 2 out of 3 in the Structure of the Family GH92 Alpha-Mannosidase BT3130 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 BT3130 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:55.9 occ:1.00 O3 B:MVL802 2.3 69.8 1.0 O B:HOH1036 2.3 54.5 1.0 O B:HOH914 2.3 54.7 1.0 OE2 B:GLU595 2.3 57.4 1.0 O B:HOH916 2.3 52.6 1.0 OD2 B:ASP637 2.3 60.4 1.0 OD1 B:ASN594 2.3 54.1 1.0 O2 B:MVL802 2.3 63.8 1.0 CG B:ASP637 3.3 59.5 1.0 CD B:GLU595 3.4 51.9 1.0 C2 B:MVL802 3.5 67.5 1.0 C3 B:MVL802 3.5 69.9 1.0 CG B:ASN594 3.6 54.0 1.0 OD1 B:ASP637 3.6 63.2 1.0 OD1 B:ASP353 4.0 52.2 1.0 OE1 B:GLU595 4.1 51.8 1.0 C1 B:MVL802 4.3 69.0 1.0 CB B:ASN635 4.4 55.6 1.0 CG B:GLU595 4.4 50.4 1.0 C4 B:MVL802 4.4 68.2 1.0 ND2 B:ASN594 4.5 53.8 1.0 CA B:ASN594 4.5 46.9 1.0 O B:GLY593 4.6 47.7 1.0 OE1 B:GLU535 4.6 68.7 1.0 CB B:ASN594 4.6 52.8 1.0 O B:HOH1049 4.6 57.0 1.0 OD1 B:ASN635 4.6 48.8 1.0 CZ3 B:TRP352 4.7 40.4 1.0 CB B:ASP637 4.7 54.0 1.0 O B:ASN635 4.7 51.4 1.0 N1 B:MVL802 4.8 69.9 1.0 ND2 B:ASN582 4.8 93.8 1.0 CG B:ASP353 4.9 53.4 1.0 N B:GLU595 4.9 46.7 1.0 CG B:ASN635 5.0 51.5 1.0

Calcium binding site 3 out of 3 in the Structure of the Family GH92 Alpha-Mannosidase BT3130 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 BT3130 From Bacteroides Thetaiotaomicron in Complex with Mannoimidazole (Mani) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:0.6 occ:1.00 O C:HOH901 2.3 98.2 1.0 O3 C:MVL802 2.3 97.6 1.0 OD1 C:ASN594 2.3 0.2 1.0 O2 C:MVL802 2.3 0.5 1.0 O C:HOH925 2.3 95.8 1.0 OD2 C:ASP637 2.3 99.8 1.0 O C:HOH902 2.3 82.8 1.0 OE1 C:GLU595 2.3 97.3 1.0 C2 C:MVL802 3.4 99.2 1.0 C3 C:MVL802 3.4 0.5 1.0 CG C:ASP637 3.5 91.8 1.0 CD C:GLU595 3.5 91.0 1.0 CG C:ASN594 3.6 0.4 1.0 OE2 C:GLU595 3.9 86.1 1.0 OD1 C:ASP637 3.9 94.9 1.0 OD1 C:ASP353 4.0 82.6 1.0 CZ3 C:TRP352 4.3 86.1 1.0 C1 C:MVL802 4.3 0.1 1.0 C4 C:MVL802 4.4 98.2 1.0 ND2 C:ASN594 4.4 1.0 1.0 CA C:ASN594 4.4 0.9 1.0 CB C:ASN635 4.4 92.0 1.0 CB C:ASN594 4.6 0.1 1.0 N C:GLU595 4.6 0.2 1.0 O C:GLY593 4.6 0.5 1.0 O C:ASN635 4.7 78.3 1.0 CB C:ASP637 4.7 86.9 1.0 CG C:GLU595 4.7 93.2 1.0 N1 C:MVL802 4.9 0.9 1.0 ND2 C:ASN635 4.9 94.1 1.0 CG C:ASP353 5.0 85.8 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