Calcium in PDB 6f8z: Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron

The structure of Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron, PDB code: 6f8z 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)	49.67 / 2.50
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	272.301, 272.301, 190.047, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 22.2

The binding sites of Calcium atom in the Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron (pdb code 6f8z). 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, PDB code: 6f8z:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:58.5 occ:1.00 O A:HOH1348 2.3 59.1 1.0 OE2 A:GLU595 2.3 45.3 1.0 O A:HOH901 2.3 52.4 1.0 OD1 A:ASN594 2.3 50.2 1.0 O A:HOH974 2.3 44.8 1.0 OD2 A:ASP637 2.4 47.5 1.0 O A:GLY593 2.4 53.6 1.0 CD A:GLU595 3.4 39.8 1.0 CG A:ASP637 3.5 40.7 1.0 CG A:ASN594 3.5 50.9 1.0 C A:GLY593 3.6 44.1 1.0 OE1 A:GLU595 3.7 36.4 1.0 CA A:ASN594 3.8 47.5 1.0 OD1 A:ASP637 3.9 46.9 1.0 CB A:ASN594 4.2 54.2 1.0 N A:ASN594 4.2 42.4 1.0 O A:ASN635 4.3 32.0 1.0 O A:HOH912 4.4 46.1 1.0 O A:HOH1244 4.4 49.2 1.0 OD1 A:ASP353 4.4 33.1 1.0 ND2 A:ASN594 4.5 48.2 1.0 N A:GLU595 4.5 40.1 1.0 CG A:GLU595 4.6 40.6 1.0 CE A:MET641 4.7 45.7 1.0 C A:ASN594 4.7 45.1 1.0 CB A:ASP637 4.8 37.4 1.0 CB A:ASN635 4.8 36.5 1.0 CA A:GLY593 4.9 41.4 1.0 O A:ASN582 4.9 0.8 1.0

Calcium binding site 2 out of 3 in the Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca900 b:49.9 occ:1.00 OE2 B:GLU595 2.3 43.0 1.0 O B:HOH1093 2.3 40.4 1.0 O B:HOH1230 2.3 54.1 1.0 O B:HOH1183 2.3 55.0 1.0 O B:HOH1058 2.3 53.4 1.0 O B:HOH1055 2.3 54.0 1.0 OD2 B:ASP637 2.4 46.5 1.0 O B:GLY593 2.4 45.7 1.0 CG B:ASP637 3.3 43.2 1.0 CD B:GLU595 3.4 41.2 1.0 OD1 B:ASP637 3.6 44.3 1.0 C B:GLY593 3.6 40.9 1.0 OE1 B:GLU595 4.2 43.6 1.0 CG B:GLU595 4.3 44.0 1.0 O B:ASN635 4.4 40.1 1.0 CA B:GLY593 4.5 40.1 1.0 O B:HOH1233 4.5 59.0 1.0 OD1 B:ASP353 4.5 36.9 1.0 N B:GLU595 4.5 42.2 1.0 N B:ASN594 4.6 41.8 1.0 CA B:ASN594 4.7 49.0 1.0 CB B:ASP637 4.8 41.9 1.0

Calcium binding site 3 out of 3 in the Structure of the Family GH92 Alpha-Mannosidase BT3130 From Bacteroides Thetaiotaomicron


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca900 b:81.4 occ:1.00 O C:HOH1012 2.3 70.2 1.0 O C:HOH1179 2.3 84.9 1.0 OE1 C:GLU595 2.3 68.0 1.0 O C:HOH1141 2.3 77.7 1.0 O C:HOH1002 2.3 81.0 1.0 OD2 C:ASP637 2.3 77.1 1.0 O C:GLY593 2.4 91.7 1.0 CD C:GLU595 3.4 63.1 1.0 CG C:ASP637 3.5 73.0 1.0 C C:GLY593 3.6 82.8 1.0 OE2 C:GLU595 3.8 60.9 1.0 OD1 C:ASP637 3.9 77.3 1.0 CA C:ASN594 4.3 91.9 1.0 N C:ASN594 4.4 85.7 1.0 O C:ASN635 4.4 57.5 1.0 OD1 C:ASP353 4.4 64.4 1.0 N C:GLU595 4.4 78.0 1.0 CA C:GLY593 4.6 78.7 1.0 CG C:GLU595 4.7 65.2 1.0 CB C:ASP637 4.7 70.6 1.0 C C:ASN594 4.9 84.8 1.0 CB C:GLU595 5.0 67.4 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