Calcium in PDB 8dl2: BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose

The structure of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose, PDB code: 8dl2 was solved by H.A.Brown, A.L.Deveaux, N.M.Koropatkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.60 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	100.08, 125.31, 150.78, 90, 102.11, 90
R / Rfree (%)	17.5 / 21.9

The structure of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose (pdb code 8dl2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose, PDB code: 8dl2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:13.2 occ:1.00 OE2 A:GLU356 2.2 22.6 1.0 O A:PHE357 2.2 12.0 1.0 OD2 A:ASP374 2.3 14.2 1.0 OE1 A:GLU274 2.3 13.8 1.0 O A:HOH976 2.4 18.9 1.0 O A:GLY359 2.4 13.5 1.0 CD A:GLU356 3.1 21.2 1.0 OE1 A:GLU356 3.3 26.8 1.0 CG A:ASP374 3.3 15.0 1.0 C A:PHE357 3.5 12.8 1.0 CD A:GLU274 3.5 15.6 1.0 C A:GLY359 3.5 14.4 1.0 OD1 A:ASP374 3.7 18.0 1.0 N A:GLY359 3.8 13.8 1.0 N A:PHE357 3.9 13.3 1.0 CA A:GLY359 4.1 14.2 1.0 OE2 A:GLU274 4.1 14.8 1.0 C A:ALA358 4.2 14.6 1.0 CD1 A:PHE357 4.3 13.4 1.0 OH A:TYR289 4.3 22.4 1.0 CA A:PHE357 4.3 12.8 1.0 CG A:GLU356 4.4 19.1 1.0 N A:ALA358 4.4 12.9 1.0 O A:HOH906 4.5 27.6 1.0 N A:ASN360 4.6 15.8 1.0 CA A:ALA358 4.6 14.1 1.0 CG A:GLU274 4.6 15.7 1.0 CB A:ASP374 4.7 13.9 1.0 CE1 A:PHE357 4.7 13.6 1.0 O A:HOH1248 4.7 39.3 1.0 C A:GLU356 4.7 14.0 1.0 CB A:GLU274 4.8 16.0 1.0 O A:ALA358 4.8 13.2 1.0 CG A:PHE357 4.8 12.4 1.0 CA A:ASN360 4.9 17.5 1.0 CA A:GLU356 4.9 15.1 1.0 CG2 A:VAL277 4.9 22.8 1.0

Calcium binding site 2 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:13.8 occ:1.00 OE2 B:GLU356 2.1 19.9 1.0 O B:PHE357 2.3 12.5 1.0 OE1 B:GLU274 2.3 12.7 1.0 O B:GLY359 2.4 13.0 1.0 OD2 B:ASP374 2.4 11.3 1.0 O B:HOH1112 2.5 9.7 1.0 CD B:GLU356 3.1 17.8 1.0 CG B:ASP374 3.4 12.9 1.0 CD B:GLU274 3.4 15.4 1.0 C B:PHE357 3.5 11.0 1.0 C B:GLY359 3.5 12.4 1.0 OE1 B:GLU356 3.5 23.5 1.0 OD1 B:ASP374 3.7 12.4 1.0 N B:GLY359 3.8 13.2 1.0 N B:PHE357 3.9 11.7 1.0 OE2 B:GLU274 4.0 15.3 1.0 C B:ALA358 4.2 13.9 1.0 CA B:GLY359 4.2 12.6 1.0 CD1 B:PHE357 4.3 11.7 1.0 CA B:PHE357 4.3 11.8 1.0 CG B:GLU356 4.3 17.6 1.0 OH B:TYR289 4.4 25.3 1.0 N B:ALA358 4.4 11.5 1.0 O B:HOH1407 4.5 31.4 1.0 CA B:ALA358 4.5 12.0 1.0 N B:ASN360 4.5 13.8 1.0 O B:HOH903 4.6 21.2 1.0 CE1 B:PHE357 4.6 11.3 1.0 CG B:GLU274 4.7 15.7 1.0 O B:ALA358 4.7 12.8 1.0 CB B:ASP374 4.7 13.3 1.0 C B:GLU356 4.7 12.8 1.0 CB B:GLU274 4.8 16.0 1.0 CA B:ASN360 4.8 15.1 1.0 CG B:PHE357 4.8 11.1 1.0 CA B:GLU356 5.0 13.8 1.0 CG2 B:VAL277 5.0 21.5 1.0

Calcium binding site 3 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:21.1 occ:1.00 OE1 C:GLU274 2.3 21.0 1.0 OE2 C:GLU356 2.3 25.2 1.0 O C:PHE357 2.3 20.1 1.0 O C:HOH1067 2.4 17.7 1.0 OD2 C:ASP374 2.4 22.6 1.0 O C:GLY359 2.4 17.2 1.0 CD C:GLU356 3.2 25.0 1.0 CG C:ASP374 3.4 23.5 1.0 OE1 C:GLU356 3.4 24.8 1.0 CD C:GLU274 3.4 21.2 1.0 C C:PHE357 3.5 20.0 1.0 C C:GLY359 3.6 17.2 1.0 OD1 C:ASP374 3.7 25.8 1.0 N C:GLY359 3.8 18.2 1.0 N C:PHE357 3.9 18.6 1.0 OE2 C:GLU274 3.9 19.2 1.0 CA C:GLY359 4.2 17.4 1.0 C C:ALA358 4.2 19.2 1.0 CD1 C:PHE357 4.3 19.5 1.0 CA C:PHE357 4.4 18.9 1.0 OH C:TYR289 4.4 25.8 1.0 O C:HOH949 4.4 31.3 1.0 CG C:GLU356 4.5 23.3 1.0 N C:ALA358 4.5 20.0 1.0 N C:ASN360 4.6 17.9 1.0 CA C:ALA358 4.6 20.2 1.0 CB C:ASP374 4.7 21.9 1.0 CG C:GLU274 4.7 19.9 1.0 CE1 C:PHE357 4.7 19.3 1.0 C C:GLU356 4.8 19.9 1.0 CB C:GLU274 4.8 19.9 1.0 O C:ALA358 4.8 16.9 1.0 CA C:ASN360 4.8 21.0 1.0 CG C:PHE357 4.8 18.6 1.0 CG2 C:VAL277 4.8 25.3 1.0 CA C:GLU356 5.0 20.6 1.0

Calcium binding site 4 out of 4 in the BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:18.5 occ:1.00 OE1 D:GLU274 2.2 16.8 1.0 O D:PHE357 2.3 16.7 1.0 O D:GLY359 2.4 15.7 1.0 OD2 D:ASP374 2.4 19.1 1.0 O D:HOH940 2.4 17.0 1.0 OE2 D:GLU356 2.7 25.6 1.0 OE1 D:GLU356 2.7 31.7 1.0 CD D:GLU356 3.0 25.1 1.0 CG D:ASP374 3.3 18.7 1.0 CD D:GLU274 3.3 18.8 1.0 C D:PHE357 3.5 17.9 1.0 OD1 D:ASP374 3.6 19.6 1.0 C D:GLY359 3.6 16.6 1.0 N D:PHE357 3.9 18.1 1.0 N D:GLY359 3.9 17.3 1.0 OE2 D:GLU274 3.9 21.7 1.0 O D:HOH1246 4.2 36.0 1.0 CA D:GLY359 4.2 16.8 1.0 C D:ALA358 4.3 16.6 1.0 CD2 D:PHE357 4.3 16.9 1.0 CA D:PHE357 4.3 17.6 1.0 OH D:TYR289 4.4 22.6 1.0 CG D:GLU356 4.5 23.6 1.0 O D:HOH919 4.5 25.2 1.0 N D:ALA358 4.5 17.6 1.0 CG D:GLU274 4.5 19.6 1.0 CE2 D:PHE357 4.6 16.3 1.0 N D:ASN360 4.6 17.6 1.0 CB D:ASP374 4.7 18.7 1.0 CA D:ALA358 4.7 17.8 1.0 CB D:GLU274 4.7 17.7 1.0 C D:GLU356 4.7 18.0 1.0 O D:ALA358 4.8 18.6 1.0 CG D:PHE357 4.8 17.3 1.0 CG2 D:VAL277 4.9 23.5 1.0 CA D:ASN360 4.9 19.0 1.0 CA D:GLU356 4.9 18.3 1.0

H.A.Brown, A.L.Deveaux, N.M.Koropatkin. BOGH13ASUS From Bacteroides Ovatus Bound to Acarbose To Be Published.