Calcium in PDB 8dge: BOGH13ASUS From Bacteroides Ovatus

The structure of BOGH13ASUS From Bacteroides Ovatus, PDB code: 8dge 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)	62.00 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	100.387, 148.443, 112.77, 90, 91, 90
R / Rfree (%)	20.9 / 27.1

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the BOGH13ASUS From Bacteroides Ovatus (pdb code 8dge). 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, PDB code: 8dge:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:25.9 occ:1.00 O A:PHE357 2.2 24.3 1.0 OD2 A:ASP374 2.3 24.1 1.0 OE1 A:GLU274 2.4 23.7 1.0 O A:HOH1048 2.4 26.0 1.0 O A:GLY359 2.4 24.3 1.0 OE1 A:GLU356 2.5 32.0 1.0 OE2 A:GLU356 2.8 32.9 1.0 CD A:GLU356 2.9 27.8 1.0 CG A:ASP374 3.3 24.8 1.0 C A:PHE357 3.5 23.8 1.0 CD A:GLU274 3.6 26.5 1.0 C A:GLY359 3.6 23.7 1.0 OD1 A:ASP374 3.7 26.4 1.0 N A:PHE357 3.9 25.2 1.0 N A:GLY359 3.9 25.7 1.0 OE2 A:GLU274 4.1 27.2 1.0 CA A:GLY359 4.3 25.2 1.0 C A:ALA358 4.3 26.1 1.0 CA A:PHE357 4.3 24.4 1.0 CD1 A:PHE357 4.4 26.7 1.0 CG A:GLU356 4.4 29.4 1.0 N A:ALA358 4.5 25.1 1.0 OH A:TYR289 4.6 30.5 1.0 CB A:ASP374 4.6 24.3 1.0 CA A:ALA358 4.6 26.4 1.0 CE1 A:PHE357 4.6 30.3 1.0 N A:ASN360 4.7 23.2 1.0 C A:GLU356 4.7 25.1 1.0 CG A:GLU274 4.7 27.5 1.0 O A:HOH971 4.7 33.5 1.0 CB A:GLU274 4.8 28.0 1.0 CG A:PHE357 4.8 26.9 1.0 O A:ALA358 4.8 23.7 1.0 CA A:GLU356 4.8 25.9 1.0 O A:HOH942 4.9 38.0 1.0 CA A:ASN360 4.9 25.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:25.8 occ:1.00 O B:PHE357 2.2 26.3 1.0 OE1 B:GLU274 2.4 23.3 1.0 OD2 B:ASP374 2.4 22.2 1.0 O B:GLY359 2.4 23.9 1.0 OE1 B:GLU356 2.5 28.5 1.0 O B:HOH972 2.6 23.5 1.0 OE2 B:GLU356 2.6 32.1 1.0 CD B:GLU356 2.9 25.7 1.0 CG B:ASP374 3.3 24.0 1.0 C B:PHE357 3.4 25.0 1.0 CD B:GLU274 3.5 26.1 1.0 OD1 B:ASP374 3.6 26.5 1.0 C B:GLY359 3.6 25.2 1.0 N B:PHE357 3.8 24.9 1.0 N B:GLY359 3.9 26.1 1.0 OE2 B:GLU274 4.1 26.5 1.0 C B:ALA358 4.2 25.0 1.0 CA B:PHE357 4.3 24.8 1.0 CA B:GLY359 4.3 25.4 1.0 CG B:GLU356 4.3 27.6 1.0 CD1 B:PHE357 4.4 26.9 1.0 N B:ALA358 4.4 26.0 1.0 CA B:ALA358 4.5 25.1 1.0 C B:GLU356 4.6 24.4 1.0 O B:HOH1231 4.6 34.5 1.0 O B:HOH932 4.6 41.1 1.0 N B:ASN360 4.7 26.8 1.0 CB B:ASP374 4.7 23.6 1.0 CG B:GLU274 4.7 28.4 1.0 OH B:TYR289 4.7 28.4 1.0 CE1 B:PHE357 4.7 26.8 1.0 CB B:GLU274 4.7 28.4 1.0 CG2 B:VAL277 4.8 30.6 1.0 O B:ALA358 4.8 22.8 1.0 CA B:GLU356 4.8 26.3 1.0 CG B:PHE357 4.8 25.3 1.0 CA B:ASN360 4.9 29.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:28.8 occ:1.00 O C:PHE357 2.3 23.8 1.0 O C:HOH1097 2.4 25.4 1.0 O C:GLY359 2.4 23.3 1.0 OE1 C:GLU274 2.4 23.8 1.0 OD2 C:ASP374 2.5 24.0 1.0 OE1 C:GLU356 2.6 30.0 1.0 OE2 C:GLU356 2.7 29.6 1.0 CD C:GLU356 3.0 27.3 1.0 CG C:ASP374 3.4 24.1 1.0 C C:PHE357 3.5 23.9 1.0 C C:GLY359 3.6 24.2 1.0 CD C:GLU274 3.6 25.9 1.0 OD1 C:ASP374 3.7 26.9 1.0 N C:GLY359 3.9 25.2 1.0 N C:PHE357 4.0 22.5 1.0 OE2 C:GLU274 4.1 24.6 1.0 CA C:GLY359 4.2 26.1 1.0 C C:ALA358 4.3 26.6 1.0 CD1 C:PHE357 4.4 26.6 1.0 CA C:PHE357 4.4 23.9 1.0 CG C:GLU356 4.5 29.5 1.0 N C:ALA358 4.5 25.3 1.0 O C:HOH993 4.6 33.0 1.0 O C:HOH1171 4.6 35.8 1.0 N C:ASN360 4.6 23.6 1.0 OH C:TYR289 4.7 30.3 1.0 CE1 C:PHE357 4.7 26.8 1.0 CA C:ALA358 4.7 26.1 1.0 C C:GLU356 4.7 24.5 1.0 CB C:ASP374 4.7 25.4 1.0 CG C:GLU274 4.8 26.0 1.0 CB C:GLU274 4.8 27.4 1.0 CG C:PHE357 4.9 26.2 1.0 CG2 C:VAL277 4.9 27.6 1.0 CA C:ASN360 4.9 25.8 1.0 CA C:GLU356 4.9 26.1 1.0 O C:ALA358 4.9 25.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:27.4 occ:1.00 O D:PHE357 2.3 23.6 1.0 OD2 D:ASP374 2.3 21.5 1.0 OE1 D:GLU274 2.4 21.6 1.0 O D:GLY359 2.4 23.2 1.0 O D:HOH1020 2.4 25.1 1.0 OE1 D:GLU356 2.7 29.7 1.0 OE2 D:GLU356 2.8 29.1 1.0 CD D:GLU356 3.1 25.4 1.0 CG D:ASP374 3.3 22.4 1.0 C D:PHE357 3.5 24.7 1.0 CD D:GLU274 3.5 24.9 1.0 C D:GLY359 3.6 24.4 1.0 OD1 D:ASP374 3.7 24.3 1.0 N D:GLY359 3.9 25.5 1.0 N D:PHE357 3.9 23.1 1.0 OE2 D:GLU274 4.1 26.8 1.0 CA D:GLY359 4.2 24.7 1.0 CD1 D:PHE357 4.3 24.9 1.0 C D:ALA358 4.3 26.5 1.0 CA D:PHE357 4.3 25.0 1.0 N D:ALA358 4.5 25.1 1.0 OH D:TYR289 4.5 28.5 1.0 O D:HOH909 4.5 31.1 1.0 CG D:GLU356 4.5 25.6 1.0 N D:ASN360 4.6 25.6 1.0 CE1 D:PHE357 4.6 24.6 1.0 CA D:ALA358 4.6 24.2 1.0 CB D:ASP374 4.7 21.6 1.0 CG D:GLU274 4.7 24.9 1.0 CB D:GLU274 4.7 25.6 1.0 C D:GLU356 4.7 24.1 1.0 CG2 D:VAL277 4.8 27.0 1.0 CG D:PHE357 4.8 24.5 1.0 CA D:ASN360 4.9 27.3 1.0 CA D:GLU356 4.9 24.7 1.0 O D:ALA358 5.0 27.1 1.0

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