Calcium in PDB 7lnp: Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside

The structure of Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside, PDB code: 7lnp was solved by A.B.Boraston, C.S.Robb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.57 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.325, 106.637, 155.896, 90, 114.97, 90
R / Rfree (%)	23 / 28.4

The structure of Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Nickel	(Ni)	9 atoms
Sodium	(Na)	10 atoms

The binding sites of Calcium atom in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside (pdb code 7lnp). 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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside, PDB code: 7lnp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:22.1 occ:1.00 O A:LEU445 2.3 16.6 1.0 OD1 A:ASP347 2.3 21.6 1.0 O A:TYR500 2.4 14.8 1.0 OD1 A:ASP351 2.5 19.3 1.0 OD2 A:ASP351 2.5 17.1 1.0 CG A:ASP351 2.8 17.1 1.0 O A:HOH790 2.9 15.2 1.0 O A:HOH819 2.9 14.1 1.0 C A:LEU445 3.3 16.1 1.0 CG A:ASP347 3.3 18.7 1.0 C A:TYR500 3.4 14.4 1.0 O A:HOH835 3.4 22.0 1.0 OD2 A:ASP347 3.7 23.7 1.0 CA A:TYR500 3.9 14.4 1.0 CA A:LEU445 4.1 14.8 1.0 N A:ALA446 4.2 15.3 1.0 CA A:ALA446 4.3 18.0 1.0 CB A:ASP351 4.4 13.2 1.0 CB A:LEU445 4.4 13.7 1.0 N A:ALA501 4.5 16.9 1.0 CB A:ASP347 4.6 15.7 1.0 O A:ASP347 4.7 12.7 1.0 CB A:TYR500 4.8 14.2 1.0 CB A:ALA446 4.8 15.5 1.0 N A:TYR500 4.9 11.8 1.0 CA A:ALA501 4.9 14.3 1.0

Calcium binding site 2 out of 4 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:16.5 occ:1.00 O C:LEU445 2.4 13.4 1.0 OD2 C:ASP351 2.4 15.4 1.0 OD2 C:ASP347 2.4 20.8 1.0 OD1 C:ASP351 2.6 18.7 1.0 O C:TYR500 2.6 15.4 1.0 CG C:ASP351 2.8 16.6 1.0 CG C:ASP347 3.3 16.0 1.0 OD1 C:ASP347 3.5 15.8 1.0 C C:LEU445 3.5 15.9 1.0 C C:TYR500 3.6 15.4 1.0 CA C:TYR500 4.0 15.7 1.0 CA C:LEU445 4.3 15.5 1.0 CB C:ASP351 4.3 14.6 1.0 N C:ALA446 4.4 16.2 1.0 O C:ASP347 4.5 13.9 1.0 CA C:ALA446 4.5 19.8 1.0 CB C:LEU445 4.5 14.2 1.0 CB C:ASP347 4.7 16.2 1.0 O C:HOH732 4.7 12.4 1.0 N C:ALA501 4.7 15.0 1.0 CB C:ALA446 4.9 14.1 1.0 CB C:TYR500 4.9 15.6 1.0

Calcium binding site 3 out of 4 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:30.8 occ:1.00 O D:LEU445 2.4 16.8 1.0 OD1 D:ASP347 2.4 20.0 1.0 O D:TYR500 2.5 21.6 1.0 OD2 D:ASP351 2.5 21.4 1.0 OD1 D:ASP351 3.0 22.9 1.0 CG D:ASP351 3.1 21.1 1.0 CG D:ASP347 3.4 18.9 1.0 C D:LEU445 3.5 18.0 1.0 C D:TYR500 3.5 20.8 1.0 OD2 D:ASP347 3.7 19.4 1.0 CA D:TYR500 3.9 19.2 1.0 CA D:ALA446 4.2 18.1 1.0 N D:ALA446 4.2 18.1 1.0 CA D:LEU445 4.4 16.5 1.0 CB D:ALA446 4.6 18.7 1.0 CB D:ASP351 4.6 17.1 1.0 N D:ALA501 4.6 19.6 1.0 O D:ASP347 4.7 18.2 1.0 CB D:ASP347 4.7 20.4 1.0 CB D:LEU445 4.8 18.8 1.0 CB D:TYR500 4.8 17.4 1.0 N D:TYR500 5.0 18.1 1.0

Calcium binding site 4 out of 4 in the Structure of the Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside


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 Exo-Alpha-L-Galactosidase BPGH29 (D264N Mutant) From Bacteroides Plebeius in Complex with Paranitrophenyl-Alpha-L- Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca601 b:25.2 occ:1.00 O E:LEU445 2.3 16.7 1.0 OD2 E:ASP347 2.4 19.7 1.0 O E:TYR500 2.5 20.2 1.0 OD1 E:ASP351 2.6 17.3 1.0 OD1 E:ASP347 3.0 22.6 1.0 CG E:ASP347 3.0 21.2 1.0 OD2 E:ASP351 3.1 18.7 1.0 CG E:ASP351 3.2 20.0 1.0 C E:LEU445 3.4 14.9 1.0 C E:TYR500 3.6 17.2 1.0 CA E:TYR500 4.0 17.0 1.0 CA E:ALA446 4.1 17.8 1.0 N E:ALA446 4.2 14.2 1.0 CA E:LEU445 4.4 14.2 1.0 CB E:ASP347 4.5 17.8 1.0 CB E:ALA446 4.5 20.5 1.0 CB E:ASP351 4.7 17.7 1.0 N E:ALA501 4.7 15.4 1.0 CB E:LEU445 4.7 16.6 1.0 O E:ASP347 4.9 16.5 1.0 CB E:TYR500 5.0 16.7 1.0 O E:HOH803 5.0 20.6 1.0

C.S.Robb, J.K.Hobbs, B.Pluvinage, G.Reintjes, L.Klassen, S.Monteith, G.Giljan, C.Amundsen, C.Vickers, A.G.Hettle, R.Hills, X.Xing, T.Montina, W.F.Zandberg, D.W.Abbott, A.B.Boraston. Metabolism of A Hybrid Algal Galactan By Members of the Human Gut Microbiome. Nat.Chem.Biol. V. 18 501 2022.
ISSN: ESSN 1552-4469
PubMed: 35289327
DOI: 10.1038/S41589-022-00983-Y