Calcium in PDB 8xph: Marine Planctomycetes Laminarinase Ptlam

The structure of Marine Planctomycetes Laminarinase Ptlam, PDB code: 8xph was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.47 / 2.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.096, 77.336, 90.191, 90, 90, 90
R / Rfree (%)	22.1 / 26.7

The binding sites of Calcium atom in the Marine Planctomycetes Laminarinase Ptlam (pdb code 8xph). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Marine Planctomycetes Laminarinase Ptlam, PDB code: 8xph:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:8.2 occ:1.00 O A:HOH566 2.3 15.5 1.0 O A:HOH519 2.4 10.8 1.0 O A:GLU46 2.4 8.0 1.0 O A:GLY86 2.5 15.1 1.0 O A:ASP278 2.5 3.7 1.0 OD1 A:ASP278 2.6 11.7 1.0 C A:GLY86 3.4 11.1 1.0 C A:GLU46 3.5 9.6 1.0 C A:ASP278 3.6 8.2 1.0 CG A:ASP278 3.7 13.0 1.0 CA A:GLY86 3.9 16.0 1.0 CA A:ASP278 4.1 10.3 1.0 CA A:GLU46 4.2 10.5 1.0 CB A:GLU46 4.4 16.2 1.0 O A:PHE47 4.4 14.9 1.0 OE1 A:GLU46 4.4 14.4 1.0 CB A:ASP278 4.5 12.6 1.0 O A:HOH681 4.5 9.0 1.0 OD2 A:ASP278 4.5 10.1 1.0 C A:PHE47 4.6 8.3 1.0 O A:HOH517 4.6 18.9 1.0 N A:ASN87 4.6 9.8 1.0 N A:PHE47 4.6 10.0 1.0 CD1 A:TRP279 4.6 6.7 1.0 CB A:TRP279 4.7 8.5 1.0 N A:TRP279 4.7 13.7 1.0 CB A:PHE47 4.8 11.7 1.0 CA A:PHE47 4.9 7.6 1.0

Calcium binding site 2 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:3.9 occ:1.00 O A:ALA182 2.3 3.6 1.0 O A:GLU235 2.3 6.5 1.0 O A:HOH633 2.3 9.8 1.0 O A:HOH569 2.4 8.1 1.0 OE1 A:GLU238 2.4 11.9 1.0 OE2 A:GLU238 2.4 13.7 1.0 CD A:GLU238 2.6 21.9 1.0 O A:HOH630 2.7 23.0 1.0 C A:GLU235 3.3 6.7 1.0 C A:ALA182 3.4 6.4 1.0 CG A:GLU238 3.9 26.5 1.0 CA A:GLU235 3.9 21.4 1.0 CB A:ALA182 4.1 10.8 1.0 CA A:ALA182 4.2 7.2 1.0 N A:MET236 4.2 9.4 1.0 N A:ALA182 4.4 6.9 1.0 CB A:GLU235 4.4 14.6 1.0 O A:GLY183 4.4 22.3 1.0 O A:HOH601 4.4 8.0 1.0 N A:GLY183 4.5 12.7 1.0 OE1 A:GLU186 4.5 3.5 1.0 CA A:MET236 4.6 9.1 1.0 OE2 A:GLU186 4.7 7.5 1.0 N A:LYS237 4.7 13.4 1.0 CD2 A:PHE181 4.7 8.0 1.0 CA A:GLY183 4.8 23.6 1.0 C A:GLY183 4.9 30.9 1.0 CD A:GLU186 4.9 6.0 1.0 N A:GLU238 5.0 7.6 1.0

Calcium binding site 3 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:19.5 occ:1.00 O B:HOH589 2.3 17.3 1.0 O B:GLU235 2.3 18.3 1.0 O B:ALA182 2.4 10.8 1.0 OE1 B:GLU238 2.4 35.1 1.0 O B:HOH626 2.5 8.7 1.0 OE2 B:GLU238 2.6 46.6 1.0 CD B:GLU238 2.6 38.7 1.0 C B:GLU235 3.2 26.4 1.0 C B:ALA182 3.5 17.6 1.0 CA B:GLU235 3.9 22.3 1.0 CG B:GLU238 3.9 44.0 1.0 CB B:ALA182 4.1 20.2 1.0 N B:MET236 4.2 21.8 1.0 CA B:ALA182 4.3 18.3 1.0 CB B:GLU235 4.3 24.4 1.0 O B:GLY183 4.4 36.0 1.0 N B:ALA182 4.5 15.5 1.0 CA B:MET236 4.5 23.3 1.0 N B:GLY183 4.6 15.0 1.0 O B:HOH635 4.6 15.1 1.0 N B:LYS237 4.7 19.8 1.0 CA B:GLY183 4.9 22.4 1.0 CD2 B:PHE181 4.9 17.1 1.0 C B:GLY183 4.9 32.0 1.0 N B:GLU238 4.9 15.8 1.0

Calcium binding site 4 out of 4 in the Marine Planctomycetes Laminarinase Ptlam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Marine Planctomycetes Laminarinase Ptlam within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:19.6 occ:1.00 O B:HOH541 2.1 11.6 1.0 O B:GLU46 2.3 6.9 1.0 O B:GLY86 2.3 10.6 1.0 OD1 B:ASP48 2.5 21.7 1.0 O B:ASP278 2.7 36.2 1.0 OD1 B:ASP278 2.7 15.3 1.0 O B:HOH530 2.8 15.4 1.0 C B:GLY86 3.2 12.2 1.0 C B:GLU46 3.5 15.5 1.0 CA B:GLY86 3.5 9.4 1.0 CG B:ASP48 3.5 42.5 1.0 C B:ASP278 3.8 13.4 1.0 CG B:ASP278 3.9 17.6 1.0 OD2 B:ASP48 4.1 35.8 1.0 O B:PHE47 4.2 20.9 1.0 C B:PHE47 4.2 17.1 1.0 CA B:ASP278 4.3 20.4 1.0 CA B:GLU46 4.3 16.2 1.0 N B:ASN87 4.3 18.1 1.0 CB B:GLU46 4.5 14.7 1.0 N B:PHE47 4.5 22.3 1.0 N B:ASP48 4.5 29.7 1.0 CB B:PHE47 4.7 31.7 1.0 CB B:ASP278 4.7 14.3 1.0 CB B:ASP48 4.7 27.1 1.0 CA B:PHE47 4.7 18.5 1.0 CA B:ASP48 4.7 21.0 1.0 OE1 B:GLU46 4.7 19.5 1.0 OD2 B:ASP278 4.8 21.5 1.0 O B:HOH501 4.9 14.0 1.0 CA B:ASN87 4.9 6.8 1.0 N B:TRP279 4.9 17.1 1.0 CD1 B:TRP279 4.9 10.8 1.0 CB B:TRP279 4.9 21.3 1.0 N B:GLY86 5.0 16.9 1.0

J.Yang, J.Yang. N/A N/A.