Calcium in PDB 5olr: Rhamnogalacturonan Lyase

The structure of Rhamnogalacturonan Lyase, PDB code: 5olr was solved by A.Basle, A.S.Luis, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 1.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.458, 123.872, 137.628, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 16.6

The binding sites of Calcium atom in the Rhamnogalacturonan Lyase (pdb code 5olr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Rhamnogalacturonan Lyase, PDB code: 5olr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Rhamnogalacturonan Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rhamnogalacturonan Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:10.8 occ:1.00 OD2 A:ASP246 2.3 7.8 1.0 O A:GLY212 2.4 8.4 1.0 OD2 A:ASP280 2.4 12.4 1.0 O4 A:PO4601 2.5 6.6 1.0 O A:HOH847 2.5 13.4 1.0 O A:HOH1115 2.5 15.6 1.0 O A:HOH773 2.7 9.8 1.0 OD1 A:ASP246 2.8 8.4 1.0 CG A:ASP246 2.9 6.8 1.0 CG A:ASP280 3.5 11.6 1.0 P A:PO4601 3.5 7.7 1.0 C A:GLY212 3.6 7.4 1.0 CA A:CA603 3.8 5.9 1.0 O2 A:PO4601 3.8 9.1 1.0 O A:HOH1077 3.8 8.3 1.0 O A:HOH829 3.9 18.8 1.0 O1 A:PO4601 4.1 9.2 1.0 OD1 A:ASP280 4.1 16.1 1.0 CA A:GLY212 4.2 8.2 1.0 CB A:ASP246 4.2 6.6 1.0 O A:HOH1116 4.3 28.8 1.0 CB A:ASP280 4.4 9.6 1.0 NZ A:LYS285 4.6 7.1 1.0 OD1 A:ASN213 4.6 10.2 1.0 N A:ASN213 4.6 7.3 1.0 OD2 A:ASP247 4.6 6.3 1.0 O A:HOH1258 4.7 31.4 1.0 CA A:ASN213 4.8 7.4 1.0 O3 A:PO4601 4.9 10.1 1.0 O1 A:RAM606 4.9 8.8 1.0

Calcium binding site 2 out of 6 in the Rhamnogalacturonan Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rhamnogalacturonan Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:5.9 occ:1.00 OD2 A:ASP250 2.3 6.3 1.0 OD2 A:ASP246 2.3 7.8 1.0 O A:HOH1077 2.3 8.3 1.0 OD2 A:ASP247 2.4 6.3 1.0 O4 A:PO4601 2.4 6.6 1.0 OD1 A:ASP215 2.5 6.1 1.0 OD2 A:ASP215 2.5 6.4 1.0 CG A:ASP215 2.9 5.8 1.0 CG A:ASP247 3.4 6.1 1.0 CG A:ASP250 3.4 5.5 1.0 CG A:ASP246 3.5 6.8 1.0 P A:PO4601 3.6 7.7 1.0 O3 A:PO4601 3.7 10.1 1.0 CA A:CA602 3.8 10.8 1.0 CB A:ASP250 3.8 5.5 1.0 CB A:ASP247 3.9 5.4 1.0 CB A:ASP246 4.1 6.6 1.0 NZ A:LYS285 4.2 7.1 1.0 O A:HOH773 4.2 9.8 1.0 N A:ASP247 4.3 5.4 1.0 CB A:ASP215 4.4 5.5 1.0 OD1 A:ASP246 4.5 8.4 1.0 OD1 A:ASP247 4.5 6.6 1.0 OD1 A:ASP250 4.5 6.5 1.0 O1 A:PO4601 4.6 9.2 1.0 O A:HOH777 4.7 8.1 1.0 CD A:LYS285 4.7 7.0 1.0 O A:GLY212 4.7 8.4 1.0 OD2 A:ASP280 4.7 12.4 1.0 O2 A:PO4601 4.7 9.1 1.0 CA A:ASP247 4.8 5.6 1.0 O A:HOH796 4.9 7.4 1.0

Calcium binding site 3 out of 6 in the Rhamnogalacturonan Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rhamnogalacturonan Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:11.5 occ:1.00 OD2 B:ASP246 2.4 8.2 1.0 O B:GLY212 2.4 8.9 1.0 O B:HOH854 2.5 14.0 1.0 O B:HOH1069 2.5 17.0 1.0 O4 B:PO4601 2.5 7.5 1.0 OD2 B:ASP280 2.5 13.4 1.0 O B:HOH814 2.6 10.9 1.0 OD1 B:ASP246 2.9 8.8 1.0 CG B:ASP246 2.9 7.4 1.0 CG B:ASP280 3.5 12.9 1.0 P B:PO4601 3.6 8.1 1.0 C B:GLY212 3.6 8.7 1.0 CA B:CA603 3.8 6.5 1.0 O2 B:PO4601 3.8 9.0 1.0 O B:HOH1043 3.8 7.9 1.0 O B:HOH712 3.8 18.0 1.0 O3 B:PO4601 4.0 9.9 1.0 OD1 B:ASP280 4.1 17.8 1.0 CA B:GLY212 4.2 8.2 1.0 O B:HOH1067 4.3 25.3 1.0 CB B:ASP246 4.3 6.7 1.0 CB B:ASP280 4.5 10.2 1.0 OD1 B:ASN213 4.6 11.0 1.0 NZ B:LYS285 4.6 7.7 1.0 N B:ASN213 4.6 7.9 1.0 OD2 B:ASP247 4.6 7.0 1.0 O B:HOH1173 4.8 82.2 1.0 CA B:ASN213 4.8 8.2 1.0 O1 B:RAM606 4.8 10.8 1.0 O1 B:PO4601 4.9 10.3 1.0

Calcium binding site 4 out of 6 in the Rhamnogalacturonan Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rhamnogalacturonan Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:6.5 occ:1.00 OD2 B:ASP246 2.3 8.2 1.0 O B:HOH1043 2.3 7.9 1.0 OD2 B:ASP250 2.3 6.7 1.0 OD2 B:ASP247 2.4 7.0 1.0 O4 B:PO4601 2.4 7.5 1.0 OD1 B:ASP215 2.5 6.3 1.0 OD2 B:ASP215 2.5 6.7 1.0 CG B:ASP215 2.9 6.1 1.0 CG B:ASP250 3.4 5.8 1.0 CG B:ASP247 3.4 6.2 1.0 CG B:ASP246 3.5 7.4 1.0 P B:PO4601 3.7 8.1 1.0 O1 B:PO4601 3.8 10.3 1.0 CA B:CA602 3.8 11.5 1.0 CB B:ASP250 3.9 6.1 1.0 CB B:ASP247 3.9 5.9 1.0 CB B:ASP246 4.1 6.7 1.0 NZ B:LYS285 4.2 7.7 1.0 O B:HOH814 4.2 10.9 1.0 N B:ASP247 4.3 5.6 1.0 CB B:ASP215 4.4 6.0 1.0 OD1 B:ASP246 4.4 8.8 1.0 OD1 B:ASP247 4.5 6.5 1.0 OD1 B:ASP250 4.5 7.1 1.0 O3 B:PO4601 4.5 9.9 1.0 CD B:LYS285 4.6 8.7 1.0 O B:HOH754 4.6 9.2 1.0 O B:GLY212 4.7 8.9 1.0 OD2 B:ASP280 4.7 13.4 1.0 O2 B:PO4601 4.8 9.0 1.0 CA B:ASP247 4.8 5.5 1.0 O B:HOH786 4.9 7.6 1.0

Calcium binding site 5 out of 6 in the Rhamnogalacturonan Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rhamnogalacturonan Lyase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca602 b:5.5 occ:1.00 O C:HOH1082 2.3 7.4 1.0 OD2 C:ASP246 2.3 7.2 1.0 OD2 C:ASP250 2.4 6.3 1.0 OD2 C:ASP247 2.4 6.4 1.0 O4 C:PO4601 2.4 6.4 1.0 OD1 C:ASP215 2.5 5.5 1.0 OD2 C:ASP215 2.5 5.8 1.0 CG C:ASP215 2.9 5.4 1.0 CG C:ASP247 3.4 5.7 1.0 CG C:ASP250 3.5 5.3 1.0 CG C:ASP246 3.5 5.8 1.0 P C:PO4601 3.7 7.4 1.0 O3 C:PO4601 3.8 10.3 1.0 CA C:CA603 3.8 9.9 1.0 CB C:ASP250 3.8 5.2 1.0 CB C:ASP247 3.9 5.5 1.0 CB C:ASP246 4.1 5.8 1.0 O C:HOH829 4.2 9.0 1.0 NZ C:LYS285 4.3 6.6 1.0 N C:ASP247 4.3 5.4 1.0 CB C:ASP215 4.4 5.3 1.0 OD1 C:ASP247 4.5 6.3 1.0 OD1 C:ASP246 4.5 7.3 1.0 OD1 C:ASP250 4.5 6.3 1.0 O1 C:PO4601 4.6 9.3 1.0 CD C:LYS285 4.6 7.0 1.0 O C:HOH759 4.6 7.6 1.0 OD2 C:ASP280 4.7 11.6 1.0 O C:GLY212 4.7 8.0 1.0 O2 C:PO4601 4.7 9.1 1.0 CA C:ASP247 4.8 5.2 1.0 O C:HOH839 4.9 6.7 1.0

Calcium binding site 6 out of 6 in the Rhamnogalacturonan Lyase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rhamnogalacturonan Lyase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:9.9 occ:1.00 OD2 C:ASP246 2.4 7.2 1.0 O C:GLY212 2.4 8.0 1.0 OD2 C:ASP280 2.5 11.6 1.0 O4 C:PO4601 2.5 6.4 1.0 O C:HOH855 2.5 12.6 1.0 O C:HOH1108 2.5 15.1 1.0 O C:HOH829 2.6 9.0 1.0 OD1 C:ASP246 2.8 7.3 1.0 CG C:ASP246 2.9 5.8 1.0 CG C:ASP280 3.5 10.5 1.0 P C:PO4601 3.5 7.4 1.0 C C:GLY212 3.6 6.7 1.0 CA C:CA602 3.8 5.5 1.0 O2 C:PO4601 3.8 9.1 1.0 O C:HOH1082 3.8 7.4 1.0 O C:HOH711 3.8 15.8 1.0 O1 C:PO4601 4.1 9.3 1.0 OD1 C:ASP280 4.1 15.7 1.0 CA C:GLY212 4.2 7.3 1.0 CB C:ASP246 4.3 5.8 1.0 O C:HOH1133 4.4 19.1 1.0 CB C:ASP280 4.4 9.0 1.0 NZ C:LYS285 4.6 6.6 1.0 OD1 C:ASN213 4.6 8.5 1.0 OD2 C:ASP247 4.6 6.4 1.0 N C:ASN213 4.6 6.6 1.0 CA C:ASN213 4.8 6.5 1.0 O1 C:RAM606 4.8 8.7 1.0 O3 C:PO4601 4.9 10.3 1.0

A.S.Luis, J.Briggs, X.Zhang, B.Farnell, D.Ndeh, A.Labourel, A.Basle, A.Cartmell, N.Terrapon, K.Stott, E.C.Lowe, R.Mclean, K.Shearer, J.Schuckel, I.Venditto, M.C.Ralet, B.Henrissat, E.C.Martens, S.C.Mosimann, D.W.Abbott, H.J.Gilbert. Dietary Pectic Glycans Are Degraded By Coordinated Enzyme Pathways in Human Colonic Bacteroides. Nat Microbiol V. 3 210 2018.
ISSN: ESSN 2058-5276
PubMed: 29255254
DOI: 10.1038/S41564-017-0079-1