Calcium in PDB 5i0f: Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate

The structure of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate, PDB code: 5i0f was solved by S.H.Light, G.Minasov, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.59 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	195.127, 103.128, 44.094, 90.00, 92.14, 90.00
R / Rfree (%)	15.9 / 19

The binding sites of Calcium atom in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate (pdb code 5i0f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate, PDB code: 5i0f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca805 b:25.5 occ:0.75 O B:HOH1260 2.3 31.6 1.0 O B:HOH1008 2.3 39.2 1.0 OD1 B:ASP66 2.4 40.5 1.0 CG B:ASP66 3.3 41.9 1.0 OD2 B:ASP66 3.6 41.5 1.0 OE1 B:GLU76 4.5 43.9 1.0 OE2 B:GLU76 4.5 44.7 1.0 O B:HOH1249 4.5 45.2 1.0 CB B:ASP66 4.7 42.3 1.0 O B:ASP66 4.7 40.7 1.0 CD B:GLU76 4.9 42.0 1.0

Calcium binding site 2 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca806 b:43.7 occ:1.00 O B:HOH1495 2.3 33.1 1.0 O B:HOH1433 2.3 34.4 1.0 O B:HOH1020 2.4 25.9 1.0 O B:HOH1283 2.5 26.7 1.0 O B:HOH1417 2.5 37.9 1.0 OD1 B:ASP534 2.5 22.8 1.0 CG B:ASP534 3.3 22.6 1.0 CB B:ASP534 3.9 21.3 1.0 OD2 B:ASP534 4.2 23.7 1.0 O B:SER566 4.4 19.4 1.0 NZ B:LYS201 4.4 24.6 1.0 O B:HOH956 4.5 26.2 1.0 CA B:GLY567 4.5 18.9 1.0 O B:HOH1041 4.6 30.7 1.0 CA B:ASP534 4.7 19.9 1.0 C B:SER566 4.9 18.7 1.0 N B:GLY567 5.0 18.4 1.0

Calcium binding site 3 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca807 b:48.7 occ:1.00 O B:HOH970 2.3 32.3 1.0 O B:HOH1370 2.4 55.5 1.0 O B:HOH1372 2.4 39.6 1.0 O B:HOH1378 2.4 47.9 1.0 O B:ALA133 2.4 37.4 1.0 O B:HOH1246 2.6 39.3 1.0 C B:ALA133 3.6 37.6 1.0 CA B:ALA133 4.2 36.0 1.0 O B:PRO151 4.3 29.5 1.0 CB B:ALA133 4.3 36.3 1.0 C B:GLU134 4.6 40.8 1.0 O B:HOH1318 4.6 35.8 1.0 N B:GLU134 4.6 38.6 1.0 O B:GLU134 4.7 39.0 1.0 N B:PRO135 4.8 40.9 1.0 CA B:GLU134 4.8 41.4 1.0 O B:ASP149 4.9 30.7 1.0

Calcium binding site 4 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca808 b:40.2 occ:1.00 O B:HOH994 2.3 33.2 1.0 OD1 B:ASN349 2.4 41.6 1.0 O B:HOH1066 2.5 28.1 1.0 CG B:ASN349 3.5 38.9 1.0 OD2 B:ASP358 3.9 32.6 1.0 ND2 B:ASN349 4.1 38.5 1.0 OD1 B:ASP358 4.1 32.0 1.0 CG B:ASP358 4.1 31.1 1.0 O B:VAL347 4.4 32.6 1.0 ND1 B:HIS354 4.6 28.9 1.0 CE1 B:HIS354 4.7 29.1 1.0 O B:HOH1082 4.7 31.7 1.0 CB B:ASN349 4.8 37.9 1.0 O B:HOH1445 4.8 55.2 1.0 CA B:ASN349 4.8 39.8 1.0 O B:PRO348 4.8 38.9 1.0 CG1 B:VAL347 5.0 34.4 1.0

Calcium binding site 5 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca809 b:26.4 occ:0.80 O B:HOH1059 2.3 35.3 1.0 O B:GLU76 2.4 32.6 1.0 O B:HOH1197 2.4 36.1 1.0 O B:LEU79 2.4 34.9 1.0 O B:HOH1415 2.6 39.2 1.0 C B:GLU76 3.5 33.5 1.0 C B:LEU79 3.6 35.5 1.0 CA B:GLU76 4.2 34.3 1.0 CB B:GLU76 4.3 37.1 1.0 N B:LEU79 4.4 35.0 1.0 CA B:LEU79 4.4 36.0 1.0 N B:GLY77 4.5 32.1 1.0 N B:ALA80 4.6 34.9 1.0 OE1 B:GLU76 4.7 43.9 1.0 CB B:LEU79 4.7 38.7 1.0 CA B:GLY77 4.7 32.8 1.0 O B:HOH1436 4.7 40.9 1.0 CA B:ALA80 4.8 34.6 1.0 O B:HOH1460 4.8 33.8 1.0 O B:HOH1231 4.9 42.3 1.0 C B:GLY77 4.9 32.2 1.0 CB B:ALA80 5.0 34.3 1.0

Calcium binding site 6 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca810 b:50.0 occ:1.00 O B:HOH1285 2.3 47.8 1.0 OD1 B:ASP396 2.7 52.8 1.0 OD2 B:ASP396 2.8 55.0 1.0 CG B:ASP396 3.1 53.5 1.0 CB B:ASP396 4.6 53.2 1.0

Calcium binding site 7 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca811 b:64.5 occ:1.00 O B:HOH930 2.5 28.8 1.0 O B:HOH1035 2.6 34.8 1.0 O B:GLY116 4.2 29.7 1.0 OG1 B:THR118 4.6 33.0 1.0 CD1 B:LEU112 4.8 30.0 1.0

Calcium binding site 8 out of 8 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes in Complex with Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca812 b:42.8 occ:1.00 O B:LEU254 2.3 31.8 1.0 O B:HOH1369 2.3 35.9 1.0 O B:HOH1323 2.5 41.6 1.0 O B:HOH1123 2.5 42.9 1.0 OD1 B:ASP253 2.6 27.7 1.0 OD2 B:ASP253 2.6 28.6 1.0 OD2 B:ASP486 2.8 34.2 1.0 CG B:ASP253 3.0 27.2 1.0 C B:LEU254 3.5 32.6 1.0 CG B:ASP486 3.7 30.1 1.0 O B:GLY255 3.7 51.1 1.0 CB B:ASP486 3.8 27.9 1.0 C B:GLY255 4.1 46.7 1.0 N B:LEU254 4.2 27.6 1.0 CD B:ARG234 4.3 24.3 1.0 N B:GLY255 4.4 35.7 1.0 CA B:GLY255 4.4 40.9 1.0 CB B:ASP253 4.4 25.1 1.0 CA B:LEU254 4.5 29.7 1.0 NE B:ARG234 4.5 25.2 1.0 C B:ASP253 4.7 25.7 1.0 OD1 B:ASP486 4.8 32.1 1.0 O B:HIS161 4.9 26.0 1.0 N B:PHE256 5.0 54.8 1.0

S.H.Light, L.A.Cahoon, K.V.Mahasenan, M.Lee, B.Boggess, A.S.Halavaty, S.Mobashery, N.E.Freitag, W.F.Anderson. Transferase Versus Hydrolase: the Role of Conformational Flexibility in Reaction Specificity. Structure V. 25 295 2017.
ISSN: ISSN 1878-4186
PubMed: 28089449
DOI: 10.1016/J.STR.2016.12.007