Calcium in PDB 5f7s: Cycloalternan-Degrading Enzyme From Trueperella Pyogenes

The structure of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes, PDB code: 5f7s was solved by S.H.Light, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	197.126, 104.663, 89.030, 90.00, 90.74, 90.00
R / Rfree (%)	17 / 21.1

The binding sites of Calcium atom in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes (pdb code 5f7s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes, PDB code: 5f7s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:53.5 occ:1.00 O B:HOH1101 2.4 55.4 1.0 O B:HOH1065 2.4 41.5 1.0 O B:HOH951 2.6 44.2 1.0 O A:HOH1201 2.6 46.4 1.0 OE1 A:GLN645 2.6 50.4 1.0 O B:HOH1236 2.7 56.8 1.0 CD A:GLN645 3.7 48.5 1.0 O B:HOH1107 4.1 28.2 1.0 NE2 A:GLN645 4.3 50.8 1.0 O B:HOH998 4.5 27.7 1.0 O B:SER535 4.6 29.9 1.0 O A:HOH1089 4.7 33.0 1.0 O B:HOH1228 4.8 53.9 1.0 CA A:GLN645 4.8 38.9 1.0 OE2 B:GLU571 4.8 38.0 1.0 CB B:PRO568 4.8 29.7 1.0 O B:VAL569 4.9 28.0 1.0 O B:PRO568 4.9 27.9 1.0 CG A:GLN645 4.9 45.4 1.0 CB A:GLN645 5.0 41.1 1.0

Calcium binding site 2 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:58.1 occ:1.00 O A:ALA133 2.3 47.0 1.0 O A:HOH934 2.4 41.3 1.0 O A:HOH1191 2.4 48.9 1.0 O A:HOH1183 2.5 46.1 1.0 C A:ALA133 3.4 45.8 1.0 CA A:ALA133 4.2 43.6 1.0 C A:GLU134 4.3 47.8 1.0 O A:PRO151 4.3 34.7 1.0 O A:GLU134 4.3 47.0 1.0 CB A:ALA133 4.4 45.5 1.0 N A:GLU134 4.4 48.2 1.0 CA A:GLU134 4.6 50.2 1.0 N A:PRO135 4.6 46.7 1.0 O A:HOH1131 4.9 34.8 1.0

Calcium binding site 3 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:49.4 occ:1.00 O A:HOH942 2.3 43.2 1.0 O A:HOH966 2.4 40.0 1.0 OD1 A:ASN349 2.4 49.8 1.0 O A:HOH1040 2.6 36.5 1.0 CG A:ASN349 3.5 48.5 1.0 ND2 A:ASN349 3.9 47.8 1.0 O A:VAL347 4.3 42.8 1.0 OD2 A:ASP358 4.4 43.8 1.0 CG A:ASP358 4.6 43.9 1.0 OD1 A:ASP358 4.7 47.7 1.0 ND1 A:HIS354 4.8 37.6 1.0 CB A:ASN349 4.8 49.7 1.0 O A:PRO348 4.9 45.4 1.0 O A:HOH1085 4.9 33.1 1.0 CE1 A:HIS354 5.0 37.8 1.0

Calcium binding site 4 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:42.5 occ:1.00 O A:HOH1208 2.3 57.0 1.0 O A:HOH1176 2.5 36.3 1.0 O A:HOH1034 2.5 42.9 1.0 O A:HOH1068 2.5 33.1 1.0 O A:HOH1035 2.6 44.1 1.0 CD A:PRO568 4.4 30.6 1.0 OD1 A:ASP534 4.5 34.2 1.0 O A:HOH1002 4.7 32.6 1.0 O A:HOH1076 4.8 38.2 1.0 O A:SER535 4.8 28.0 1.0 CB A:ASP534 4.8 32.4 1.0 CA A:GLY567 4.9 27.8 1.0 O A:SER566 4.9 26.0 1.0 CG A:ASP534 4.9 33.6 1.0 N A:SER535 4.9 29.9 1.0 N A:PRO568 5.0 29.8 1.0 O A:HOH1218 5.0 40.7 1.0

Calcium binding site 5 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca805 b:55.6 occ:1.00 O A:HOH947 2.4 45.6 1.0 O A:HOH1132 2.5 53.0 1.0 OD2 A:ASP467 2.5 23.6 1.0 O A:HOH1097 2.8 40.9 1.0 CG A:ASP467 3.4 24.7 1.0 OD1 A:ASP467 3.8 25.9 1.0 NH1 A:ARG516 4.1 34.0 1.0 O A:HOH1163 4.1 34.3 1.0 CH2 A:TRP430 4.1 94.1 1.0 NE1 A:TRP387 4.3 24.6 1.0 O A:HOH981 4.4 36.4 1.0 CZ2 A:TRP387 4.5 25.1 1.0 CZ2 A:TRP430 4.6 92.1 1.0 CB A:ASP467 4.7 24.8 1.0 OD2 A:ASP532 4.7 31.8 1.0 CE2 A:TRP387 4.8 24.3 1.0 CZ3 A:TRP430 4.8 92.5 1.0 OD1 A:ASP532 4.9 30.9 1.0 CZ A:ARG516 5.0 33.1 1.0

Calcium binding site 6 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca806 b:77.1 occ:1.00 O A:HOH1203 2.4 50.7 1.0 O A:HOH1212 2.5 48.4 1.0 OE1 A:GLU379 2.6 60.5 1.0 O A:HOH1049 2.8 54.4 1.0 OE2 A:GLU376 2.9 41.1 1.0 OE1 A:GLU376 3.2 40.8 1.0 CD A:GLU376 3.4 39.2 1.0 CD A:GLU379 3.5 55.4 1.0 OE2 A:GLU379 3.6 59.0 1.0 CG A:GLU379 4.9 49.0 1.0 CG A:GLU376 4.9 35.9 1.0

Calcium binding site 7 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:73.3 occ:1.00 O B:HOH1184 2.3 49.0 1.0 O B:HOH1224 2.4 51.2 1.0 OE2 B:GLU376 2.5 41.4 1.0 O B:HOH1055 2.7 45.0 1.0 OE1 B:GLU379 2.9 56.2 1.0 OE2 B:GLU379 3.0 57.0 1.0 OE1 B:GLU376 3.1 42.4 1.0 CD B:GLU376 3.2 41.3 1.0 CD B:GLU379 3.3 54.0 1.0 NE B:ARG375 4.3 39.7 1.0 CG B:GLU376 4.7 39.3 1.0 CG B:GLU379 4.8 48.4 1.0 NH2 B:ARG375 4.9 41.3 1.0

Calcium binding site 8 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:74.0 occ:1.00 O B:HOH1161 2.3 51.8 1.0 O B:HOH992 2.4 44.0 1.0 O B:ALA133 2.5 45.2 1.0 O B:HOH1226 2.7 50.5 1.0 C B:ALA133 3.5 43.5 1.0 O B:PRO151 4.2 33.5 1.0 CA B:ALA133 4.3 41.2 1.0 C B:GLU134 4.3 48.8 1.0 O B:GLU134 4.4 47.4 1.0 N B:GLU134 4.5 45.8 1.0 O B:HOH1177 4.5 40.2 1.0 CB B:ALA133 4.5 42.5 1.0 N B:PRO135 4.5 51.0 1.0 CA B:GLU134 4.6 49.1 1.0 CA B:PRO135 4.9 50.3 1.0 O B:ASP149 5.0 39.6 1.0

Calcium binding site 9 out of 9 in the Cycloalternan-Degrading Enzyme From Trueperella Pyogenes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cycloalternan-Degrading Enzyme From Trueperella Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:59.3 occ:1.00 OD2 B:ASP467 2.4 25.4 1.0 O B:HOH1043 2.5 51.9 1.0 CG B:ASP467 3.4 25.2 1.0 OD1 B:ASP467 3.7 26.0 1.0 O B:HOH1134 3.9 36.0 1.0 NH1 B:ARG516 4.0 33.9 1.0 NE1 B:TRP387 4.2 22.0 1.0 CH2 B:TRP430 4.4 95.3 1.0 OD2 B:ASP532 4.6 31.7 1.0 CZ2 B:TRP387 4.7 22.4 1.0 CB B:ASP467 4.7 25.1 1.0 OD1 B:ASP532 4.7 30.6 1.0 CE2 B:TRP387 4.8 21.9 1.0 O B:HOH948 4.9 35.5 1.0 O B:HOH1115 4.9 48.4 1.0 CZ2 B:TRP430 5.0 90.0 1.0

S.H.Light, L.A.Cahoon, A.S.Halavaty, N.E.Freitag, W.F.Anderson. Structure to Function of An Alpha-Glucan Metabolic Pathway That Promotes Listeria Monocytogenes Pathogenesis. Nat Microbiol V. 2 16202 2016.
ISSN: ESSN 2058-5276
PubMed: 27819654
DOI: 10.1038/NMICROBIOL.2016.202