Calcium in PDB 4hiz: Phage PHI92 Endosialidase

All present enzymatic activity of Phage PHI92 Endosialidase:
3.2.1.129;

The structure of Phage PHI92 Endosialidase, PDB code: 4hiz was solved by D.Schwarzer, C.Browning, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.858, 137.584, 140.778, 90.00, 94.64, 90.00
R / Rfree (%)	10.7 / 14.7

The structure of Phage PHI92 Endosialidase also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms
Sodium	(Na)	12 atoms

The binding sites of Calcium atom in the Phage PHI92 Endosialidase (pdb code 4hiz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Phage PHI92 Endosialidase, PDB code: 4hiz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca823 b:16.2 occ:1.00 O A:THR152 2.4 9.6 1.0 O A:HIS586 2.4 11.7 1.0 O A:ALA588 2.5 10.8 1.0 O A:PHE154 2.5 10.3 1.0 OD2 A:ASP589 2.7 13.4 1.0 CG A:ASP589 3.2 11.3 1.0 OD1 A:ASP589 3.3 11.1 1.0 C A:ALA588 3.5 10.1 1.0 NH2 B:ARG615 3.5 12.6 1.0 C A:HIS586 3.6 11.1 1.0 C A:THR152 3.6 9.2 1.0 ND2 A:ASN156 3.7 11.9 1.0 C A:PHE154 3.8 9.9 1.0 N A:ALA588 3.8 9.7 1.0 C A:PRO587 4.0 11.1 1.0 C A:PRO153 4.1 10.1 1.0 CA A:PRO153 4.1 9.6 1.0 N A:PHE154 4.2 9.4 1.0 CA A:ALA588 4.2 10.0 1.0 CZ B:ARG615 4.2 12.6 1.0 N A:ASP589 4.3 9.0 1.0 CA A:PRO587 4.4 11.2 1.0 N A:PRO587 4.4 11.3 1.0 CB A:ASP589 4.4 9.1 1.0 N A:PRO153 4.4 10.1 1.0 O A:PRO153 4.4 10.5 1.0 N A:ASN156 4.5 9.5 1.0 N A:THR152 4.5 9.7 1.0 O A:PRO587 4.5 12.5 1.0 CG A:ASN156 4.5 11.0 1.0 CA A:HIS586 4.5 10.1 1.0 CB A:HIS586 4.6 10.4 1.0 CA A:ASP589 4.6 8.5 1.0 CA A:PHE154 4.7 8.9 1.0 CA A:THR152 4.7 9.7 1.0 N A:TYR155 4.7 9.8 1.0 O A:HOH967 4.7 14.2 1.0 CA A:TYR155 4.8 9.7 1.0 NH1 B:ARG615 4.8 12.3 1.0 CB A:ASN156 4.8 10.1 1.0 N A:HIS586 4.8 10.1 1.0 NE B:ARG615 4.9 12.8 1.0 OG1 A:THR152 4.9 11.3 1.0 CB A:ALA588 5.0 9.5 1.0

Calcium binding site 2 out of 6 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca824 b:27.4 occ:1.00 O A:HOH1899 2.3 61.7 1.0 O A:HOH1142 2.4 53.6 1.0 O A:HOH1670 2.5 39.3 1.0 O A:HOH1738 2.5 45.5 1.0 O A:GLU456 2.5 22.3 1.0 O A:HOH1017 2.6 26.2 1.0 O A:HOH1589 2.6 37.6 1.0 C A:GLU456 3.7 20.9 1.0 O A:HOH1824 4.1 53.4 1.0 O A:THR411 4.3 18.0 1.0 O A:HOH1369 4.3 36.3 1.0 CA A:GLU456 4.4 21.5 1.0 OD1 A:ASN457 4.6 26.5 1.0 N A:ASN457 4.7 19.6 1.0 O A:GLY455 4.9 20.0 1.0 O A:HOH1057 4.9 25.0 1.0 CA A:ASN457 4.9 19.6 1.0

Calcium binding site 3 out of 6 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca819 b:16.9 occ:1.00 O B:THR152 2.3 9.3 1.0 O B:HIS586 2.5 11.5 1.0 O B:ALA588 2.6 10.3 1.0 O B:PHE154 2.6 9.9 1.0 OD2 B:ASP589 2.7 12.2 1.0 CG B:ASP589 3.2 11.5 1.0 OD1 B:ASP589 3.3 10.8 1.0 C B:ALA588 3.5 10.3 1.0 NH2 C:ARG615 3.5 12.0 1.0 C B:THR152 3.6 9.9 1.0 C B:HIS586 3.6 11.4 1.0 ND2 B:ASN156 3.7 10.8 1.0 C B:PHE154 3.8 9.7 1.0 N B:ALA588 3.8 10.2 1.0 C B:PRO587 4.0 11.4 1.0 C B:PRO153 4.1 10.3 1.0 CA B:PRO153 4.2 10.6 1.0 CZ C:ARG615 4.2 12.6 1.0 N B:PHE154 4.3 8.9 1.0 CA B:ALA588 4.3 10.4 1.0 N B:ASP589 4.4 9.4 1.0 N B:PRO153 4.4 10.4 1.0 CB B:ASP589 4.4 9.9 1.0 O B:PRO153 4.4 10.7 1.0 CA B:PRO587 4.4 11.8 1.0 N B:PRO587 4.4 11.3 1.0 N B:THR152 4.4 10.1 1.0 N B:ASN156 4.5 8.8 1.0 O B:PRO587 4.5 12.3 1.0 CG B:ASN156 4.5 10.5 1.0 CA B:HIS586 4.6 10.6 1.0 CB B:HIS586 4.6 10.1 1.0 CA B:ASP589 4.6 8.8 1.0 CA B:THR152 4.6 10.5 1.0 CA B:PHE154 4.7 8.9 1.0 N B:TYR155 4.7 10.4 1.0 O B:HOH944 4.7 14.3 1.0 NH1 C:ARG615 4.8 12.5 1.0 CA B:TYR155 4.8 9.9 1.0 N B:HIS586 4.8 10.8 1.0 CB B:ASN156 4.8 9.3 1.0 NE C:ARG615 4.9 13.6 1.0 OG1 B:THR152 4.9 10.9 1.0

Calcium binding site 4 out of 6 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca820 b:22.3 occ:1.00 O B:HOH1687 2.4 42.7 1.0 O B:HOH1684 2.5 48.2 1.0 O B:HOH1381 2.5 43.6 1.0 O B:GLU456 2.5 20.4 1.0 O B:HOH1006 2.6 21.9 1.0 O B:HOH1206 2.6 30.0 1.0 O B:HOH1761 2.7 67.7 1.0 C B:GLU456 3.7 18.9 1.0 O B:HOH1737 4.3 56.6 1.0 O B:THR411 4.3 16.3 1.0 O B:HOH1227 4.4 32.5 1.0 CA B:GLU456 4.4 19.5 1.0 OD1 B:ASN457 4.6 23.0 1.0 N B:ASN457 4.7 18.1 1.0 O B:HOH966 4.8 23.1 1.0 O B:GLY455 4.9 20.4 1.0 OE1 B:GLU456 4.9 49.2 1.0 CA B:ASN457 4.9 17.9 1.0

Calcium binding site 5 out of 6 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca819 b:16.4 occ:1.00 O C:HIS586 2.4 10.9 1.0 O C:THR152 2.4 11.1 1.0 O C:ALA588 2.6 10.8 1.0 O C:PHE154 2.6 10.3 1.0 OD2 C:ASP589 2.6 12.6 1.0 CG C:ASP589 3.2 11.8 1.0 OD1 C:ASP589 3.3 11.6 1.0 C C:ALA588 3.5 10.2 1.0 NH2 A:ARG615 3.5 13.9 1.0 C C:HIS586 3.6 11.5 1.0 C C:THR152 3.6 10.2 1.0 ND2 C:ASN156 3.7 11.1 1.0 C C:PHE154 3.8 10.7 1.0 N C:ALA588 3.8 10.2 1.0 C C:PRO587 4.0 11.1 1.0 C C:PRO153 4.1 11.0 1.0 CA C:PRO153 4.2 11.2 1.0 CZ A:ARG615 4.2 13.5 1.0 CA C:ALA588 4.2 10.3 1.0 N C:PHE154 4.3 9.7 1.0 CA C:PRO587 4.3 11.3 1.0 N C:ASP589 4.3 9.6 1.0 N C:PRO587 4.4 11.2 1.0 CB C:ASP589 4.4 9.9 1.0 N C:PRO153 4.4 10.3 1.0 O C:PRO153 4.4 10.9 1.0 O C:PRO587 4.4 12.3 1.0 N C:ASN156 4.5 10.7 1.0 N C:THR152 4.5 10.6 1.0 CA C:HIS586 4.5 11.0 1.0 CG C:ASN156 4.5 11.3 1.0 CB C:HIS586 4.6 10.9 1.0 CA C:ASP589 4.6 9.2 1.0 CA C:PHE154 4.7 10.8 1.0 O C:HOH922 4.7 14.7 1.0 CA C:THR152 4.7 10.5 1.0 N C:TYR155 4.7 10.8 1.0 N C:HIS586 4.8 10.9 1.0 NH1 A:ARG615 4.8 13.1 1.0 CA C:TYR155 4.8 11.1 1.0 NE A:ARG615 4.8 13.4 1.0 CB C:ASN156 4.8 10.8 1.0 OG1 C:THR152 5.0 11.9 1.0 CB C:ALA588 5.0 10.3 1.0

Calcium binding site 6 out of 6 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca820 b:41.6 occ:1.00 O C:GLU456 2.5 20.9 1.0 O C:HOH1292 2.7 56.1 1.0 O C:HOH1877 2.7 62.2 1.0 O C:HOH1161 2.8 26.5 1.0 O C:HOH1169 3.0 31.2 1.0 C C:GLU456 3.6 19.5 1.0 OD1 C:ASN457 4.1 25.9 1.0 O C:HOH1941 4.3 54.0 1.0 CA C:GLU456 4.5 19.5 1.0 O C:THR411 4.5 18.5 1.0 N C:ASN457 4.5 19.1 1.0 CA C:ASN457 4.6 19.7 1.0 O C:HOH1544 4.7 51.1 1.0 CG C:ASN457 4.7 23.4 1.0 O C:HOH1609 4.9 36.1 1.0 O C:HOH913 4.9 50.5 1.0

D.Schwarzer, C.Browning, A.Oberbeck, K.Stummeyer, M.Muhlenhoff, R.Gerardy-Schahn, P.G.Leiman. Crystal Structure of Endosialidase From Phage PHI92 That Cleaves ALPHA2,8- and ALPHA2,9-Linked Polysialic Acid To Be Published.