Sodium 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
Calcium	(Ca)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Phage PHI92 Endosialidase (pdb code 4hiz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Phage PHI92 Endosialidase, PDB code: 4hiz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na825 b:76.8 occ:1.00 ND2 A:ASN457 3.1 25.0 1.0 O A:HOH1969 3.7 59.6 1.0 O A:HOH1860 3.8 58.4 1.0 O A:HOH1738 4.1 45.5 1.0 CG A:ASN457 4.1 24.6 1.0 OD1 A:ASN457 4.2 26.5 1.0 O A:HOH1142 4.3 53.6 1.0 CB A:GLU456 4.3 25.3 1.0 O A:HOH1892 4.5 51.1 1.0 OD2 A:ASP453 4.9 25.6 1.0 O A:HOH1779 4.9 78.7 1.0 O A:GLU456 4.9 22.3 1.0

Sodium binding site 2 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na826 b:44.5 occ:1.00 O A:VAL550 2.7 10.8 1.0 O A:THR163 2.7 12.5 1.0 O A:HOH1389 2.8 47.0 1.0 OG1 A:THR163 3.5 11.9 1.0 C A:THR163 3.6 11.0 1.0 CE A:LYS426 3.7 16.1 1.0 O A:HOH1127 3.7 19.0 1.0 C A:VAL550 3.8 9.9 1.0 CB A:CYS551 3.8 12.3 1.0 O A:HOH1038 3.8 18.2 1.0 O A:HOH1010 3.8 15.5 1.0 CA A:CYS551 4.0 10.5 1.0 O A:HOH1294 4.1 26.5 1.0 O2 A:EDO806 4.2 26.2 1.0 O A:HOH1050 4.3 17.1 1.0 N A:CYS551 4.3 9.5 1.0 CA A:THR163 4.4 10.3 1.0 N A:PHE164 4.5 10.5 1.0 O A:HOH1519 4.5 37.4 1.0 CB A:THR163 4.5 11.3 1.0 OG A:SER549 4.5 12.6 1.0 CA A:PHE164 4.5 9.9 1.0 N A:THR163 4.6 10.1 1.0 NZ A:LYS426 4.6 15.2 1.0 O1 A:EDO806 4.8 21.9 1.0 OD1 A:ASP161 4.8 15.8 1.0 O A:HOH1817 4.9 74.7 1.0 N A:VAL550 4.9 9.5 1.0 CD A:LYS426 4.9 15.0 1.0 CA A:VAL550 4.9 9.5 1.0

Sodium binding site 3 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na827 b:48.8 occ:1.00 O A:HOH1518 2.6 47.6 1.0 OG A:SER440 2.7 20.8 1.0 O A:HOH1692 2.8 50.7 1.0 CB A:SER440 3.4 18.6 1.0 OG A:SER442 3.4 22.9 1.0 CB A:ALA443 4.2 18.8 1.0 O A:HOH1469 4.4 49.6 1.0 ND2 A:ASN419 4.5 16.5 1.0 C A:SER442 4.5 18.6 1.0 O A:SER442 4.6 19.7 1.0 N A:ALA443 4.6 17.2 1.0 CB A:SER442 4.7 20.6 1.0 O A:HOH1811 4.7 64.9 1.0 O A:HOH1193 4.8 26.0 1.0 CA A:SER440 4.9 16.1 1.0 CA A:SER442 5.0 18.0 1.0 N A:SER442 5.0 16.7 1.0

Sodium binding site 4 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na828 b:35.9 occ:1.00 O B:HOH1210 2.6 40.6 1.0 OD1 A:ASP584 2.7 16.2 1.0 O B:HOH1143 3.0 21.3 1.0 CG A:ASP584 3.6 14.5 1.0 NZ B:LYS191 3.6 19.0 1.0 CE B:LYS191 3.7 18.5 1.0 OD2 A:ASP584 3.8 15.3 1.0 OE1 B:GLU203 4.0 21.9 1.0 OG B:SER200 4.4 12.2 1.0 CB B:SER200 4.5 10.5 1.0 O A:HOH1053 4.5 18.3 1.0 C A:HIS583 4.7 11.6 1.0 O B:MET201 4.7 11.1 1.0 CB B:GLU203 4.7 12.0 1.0 O A:HIS583 4.7 12.8 1.0 N A:ASP584 4.8 11.1 1.0 CD B:LYS191 4.9 18.0 1.0 CB A:ASP584 4.9 12.3 1.0 CD B:GLU203 4.9 20.2 1.0 CG B:MET201 5.0 12.6 1.0

Sodium binding site 5 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na829 b:26.4 occ:1.00 O A:HOH1101 2.7 33.3 1.0 OG1 A:THR623 3.0 17.2 1.0 O A:HOH1596 3.1 38.3 1.0 O C:HOH989 3.3 23.8 1.0 N A:THR623 3.3 13.8 1.0 CE3 C:TRP204 3.6 13.4 1.0 CG2 A:THR623 3.7 17.2 1.0 CB A:THR623 3.8 16.6 1.0 CE1 C:HIS186 3.8 13.6 1.0 O A:HOH1554 3.9 52.8 1.0 CA C:PRO207 4.1 14.6 1.0 CA A:THR623 4.1 14.8 1.0 CA A:GLY622 4.2 12.7 1.0 C A:GLY622 4.3 13.6 1.0 CZ3 C:TRP204 4.3 14.4 1.0 O C:HOH1332 4.3 47.5 1.0 CB C:TRP204 4.4 11.3 1.0 CB C:PRO207 4.4 14.3 1.0 ND1 C:HIS186 4.4 13.6 1.0 CD2 C:TRP204 4.5 12.1 1.0 O C:THR206 4.6 14.5 1.0 NE2 C:HIS186 4.7 13.9 1.0 N C:PRO207 4.8 14.7 1.0 N A:ASP624 4.9 15.7 1.0 CG C:TRP204 4.9 10.9 1.0 O C:HOH1010 4.9 16.2 1.0 C A:THR623 5.0 15.6 1.0

Sodium binding site 6 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na821 b:31.3 occ:1.00 O B:HOH902 2.7 16.6 1.0 OD2 B:ASP386 2.7 26.6 1.0 O B:HOH1204 3.0 25.7 1.0 NH1 B:ARG238 3.5 15.3 1.0 CG B:ASP386 3.5 25.0 1.0 OD1 B:ASP386 3.6 28.5 1.0 CG2 B:THR363 3.8 15.8 1.0 O B:HOH1385 3.9 39.3 1.0 CA B:ARG244 4.0 13.6 1.0 O B:HOH1619 4.1 49.4 1.0 O B:HOH1824 4.1 48.0 1.0 CA B:THR363 4.2 14.8 1.0 CG B:ARG244 4.2 16.7 1.0 O B:MET243 4.2 15.9 1.0 O B:THR363 4.2 16.0 1.0 CD1 B:TYR354 4.2 16.8 1.0 CB B:THR363 4.4 14.8 1.0 OG1 B:THR363 4.4 16.0 1.0 N B:LEU245 4.6 13.4 1.0 CB B:ARG244 4.6 14.3 1.0 C B:THR363 4.7 15.4 1.0 N B:ARG244 4.7 13.8 1.0 C B:MET243 4.7 14.8 1.0 CZ B:ARG238 4.8 15.6 1.0 CE1 B:TYR354 4.8 18.5 1.0 C B:ARG244 4.8 13.8 1.0 CB B:ASP386 4.9 19.9 1.0

Sodium binding site 7 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na821 b:19.3 occ:1.00 O C:ASN156 2.7 12.2 1.0 O C:HOH1665 2.7 12.7 1.0 O C:ASP589 2.8 12.1 1.0 CA C:GLY562 3.4 11.0 1.0 N C:ASP589 3.4 9.6 1.0 CB C:ALA544 3.5 13.4 1.0 CA C:ALA157 3.5 10.0 1.0 C C:ASP589 3.6 10.7 1.0 CB C:ALA157 3.6 10.4 1.0 C C:ASN156 3.7 11.4 1.0 CB C:ALA588 3.8 10.3 1.0 C C:ALA588 3.8 10.2 1.0 O C:ALA544 3.8 12.6 1.0 N C:GLY563 3.9 9.4 1.0 CD2 C:LEU590 3.9 11.4 1.0 CA C:ASP589 3.9 9.2 1.0 CA C:ALA588 4.0 10.3 1.0 C C:GLY562 4.1 11.5 1.0 O C:GLY563 4.1 11.3 1.0 N C:ALA157 4.1 9.9 1.0 C C:ALA544 4.5 12.2 1.0 N C:LEU590 4.5 9.7 1.0 N C:GLY562 4.5 10.5 1.0 O C:ALA588 4.6 10.8 1.0 CA C:ALA544 4.6 12.5 1.0 C C:ALA157 4.8 9.8 1.0 CA C:LEU590 4.8 9.3 1.0 C C:GLY563 4.8 10.5 1.0 N C:TRP158 4.9 9.4 1.0 CG C:LEU590 4.9 11.9 1.0 O C:HOH1622 5.0 10.7 1.0 CA C:GLY563 5.0 9.7 1.0

Sodium binding site 8 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na822 b:23.4 occ:1.00 O C:HOH901 2.7 16.0 1.0 O C:HOH1046 2.7 19.5 1.0 O C:HOH983 2.9 15.1 1.0 NE1 C:TRP493 2.9 13.8 1.0 CD1 C:TRP493 3.4 14.0 1.0 CD1 C:TRP528 3.7 14.1 1.0 CG2 C:VAL467 3.8 15.4 1.0 NE1 C:TRP528 3.8 13.8 1.0 O C:HOH1164 3.8 23.6 1.0 CE2 C:TRP493 4.0 12.9 1.0 CB C:ASN465 4.1 16.1 1.0 O C:PRO464 4.2 15.2 1.0 O C:HOH1084 4.2 19.6 1.0 CD2 C:LEU134 4.4 16.7 1.0 O C:ASN465 4.6 15.9 1.0 CG C:TRP493 4.7 12.9 1.0 CZ2 C:TRP493 4.7 13.6 1.0 OE1 C:GLN132 4.7 17.2 1.0 CG C:TRP528 4.8 13.1 1.0 CE2 C:TRP528 4.8 13.4 1.0 O C:TRP493 4.8 14.4 1.0 ND2 C:ASN465 4.9 17.9 1.0 CD2 C:TRP493 5.0 12.4 1.0

Sodium binding site 9 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na823 b:28.6 occ:1.00 O B:HOH908 2.5 39.0 1.0 OE2 C:GLU650 2.7 26.2 1.0 N C:ASP652 3.0 13.8 1.0 CG C:ASP652 3.3 18.1 1.0 CG C:GLU650 3.4 21.5 1.0 OD1 C:ASP652 3.5 17.0 1.0 CD C:GLU650 3.5 24.0 1.0 CB C:ASP652 3.5 16.2 1.0 N C:HIS651 3.5 12.9 1.0 CB C:HIS651 3.6 13.2 1.0 CB C:GLU650 3.7 18.3 1.0 OD2 C:ASP652 3.8 20.6 1.0 CA C:ASP652 3.8 15.3 1.0 O B:HOH1232 3.9 29.4 1.0 C C:HIS651 3.9 12.8 1.0 CA C:HIS651 3.9 12.8 1.0 O C:HOH1585 4.1 40.5 1.0 C C:GLU650 4.2 12.8 1.0 O C:HOH1302 4.2 34.5 1.0 O B:HOH903 4.2 15.6 1.0 OD1 B:ASN184 4.3 15.0 1.0 O C:HOH1465 4.5 47.9 1.0 O B:HOH1545 4.5 16.6 1.0 CA C:GLU650 4.6 14.1 1.0 CG C:HIS651 4.6 13.1 1.0 O B:HOH1820 4.7 41.5 1.0 OE1 C:GLU650 4.7 23.4 1.0 CD2 C:HIS651 4.9 12.7 1.0 C C:ASP652 4.9 15.5 1.0 O C:GLU650 4.9 13.5 1.0

Sodium binding site 10 out of 12 in the Phage PHI92 Endosialidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Phage PHI92 Endosialidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na824 b:34.6 occ:1.00 O C:HOH1438 2.8 50.1 1.0 N C:VAL308 2.9 18.9 1.0 O C:HOH1105 3.4 38.3 1.0 O C:VAL308 3.5 23.6 1.0 CA C:SER307 3.5 21.5 1.0 CG2 C:VAL285 3.7 22.2 1.0 C C:SER307 3.7 21.1 1.0 CB C:SER307 3.7 22.2 1.0 CA C:VAL308 3.9 19.8 1.0 C C:VAL308 4.1 22.0 1.0 CB C:VAL308 4.2 20.7 1.0 O C:HOH1914 4.5 53.5 1.0 OG C:SER307 4.7 24.3 1.0 CG2 C:VAL308 4.7 21.2 1.0 N C:SER307 4.8 20.6 1.0 O C:HOH1053 4.9 28.6 1.0 O C:SER307 4.9 22.9 1.0 O C:ALA306 5.0 22.4 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.