Sodium in PDB 8d4o: Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus

The structure of Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus, PDB code: 8d4o was solved by C.D.Gido, B.V.Geisbrecht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.08 / 1.45
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.623, 48.091, 55.161, 84.26, 89.92, 72.96
R / Rfree (%)	16.9 / 19.7

The binding sites of Sodium atom in the Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus (pdb code 8d4o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus, PDB code: 8d4o:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:18.6 occ:1.00 O A:HOH401 2.6 25.7 1.0 OD2 A:ASP121 2.7 12.7 1.0 O B:HOH352 2.7 11.0 1.0 OG1 B:THR109 2.8 6.7 1.0 CG A:ASP121 3.5 12.1 1.0 CB A:ASP121 3.6 8.4 1.0 CG2 B:THR109 3.7 8.0 1.0 CB B:THR109 3.7 6.2 1.0 CG2 B:VAL119 3.8 8.3 1.0 OE2 B:GLU107 4.1 24.5 1.0 O A:HOH326 4.2 16.4 1.0 CB A:SER124 4.2 12.1 1.0 O B:HOH364 4.3 19.5 1.0 OG A:SER124 4.3 15.0 1.0 OE1 B:GLU107 4.6 13.4 1.0 CD B:GLU107 4.6 15.7 1.0 OD1 A:ASP121 4.7 8.9 1.0 NZ B:LYS117 4.8 14.5 1.0 O A:HOH380 4.9 9.5 1.0 CD B:LYS117 4.9 12.9 1.0 O B:HOH308 4.9 20.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:32.6 occ:1.00 O A:HOH320 2.8 25.3 1.0 O A:HOH376 3.2 9.4 1.0 O A:ILE55 3.2 10.9 1.0 O C:HOH376 3.3 16.2 1.0 N A:THR60 3.6 19.2 1.0 OG1 A:THR60 3.6 22.2 1.0 CG2 A:THR60 3.9 24.0 1.0 OG1 A:THR56 4.0 17.5 1.0 CA A:THR56 4.1 11.1 1.0 O A:HOH389 4.1 25.0 1.0 C A:ILE55 4.2 9.9 1.0 O A:HOH311 4.2 24.7 1.0 CB A:THR60 4.2 22.6 1.0 CA A:GLY59 4.2 19.8 1.0 C A:GLY59 4.2 17.3 1.0 O A:HOH332 4.3 20.5 1.0 CA A:THR60 4.4 17.2 1.0 NH2 A:ARG93 4.4 23.0 1.0 CB A:THR56 4.5 13.5 1.0 N A:THR56 4.5 9.4 1.0 O C:HOH413 4.5 29.7 1.0 CG2 A:THR56 4.6 19.9 1.0 OG1 A:THR54 4.6 11.6 1.0 O A:THR60 4.7 23.4 1.0 N A:GLY59 4.8 17.4 1.0 C A:THR60 5.0 21.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:28.1 occ:1.00 O C:HOH314 2.6 23.2 1.0 O B:SER124 2.7 11.5 1.0 O B:HOH322 2.7 14.7 1.0 OE1 B:GLU82 2.9 18.7 1.0 OE2 B:GLU82 3.0 25.2 1.0 CD B:GLU82 3.3 18.3 1.0 C B:SER124 3.8 11.5 1.0 O C:HOH303 3.8 19.3 1.0 O B:LEU122 4.0 10.0 1.0 O B:ASP121 4.0 9.6 1.0 CG1 B:ILE126 4.2 13.0 1.0 CD1 B:ILE126 4.2 14.8 1.0 C B:LEU122 4.3 8.2 1.0 N B:SER124 4.4 9.2 1.0 CA B:GLY125 4.5 10.8 1.0 OE1 C:GLN62 4.5 19.5 1.0 O B:HOH344 4.5 14.8 1.0 N B:GLY125 4.6 13.0 1.0 CA B:LEU122 4.7 8.5 1.0 C B:GLY125 4.7 11.7 1.0 N B:ILE126 4.7 12.8 1.0 CA B:SER124 4.8 10.1 1.0 CG B:GLU82 4.9 10.2 1.0 N B:LYS123 5.0 7.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:26.8 occ:1.00 O D:HOH399 2.3 26.8 1.0 O D:HOH311 2.4 28.4 1.0 OG1 D:THR54 2.4 12.6 1.0 O D:HOH365 2.5 20.4 1.0 O D:ILE55 2.6 9.0 1.0 C D:ILE55 3.4 9.0 1.0 N D:ILE55 3.6 6.0 1.0 O D:HOH344 3.7 20.0 1.0 CB D:THR54 3.8 8.8 1.0 OG1 D:THR56 3.9 16.5 1.0 CA D:ILE55 4.2 7.0 1.0 N D:THR56 4.2 8.8 1.0 NH2 D:ARG93 4.3 20.9 1.0 C D:THR54 4.3 6.2 1.0 CA D:THR54 4.4 6.3 1.0 CG2 D:THR54 4.4 10.0 1.0 CA D:THR56 4.4 10.6 1.0 O D:HOH314 4.6 20.0 1.0 O D:HOH329 4.7 22.9 1.0 O D:HOH364 4.7 8.5 1.0 OG1 D:THR60 4.7 20.8 1.0 O D:HOH371 4.8 18.3 1.0 CB D:THR56 4.8 13.4 1.0

C.D.Gido, T.J.Herdendorf, B.V.Geisbrecht. Crystal Structure of the Neutrophil Serine Protease Inhibitor EAP1 From S. Aureus To Be Published.