Sodium in PDB 4hgu: Crystal Structure of Galleria Mellonella Silk Protease Inhibitor 2

The structure of Crystal Structure of Galleria Mellonella Silk Protease Inhibitor 2, PDB code: 4hgu was solved by S.Krzywda, M.Jaskolski, A.Dvornyk, B.Kludkiewicz, K.Grzelak, W.Zagorski, W.Bal, E.Kopera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 0.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	27.270, 31.240, 35.740, 90.00, 90.00, 90.00
R / Rfree (%)	10.7 / 12.9

The binding sites of Sodium atom in the Crystal Structure of Galleria Mellonella Silk Protease Inhibitor 2 (pdb code 4hgu). 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 Galleria Mellonella Silk Protease Inhibitor 2, PDB code: 4hgu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Galleria Mellonella Silk Protease Inhibitor 2


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 Galleria Mellonella Silk Protease Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:6.6 occ:0.66 O A:HOH242 2.4 10.8 0.3 O A:HOH204 2.4 8.0 1.0 O A:HOH212 2.4 11.3 0.9 O A:HOH210 2.5 10.4 0.8 O A:HOH208 2.5 7.5 1.0 O A:HOH242 2.5 12.5 0.5 O A:HOH205 2.5 11.6 0.8 O A:HOH211 3.7 7.3 0.4 O A:HOH207 3.8 6.4 1.0 O A:HOH214 3.8 8.9 0.7 O A:HOH206 3.9 12.3 0.9 O A:HOH209 3.9 8.2 1.0 N A:GLU1 4.3 7.0 1.0 O A:HOH226 4.6 6.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Galleria Mellonella Silk Protease Inhibitor 2


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 Galleria Mellonella Silk Protease Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:8.3 occ:0.38 O A:HOH274 2.3 19.7 0.4 OD1 A:ASP34 2.3 13.9 1.0 O A:HOH271 2.5 19.3 0.7 O A:HOH273 2.5 22.1 0.5 O A:HOH272 2.5 22.7 0.7 O A:ASP34 2.6 7.3 1.0 C A:ASP34 3.3 5.1 1.0 O A:HOH275 3.4 8.0 0.3 CG A:ASP34 3.4 7.8 1.0 CA A:ASP34 3.7 5.4 1.0 CB A:ASP34 4.1 5.6 1.0 OD2 A:ASP34 4.4 10.8 1.0 N A:HIS35 4.4 4.5 1.0 O A:HOH275 4.4 14.2 0.5 CB A:HIS35 4.7 6.0 1.0 CA A:HIS35 4.9 4.7 1.0 O A:HOH252 5.0 13.4 0.4

Sodium binding site 3 out of 4 in the Crystal Structure of Galleria Mellonella Silk Protease Inhibitor 2


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 Galleria Mellonella Silk Protease Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:10.6 occ:0.33 O A:HOH281 2.0 18.9 0.4 O A:HOH266 2.3 9.6 0.3 O A:ASP16 2.4 8.9 1.0 O A:HOH279 2.4 16.1 0.4 C A:ASP16 3.4 6.2 1.0 O A:HOH266 3.5 12.1 0.4 CA A:ASP16 4.0 6.1 1.0 CB A:ASP16 4.1 6.7 1.0 N A:GLY17 4.6 5.9 1.0 CA A:GLY17 5.0 6.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Galleria Mellonella Silk Protease Inhibitor 2


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 Galleria Mellonella Silk Protease Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:7.6 occ:0.21 O A:HOH258 2.1 21.1 0.7 OG1 A:THR7 2.3 9.3 1.0 O A:HOH234 2.4 17.7 0.8 O A:HOH257 2.5 15.8 0.4 CB A:THR7 3.5 7.1 1.0 CG2 A:THR7 3.7 11.9 1.0 N A:THR7 4.1 4.5 1.0 CA A:THR7 4.4 5.5 1.0 OE2 A:GLU8 5.0 18.4 0.4 O A:HOH262 5.0 11.9 0.4

S.Krzywda, M.Jaskolski, A.Dvornyk, B.Kludkiewicz, K.Grzelak, W.Zagorski, W.Bal, E.Kopera. A Novel Method of Protein Purification For Structural Research: An Example From Spi-2 Inhibitor, Studied at Ultrahigh Resolution By X-Ray Diffraction and By uc(Nmr) Spectroscopy To Be Published.