Sodium in PDB 9b7f: S_SAD Structure of Hewl Using Lossless Default Compression

All present enzymatic activity of S_SAD Structure of Hewl Using Lossless Default Compression:
3.2.1.17;

The structure of S_SAD Structure of Hewl Using Lossless Default Compression, PDB code: 9b7f was solved by J.Jakoncic, H.J.Bernstein, A.S.Soares, K.Horvat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 1.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.895, 78.895, 36.955, 90, 90, 90
R / Rfree (%)	15.9 / 19.8

The structure of S_SAD Structure of Hewl Using Lossless Default Compression also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the S_SAD Structure of Hewl Using Lossless Default Compression (pdb code 9b7f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the S_SAD Structure of Hewl Using Lossless Default Compression, PDB code: 9b7f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the S_SAD Structure of Hewl Using Lossless Default Compression


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S_SAD Structure of Hewl Using Lossless Default Compression within 5.0Å range: probe atom residue distance (Å) B Occ A:Na213 b:9.9 occ:1.00 O A:SER60 2.3 10.2 1.0 O A:CYS64 2.3 7.8 1.0 O A:ARG73 2.4 10.4 1.0 O A:HOH377 2.4 9.3 1.0 OG A:SER72 2.5 11.2 1.0 O A:HOH368 2.5 5.6 1.0 CB A:SER72 3.2 10.3 1.0 C A:CYS64 3.4 6.9 1.0 C A:ARG73 3.4 10.1 1.0 C A:SER60 3.5 9.2 1.0 N A:ARG73 3.9 10.0 1.0 CA A:ASN65 3.9 7.1 1.0 CA A:SER60 4.1 8.6 1.0 N A:ASN65 4.1 7.0 1.0 C A:SER72 4.1 11.3 1.0 CB A:SER60 4.2 8.2 1.0 CA A:ARG73 4.3 10.3 1.0 CA A:SER72 4.3 11.0 1.0 N A:ASN74 4.4 9.6 1.0 N A:CYS64 4.4 7.0 1.0 O A:ARG61 4.5 10.6 1.0 C A:ARG61 4.5 11.4 1.0 CA A:ASN74 4.5 9.2 1.0 N A:ARG61 4.5 10.6 1.0 CA A:CYS64 4.6 7.0 1.0 O A:HOH402 4.6 28.1 1.0 N A:ASP66 4.6 6.7 1.0 OD1 A:ASN65 4.6 9.1 1.0 CB A:ASN74 4.7 9.5 1.0 CL A:CL205 4.7 11.6 1.0 O A:SER72 4.7 11.9 1.0 CB A:THR69 4.8 9.0 1.0 CA A:ARG61 4.8 11.2 0.5 CB A:ASN65 4.8 7.5 1.0 CA A:ARG61 4.8 11.4 0.5 C A:ASN65 4.8 6.8 1.0 N A:TRP62 5.0 10.4 1.0

Sodium binding site 2 out of 4 in the S_SAD Structure of Hewl Using Lossless Default Compression


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S_SAD Structure of Hewl Using Lossless Default Compression within 5.0Å range: probe atom residue distance (Å) B Occ A:Na214 b:16.3 occ:1.00 O A:ASP87 2.6 15.0 1.0 O A:ALA82 2.6 10.9 1.0 N A:SER91 2.8 10.0 1.0 O A:HOH327 3.1 10.5 1.0 O A:HOH337 3.3 12.0 1.0 N A:ALA90 3.4 9.6 1.0 CB A:ALA90 3.5 9.9 1.0 C A:ALA90 3.6 9.7 1.0 CA A:ALA90 3.6 9.6 1.0 C A:ILE88 3.7 10.8 1.0 CA A:ILE88 3.7 10.7 1.0 C A:ASP87 3.8 11.2 1.0 C A:ALA82 3.8 8.6 1.0 O A:ILE88 3.8 10.3 1.0 CA A:LEU83 3.8 8.0 1.0 CB A:SER91 3.8 9.6 1.0 CA A:SER91 3.9 9.3 1.0 OG A:SER91 3.9 10.9 1.0 N A:THR89 4.1 10.8 1.0 C A:LEU83 4.1 7.8 1.0 CB A:SER85 4.2 9.9 1.0 O A:HOH384 4.2 21.8 1.0 N A:ILE88 4.3 11.3 1.0 N A:LEU83 4.3 7.8 1.0 O A:LEU83 4.3 8.2 1.0 C A:THR89 4.3 10.4 1.0 O A:HOH309 4.4 12.6 1.0 N A:SER85 4.5 8.8 1.0 O A:SER85 4.6 9.5 1.0 N A:LEU84 4.7 7.9 1.0 O A:ALA90 4.8 9.1 1.0 CD2 A:LEU83 4.8 8.8 1.0 CA A:SER85 4.8 9.4 1.0 CA A:THR89 4.9 10.8 1.0 CB A:ILE88 5.0 10.4 1.0

Sodium binding site 3 out of 4 in the S_SAD Structure of Hewl Using Lossless Default Compression


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of S_SAD Structure of Hewl Using Lossless Default Compression within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:12.5 occ:1.00 O A:TYR53 2.6 7.8 1.0 OG A:SER91 2.7 10.9 1.0 N A:LEU56 2.7 8.6 1.0 N A:ILE55 3.2 7.2 1.0 C A:GLY54 3.3 7.0 1.0 N A:GLN57 3.4 6.0 1.0 CA A:LEU56 3.4 7.3 1.0 CA A:GLY54 3.5 6.2 1.0 C A:LEU56 3.6 6.8 1.0 CB A:SER91 3.6 9.6 1.0 C A:TYR53 3.6 6.2 1.0 CB A:LEU56 3.7 7.7 1.0 C A:ILE55 3.8 8.8 1.0 CD1 A:ILE58 3.8 7.3 1.0 O A:GLY54 3.9 6.6 1.0 O A:HOH309 3.9 12.6 1.0 CG1 A:ILE58 3.9 6.8 1.0 N A:ILE58 4.0 6.4 1.0 N A:GLY54 4.0 6.3 1.0 CA A:ILE55 4.0 8.9 1.0 CG1 A:ILE55 4.1 11.3 1.0 CB A:ILE58 4.3 6.8 1.0 O A:LEU83 4.3 8.2 1.0 CA A:GLN57 4.4 6.1 1.0 CB A:LEU83 4.5 7.8 1.0 O A:LEU56 4.5 6.5 1.0 CD2 A:LEU83 4.6 8.8 1.0 CA A:SER91 4.6 9.3 1.0 CB A:ILE55 4.7 10.5 1.0 C A:GLN57 4.7 6.3 1.0 CG A:LEU56 4.8 7.7 1.0 CA A:ILE58 4.8 6.7 1.0 O A:ILE55 4.9 8.8 1.0 CG A:LEU83 5.0 7.9 1.0

Sodium binding site 4 out of 4 in the S_SAD Structure of Hewl Using Lossless Default Compression


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of S_SAD Structure of Hewl Using Lossless Default Compression within 5.0Å range: probe atom residue distance (Å) B Occ A:Na216 b:15.0 occ:1.00 NE A:ARG114 2.5 9.4 1.0 O A:HOH334 3.1 12.0 1.0 NH2 A:ARG114 3.4 8.2 1.0 CZ A:ARG114 3.4 8.5 1.0 CB A:ARG114 3.6 8.7 1.0 CD A:ARG114 3.6 9.0 1.0 CG A:ARG114 3.6 8.9 1.0 CZ A:PHE34 3.9 8.5 1.0 CE1 A:PHE34 4.2 8.1 1.0 CE2 A:PHE34 4.2 8.5 1.0 CA A:ARG114 4.3 8.4 1.0 O A:ARG114 4.4 9.3 1.0 NH1 A:ARG114 4.7 8.4 1.0 CD1 A:PHE34 4.8 7.7 1.0 CD2 A:PHE34 4.8 8.1 1.0 C A:ARG114 4.9 8.7 1.0

J.Jakoncic, H.J.Bernstein, A.S.Soares, K.Horvat. Investigation of Fast and Efficient Lossless Compression Algorithms For Macromolecular Crystallography Experiments To Be Published.