Sodium in PDB 4gwm: Crystal Structure of Human Promeprin Beta

All present enzymatic activity of Crystal Structure of Human Promeprin Beta:
3.4.24.63;

The structure of Crystal Structure of Human Promeprin Beta, PDB code: 4gwm was solved by J.L.Arolas, C.Broder, T.Jefferson, T.Guevara, E.E.Sterchi, W.Bode, W.Stocker, C.Becker-Pauly, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.620, 71.120, 85.740, 74.87, 80.08, 65.13
R / Rfree (%)	16.8 / 18.8

The structure of Crystal Structure of Human Promeprin Beta also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Promeprin Beta (pdb code 4gwm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Promeprin Beta, PDB code: 4gwm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Promeprin Beta


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 Human Promeprin Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:31.4 occ:1.00 O A:PHE310 2.2 25.5 1.0 OG A:SER300 2.2 33.4 1.0 O A:SER266 2.5 22.4 1.0 OD1 A:ASP298 2.5 34.7 1.0 OD2 A:ASP418 2.6 23.6 1.0 OD1 A:ASP418 2.7 24.3 1.0 OE2 A:GLU268 2.9 55.3 1.0 CG A:ASP418 3.0 23.1 1.0 CB A:SER300 3.3 36.5 1.0 C A:PHE310 3.4 27.5 1.0 CG A:ASP298 3.5 35.6 1.0 C A:SER266 3.6 23.6 1.0 CB A:ASP298 3.7 30.9 1.0 N A:PHE310 3.7 30.5 1.0 CB A:SER266 4.0 27.1 1.0 CD A:GLU268 4.0 73.0 1.0 CA A:SER266 4.1 22.0 1.0 N A:SER300 4.2 34.7 1.0 CA A:PHE310 4.2 27.7 1.0 OD1 A:ASP419 4.2 27.9 1.0 CA A:SER300 4.3 35.6 1.0 N A:PHE311 4.4 20.7 1.0 CB A:ASP418 4.6 19.8 1.0 OD2 A:ASP298 4.6 35.1 1.0 O A:HOH934 4.7 48.3 1.0 CA A:PHE311 4.7 20.8 1.0 C A:GLY309 4.7 40.9 1.0 N A:PHE267 4.7 20.2 1.0 CG A:GLU268 4.8 46.3 1.0 OG A:SER266 4.8 35.0 1.0 OE1 A:GLU268 4.9 79.3 1.0 CB A:PHE311 4.9 22.9 1.0 N A:HIS299 4.9 31.4 1.0 CA A:GLY309 4.9 46.2 1.0 CB A:PHE267 4.9 20.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Promeprin Beta


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 Human Promeprin Beta within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:27.6 occ:1.00 O B:PHE310 2.2 27.7 1.0 OG B:SER300 2.4 35.8 1.0 O B:SER266 2.4 24.6 1.0 OD1 B:ASP298 2.5 34.4 1.0 OD2 B:ASP418 2.5 24.2 1.0 OD1 B:ASP418 2.7 26.7 1.0 CG B:ASP418 2.9 24.9 1.0 OE2 B:GLU268 3.1 69.5 1.0 CB B:SER300 3.4 32.4 1.0 C B:PHE310 3.4 32.2 1.0 CG B:ASP298 3.5 40.4 1.0 C B:SER266 3.5 24.8 1.0 CB B:ASP298 3.8 33.6 1.0 N B:PHE310 3.8 37.6 1.0 CB B:SER266 4.0 24.9 1.0 CA B:SER266 4.1 20.5 1.0 N B:SER300 4.1 30.6 1.0 CA B:PHE310 4.2 34.9 1.0 OD1 B:ASP419 4.2 27.8 1.0 CD B:GLU268 4.3 82.6 1.0 N B:PHE311 4.4 29.1 1.0 CA B:SER300 4.4 31.0 1.0 CB B:ASP418 4.4 21.3 1.0 OD2 B:ASP298 4.6 43.0 1.0 CA B:PHE311 4.6 26.4 1.0 N B:PHE267 4.6 21.6 1.0 CB B:PHE267 4.7 23.9 1.0 N B:HIS299 4.7 30.2 1.0 O B:HOH1155 4.8 44.3 1.0 C B:GLY309 4.9 45.6 1.0 CB B:PHE311 4.9 27.3 1.0 C B:PHE267 5.0 29.8 1.0 CA B:ASP298 5.0 31.6 1.0 CG B:GLU268 5.0 46.9 1.0 CD1 B:PHE267 5.0 25.6 1.0

J.L.Arolas, C.Broder, T.Jefferson, T.Guevara, E.E.Sterchi, W.Bode, W.Stocker, C.Becker-Pauly, F.X.Gomis-Ruth. Structural Basis For the Sheddase Function of Human Meprin Beta Metalloproteinase at the Plasma Membrane Proc.Natl.Acad.Sci.Usa V. 109 16131 2012.
ISSN: ISSN 0027-8424
PubMed: 22988105
DOI: 10.1073/PNAS.1211076109