Sodium in PDB 1su3: X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action

All present enzymatic activity of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action:
3.4.24.7;

The structure of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action, PDB code: 1su3 was solved by D.Jozic, G.Bourenkov, N.H.Lim, H.Nagase, W.Bode, K.Maskos, Structural Proteomics In Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.746, 142.746, 295.308, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.2

The structure of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Calcium	(Ca)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action (pdb code 1su3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action, PDB code: 1su3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range: probe atom residue distance (Å) B Occ A:Na911 b:44.0 occ:1.00 O A:ILE287 2.3 41.9 1.0 O A:VAL429 2.3 40.8 1.0 O A:ALA380 2.3 42.0 1.0 O A:ALA331 2.3 40.0 1.0 O A:HOH1088 2.6 53.0 1.0 CL A:CL909 2.8 35.1 1.0 C A:ILE287 3.5 40.7 1.0 C A:VAL429 3.5 40.7 1.0 C A:ALA380 3.5 42.4 1.0 C A:ALA331 3.5 40.4 1.0 CA A:THR288 4.2 43.6 1.0 N A:ALA380 4.2 39.7 1.0 N A:VAL429 4.2 40.0 1.0 N A:ALA331 4.3 39.9 1.0 N A:THR288 4.3 42.5 1.0 N A:ILE287 4.4 38.3 1.0 CA A:ALA380 4.4 41.0 1.0 CA A:TYR332 4.4 42.2 1.0 CA A:VAL429 4.4 40.0 1.0 N A:PHE430 4.4 42.1 1.0 N A:TYR332 4.4 41.5 1.0 CB A:THR288 4.4 44.3 1.0 N A:LEU381 4.5 44.6 1.0 CA A:ALA331 4.5 39.9 1.0 CA A:PHE430 4.5 43.0 1.0 CA A:ILE287 4.5 39.3 1.0 CG1 A:VAL429 4.5 41.1 1.0 CB A:TYR332 4.5 42.0 1.0 CA A:LEU381 4.6 46.6 1.0 CB A:LEU381 4.6 47.0 1.0 CB A:PHE430 4.7 42.8 1.0 OG1 A:THR288 4.9 45.1 1.0 CB A:ILE287 5.0 39.6 1.0 CB A:ALA380 5.0 40.8 1.0 CB A:ALA331 5.0 39.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action within 5.0Å range: probe atom residue distance (Å) B Occ B:Na912 b:34.8 occ:1.00 O B:ILE287 2.2 35.0 1.0 O B:ALA380 2.3 37.5 1.0 O B:ALA331 2.3 35.7 1.0 O B:VAL429 2.4 38.6 1.0 O B:HOH980 2.6 38.9 1.0 CL B:CL910 2.9 34.4 1.0 C B:ILE287 3.4 35.2 1.0 C B:ALA331 3.5 35.6 1.0 C B:ALA380 3.6 38.2 1.0 C B:VAL429 3.6 38.3 1.0 CA B:THR288 4.1 36.9 1.0 N B:THR288 4.2 35.8 1.0 N B:VAL429 4.2 37.5 1.0 N B:ALA380 4.3 36.5 1.0 N B:ILE287 4.3 34.8 1.0 CB B:THR288 4.3 37.0 1.0 N B:ALA331 4.3 35.0 1.0 CA B:TYR332 4.3 35.0 1.0 N B:TYR332 4.4 35.8 1.0 CA B:ILE287 4.4 34.5 1.0 CA B:ALA380 4.5 37.2 1.0 CA B:PHE430 4.5 40.7 1.0 CA B:ALA331 4.5 35.0 1.0 N B:PHE430 4.5 39.6 1.0 N B:LEU381 4.5 39.6 1.0 CB B:TYR332 4.5 35.0 1.0 CA B:VAL429 4.5 37.3 1.0 CA B:LEU381 4.5 41.5 1.0 CG1 B:VAL429 4.5 37.7 1.0 CB B:PHE430 4.5 40.7 1.0 CB B:LEU381 4.5 42.2 1.0 OG1 B:THR288 4.7 38.0 1.0 CB B:ILE287 4.9 34.8 1.0 CB B:ALA331 4.9 34.8 1.0

D.Jozic, G.Bourenkov, N.H.Lim, R.Visse, H.Nagase, W.Bode, K.Maskos. X-Ray Structure of Human Prommp-1: New Insights Into Procollagenase Activation and Collagen Binding. J.Biol.Chem. V. 280 9578 2005.
ISSN: ISSN 0021-9258
PubMed: 15611040
DOI: 10.1074/JBC.M411084200