Atomistry » Sodium » PDB 1s45-1t3p » 1su3
Atomistry »
  Sodium »
    PDB 1s45-1t3p »
      1su3 »

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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 1su3:

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

Sodium Binding Sites:

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 1su3

Go back to Sodium Binding Sites List in 1su3
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 1su3

Go back to Sodium Binding Sites List in 1su3
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

Reference:

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
Page generated: Tue Dec 15 05:36:06 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy