Zinc 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:

Calcium	(Ca)	8 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action, PDB code: 1su3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn913 b:34.8 occ:1.00 NE2 A:HIS222 2.0 31.5 1.0 NE2 A:HIS228 2.0 33.8 1.0 NE2 A:HIS218 2.0 31.2 1.0 SG A:CYS92 2.2 27.4 1.0 CD2 A:HIS228 2.9 31.4 1.0 CE1 A:HIS222 2.9 33.8 1.0 CB A:CYS92 3.0 29.1 1.0 CD2 A:HIS222 3.0 34.2 1.0 CD2 A:HIS218 3.0 30.2 1.0 CE1 A:HIS218 3.0 31.5 1.0 CE1 A:HIS228 3.1 35.5 1.0 CB A:VAL94 4.0 29.8 1.0 ND1 A:HIS222 4.1 32.5 1.0 CG A:HIS228 4.1 33.2 1.0 CG A:HIS222 4.1 33.7 1.0 ND1 A:HIS228 4.1 32.4 1.0 ND1 A:HIS218 4.1 27.3 1.0 CG A:HIS218 4.1 28.8 1.0 CG2 A:VAL94 4.3 29.6 1.0 CA A:CYS92 4.4 28.7 1.0 N A:VAL94 4.7 29.6 1.0 CE A:MET236 4.7 32.3 1.0 CG1 A:VAL94 4.9 29.9 1.0 CA A:VAL94 4.9 30.1 1.0 O A:VAL94 4.9 30.5 1.0 C A:CYS92 4.9 29.1 1.0

Zinc binding site 2 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn915 b:42.3 occ:1.00 ND1 A:HIS196 1.8 31.6 1.0 OD2 A:ASP170 2.0 43.6 1.0 NE2 A:HIS183 2.1 36.3 1.0 NE2 A:HIS168 2.1 39.7 1.0 CE1 A:HIS196 2.7 35.0 1.0 CG A:HIS196 2.9 35.1 1.0 CD2 A:HIS168 2.9 39.8 1.0 CG A:ASP170 2.9 42.8 1.0 CE1 A:HIS183 3.0 36.0 1.0 CD2 A:HIS183 3.1 32.8 1.0 OD1 A:ASP170 3.1 39.9 1.0 CE1 A:HIS168 3.2 38.8 1.0 CB A:HIS196 3.4 33.9 1.0 NE2 A:HIS196 3.8 34.4 1.0 CD2 A:HIS196 4.0 36.2 1.0 O A:SER172 4.0 44.3 1.0 CG A:HIS168 4.1 41.5 1.0 ND1 A:HIS183 4.1 35.6 1.0 ND1 A:HIS168 4.2 41.1 1.0 CG A:HIS183 4.2 34.1 1.0 CE1 A:PHE185 4.3 41.1 1.0 CB A:ASP170 4.3 44.9 1.0 CZ A:PHE185 4.5 41.4 1.0 CE2 A:PHE174 4.7 35.6 1.0 CB A:SER172 4.8 45.8 1.0 CZ A:PHE174 4.8 36.8 1.0 O A:HOH978 4.9 49.4 1.0 CA A:HIS196 4.9 34.1 1.0 CG2 A:VAL164 4.9 36.7 1.0

Zinc binding site 3 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 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:Zn913 b:35.6 occ:1.00 NE2 B:HIS228 1.9 35.0 1.0 NE2 B:HIS218 2.0 33.9 1.0 NE2 B:HIS222 2.0 34.9 1.0 SG B:CYS92 2.3 40.0 1.0 CE1 B:HIS228 2.9 34.1 1.0 CD2 B:HIS228 2.9 32.7 1.0 CB B:CYS92 2.9 39.8 1.0 CD2 B:HIS222 2.9 37.1 1.0 CE1 B:HIS218 3.0 35.6 1.0 CD2 B:HIS218 3.0 33.5 1.0 CE1 B:HIS222 3.1 37.0 1.0 CB B:VAL94 3.9 39.5 1.0 ND1 B:HIS228 4.0 32.5 1.0 CG B:HIS228 4.0 33.8 1.0 ND1 B:HIS218 4.1 35.1 1.0 CG B:HIS222 4.1 35.6 1.0 CG B:HIS218 4.1 33.9 1.0 ND1 B:HIS222 4.1 37.8 1.0 CG2 B:VAL94 4.2 41.0 1.0 CA B:CYS92 4.4 40.0 1.0 CE B:MET236 4.7 35.2 1.0 CG1 B:VAL94 4.8 38.7 1.0 N B:VAL94 4.8 38.7 1.0 C B:CYS92 4.8 39.8 1.0 CA B:VAL94 4.9 39.4 1.0

Zinc binding site 4 out of 4 in the X-Ray Structure of Human Prommp-1: New Insights Into Collagenase Action


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 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:Zn915 b:45.7 occ:1.00 OD2 B:ASP170 1.7 43.2 1.0 ND1 B:HIS196 1.9 36.3 1.0 NE2 B:HIS183 2.1 41.5 1.0 NE2 B:HIS168 2.2 41.2 1.0 CG B:ASP170 2.8 46.0 1.0 CE1 B:HIS196 2.8 39.9 1.0 CD2 B:HIS168 2.9 41.8 1.0 CE1 B:HIS183 3.0 41.8 1.0 CG B:HIS196 3.0 37.6 1.0 CD2 B:HIS183 3.1 39.9 1.0 OD1 B:ASP170 3.2 41.0 1.0 CE1 B:HIS168 3.4 42.6 1.0 CB B:HIS196 3.4 36.6 1.0 NE2 B:HIS196 3.9 40.4 1.0 O B:SER172 4.0 46.6 1.0 CD2 B:HIS196 4.1 39.6 1.0 CB B:ASP170 4.1 47.4 1.0 ND1 B:HIS183 4.1 41.6 1.0 CG B:HIS168 4.2 43.6 1.0 CG B:HIS183 4.2 39.6 1.0 CE1 B:PHE185 4.3 42.0 1.0 ND1 B:HIS168 4.3 41.6 1.0 CZ B:PHE185 4.5 41.9 1.0 CE2 B:PHE174 4.7 39.6 1.0 CB B:SER172 4.7 47.6 1.0 CZ B:PHE174 4.8 39.5 1.0 CG2 B:VAL164 4.9 40.3 1.0 O B:HOH946 4.9 50.2 1.0 CA B:HIS196 4.9 36.5 1.0 C B:SER172 5.0 46.9 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