Zinc in PDB 5h0u: Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase:
3.4.24.80;

The structure of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase, PDB code: 5h0u was solved by H.Ogata, E.Decaneto, W.Lubitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.54 / 2.24
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.995, 62.995, 122.620, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.4

The structure of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase (pdb code 5h0u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase, PDB code: 5h0u:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:32.0 occ:1.00 OXT B:HIS33 2.0 35.5 1.0 NE2 A:HIS249 2.1 36.9 1.0 NE2 A:HIS239 2.1 32.3 1.0 NE2 A:HIS243 2.2 33.8 1.0 O B:HIS33 2.5 34.4 1.0 C B:HIS33 2.6 35.5 1.0 O A:HOH411 2.7 41.9 1.0 CD2 A:HIS249 2.9 35.1 1.0 CD2 A:HIS239 3.0 35.7 1.0 CE1 A:HIS239 3.1 37.1 1.0 CD2 A:HIS243 3.1 32.0 1.0 CE1 A:HIS249 3.2 35.9 1.0 CE1 A:HIS243 3.2 35.0 1.0 O B:HOH202 4.0 37.1 1.0 CA B:HIS33 4.1 38.7 1.0 CG A:HIS249 4.1 39.0 1.0 CG A:HIS239 4.2 34.5 1.0 ND1 A:HIS239 4.2 34.1 1.0 ND1 A:HIS249 4.2 38.9 1.0 CG A:HIS243 4.3 33.0 1.0 ND1 A:HIS243 4.3 34.4 1.0 O A:PRO259 4.5 40.5 1.0 O1 A:GOL311 4.5 46.1 1.0 OE2 A:GLU240 4.6 35.2 1.0 N B:HIS33 4.6 39.7 1.0 CE A:MET257 4.7 32.0 1.0 C B:HIS32 4.9 37.2 1.0 O B:HIS32 5.0 35.9 0.9

Zinc binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:32.5 occ:1.00 NE2 A:HIS201 2.0 32.3 1.0 ND1 A:HIS214 2.0 32.8 1.0 NE2 A:HIS186 2.0 32.2 1.0 OD2 A:ASP188 2.1 34.2 1.0 CE1 A:HIS201 2.8 29.6 1.0 CD2 A:HIS186 2.9 36.4 1.0 CE1 A:HIS214 2.9 31.2 1.0 CG A:ASP188 3.1 32.8 1.0 CG A:HIS214 3.1 29.0 1.0 CE1 A:HIS186 3.1 34.6 1.0 CD2 A:HIS201 3.2 31.7 1.0 OD1 A:ASP188 3.4 33.5 1.0 CB A:HIS214 3.5 28.9 1.0 OH A:TYR203 4.0 34.5 1.0 ND1 A:HIS201 4.0 35.0 1.0 NE2 A:HIS214 4.1 29.6 1.0 CG A:HIS186 4.1 35.9 1.0 O A:THR190 4.1 34.9 1.0 ND1 A:HIS186 4.1 34.4 1.0 CD2 A:HIS214 4.2 29.8 1.0 CG A:HIS201 4.2 34.7 1.0 CE1 A:TYR203 4.4 29.2 1.0 CB A:ASP188 4.4 32.5 1.0 CE2 A:PHE192 4.5 32.0 1.0 CZ A:PHE192 4.6 31.5 1.0 CZ A:TYR203 4.6 33.7 1.0 CA A:HIS214 4.9 25.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Membrane Type 1 Matrix Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn314 b:37.6 occ:1.00 OE2 A:GLU248 1.8 40.8 1.0 NE2 B:HIS32 2.0 40.1 0.8 NE2 B:HIS28 2.2 41.3 1.0 CD A:GLU248 2.7 39.8 1.0 OE1 A:GLU248 2.8 36.3 1.0 CE1 B:HIS32 2.9 38.4 1.0 CE1 B:HIS28 3.1 40.7 1.0 CD2 B:HIS32 3.2 38.7 0.8 CD2 B:HIS28 3.3 43.9 1.0 CE2 A:PHE204 3.9 39.5 1.0 CZ A:PHE204 4.0 36.5 1.0 ND1 B:HIS32 4.0 36.6 1.0 CG A:GLU248 4.1 37.0 1.0 CG B:HIS32 4.2 38.3 1.0 ND1 B:HIS28 4.3 43.4 1.0 CG B:HIS28 4.4 45.0 1.0 CD2 A:PHE204 4.6 39.4 1.0 ND1 B:HIS30 4.6 52.0 0.3 CE1 A:PHE204 4.6 37.4 1.0 CE1 B:HIS30 4.8 55.8 1.0

E.Decaneto, T.Vasilevskaya, Y.Kutin, H.Ogata, M.Grossman, I.Sagi, M.Havenith, W.Lubitz, W.Thiel, N.Cox. Solvent Water Interactions Within the Active Site of the Membrane Type I Matrix Metalloproteinase. Phys Chem Chem Phys V. 19 30316 2017.
ISSN: ESSN 1463-9084
PubMed: 28951896
DOI: 10.1039/C7CP05572B