Zinc in PDB 2d1n: Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor

The structure of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1n was solved by T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.98 / 2.37
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	96.470, 96.470, 67.520, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 23.9

The structure of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor (pdb code 2d1n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn270 b:49.1 occ:1.00 O32 A:FA41001 1.9 67.8 1.0 NE2 A:HIS232 2.0 50.3 1.0 NE2 A:HIS226 2.2 46.9 1.0 NE2 A:HIS222 2.3 36.2 1.0 O33 A:FA41001 2.3 68.8 1.0 N22 A:FA41001 2.8 63.9 1.0 C21 A:FA41001 2.9 64.1 1.0 CD2 A:HIS232 3.0 48.3 1.0 CE1 A:HIS232 3.0 50.2 1.0 CD2 A:HIS226 3.1 46.3 1.0 CE1 A:HIS226 3.2 45.2 1.0 CD2 A:HIS222 3.2 39.3 1.0 CE1 A:HIS222 3.3 39.5 1.0 ND1 A:HIS232 4.1 49.5 1.0 CG A:HIS232 4.1 49.3 1.0 OE2 A:GLU223 4.1 47.7 1.0 ND1 A:HIS226 4.3 46.8 1.0 CG A:HIS226 4.3 46.8 1.0 C18 A:FA41001 4.4 62.6 1.0 CG A:HIS222 4.4 41.2 1.0 ND1 A:HIS222 4.4 41.2 1.0 N17 A:FA41001 4.9 58.3 1.0

Zinc binding site 2 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn271 b:49.3 occ:1.00 ND1 A:HIS200 1.9 45.6 1.0 OD2 A:ASP174 2.0 55.5 1.0 NE2 A:HIS172 2.0 51.8 1.0 NE2 A:HIS187 2.1 46.6 1.0 CE1 A:HIS187 2.6 45.7 1.0 CG A:ASP174 2.8 57.6 1.0 CD2 A:HIS172 2.8 53.7 1.0 CE1 A:HIS200 2.9 45.7 1.0 OD1 A:ASP174 3.0 56.2 1.0 CG A:HIS200 3.0 44.6 1.0 CE1 A:HIS172 3.1 53.6 1.0 CD2 A:HIS187 3.3 47.7 1.0 CB A:HIS200 3.4 42.7 1.0 ND1 A:HIS187 3.8 47.5 1.0 NE2 A:HIS200 4.0 42.8 1.0 CG A:HIS172 4.0 56.1 1.0 O A:TYR176 4.0 61.5 1.0 CD2 A:HIS200 4.1 44.3 1.0 ND1 A:HIS172 4.1 55.5 1.0 CG A:HIS187 4.2 47.3 1.0 CB A:ASP174 4.2 59.6 1.0 CE1 A:PHE189 4.7 47.8 1.0 CB A:TYR176 4.7 61.6 1.0 C A:TYR176 4.8 60.2 1.0 CZ A:PHE189 4.9 48.1 1.0 CA A:HIS200 4.9 45.7 1.0 CZ A:PHE178 4.9 54.6 1.0

Zinc binding site 3 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn285 b:51.6 occ:1.00 OE1 A:GLU135 1.9 51.1 1.0 NE2 B:HIS157 2.2 51.2 1.0 O A:HOH7 2.8 31.8 1.0 O A:HOH4 2.9 48.7 1.0 CD A:GLU135 3.0 51.3 1.0 O A:HOH3 3.1 50.0 1.0 CE1 B:HIS157 3.1 50.0 1.0 CD2 B:HIS157 3.2 50.4 1.0 O A:HOH8 3.3 35.6 1.0 OE2 A:GLU135 3.4 53.9 1.0 NH2 A:ARG155 3.5 54.8 1.0 OH A:TYR125 3.9 45.9 1.0 ND1 B:HIS157 4.2 52.1 1.0 CG B:HIS157 4.3 51.1 1.0 CG A:GLU135 4.3 50.0 1.0 CZ A:ARG155 4.6 53.4 1.0 CZ A:TYR125 4.7 47.3 1.0 NH1 A:ARG155 4.9 57.3 1.0

Zinc binding site 4 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn286 b:51.6 occ:1.00 OE1 B:GLU135 1.9 51.5 1.0 NE2 A:HIS157 2.1 48.8 1.0 O A:HOH8 2.7 35.6 1.0 O B:HOH5 2.8 32.9 1.0 CD B:GLU135 2.9 50.6 1.0 CE1 A:HIS157 3.0 47.8 1.0 CD2 A:HIS157 3.1 48.4 1.0 OE2 B:GLU135 3.3 50.3 1.0 O A:HOH7 3.4 31.8 1.0 O B:HOH6 3.5 35.2 1.0 NH2 B:ARG155 3.6 54.2 1.0 OH B:TYR125 4.0 43.7 1.0 ND1 A:HIS157 4.2 49.4 1.0 CG A:HIS157 4.2 50.0 1.0 CG B:GLU135 4.3 48.8 1.0 O A:HOH47 4.4 47.5 1.0 CZ B:ARG155 4.6 55.1 1.0 NH1 B:ARG155 4.7 58.3 1.0 CZ B:TYR125 4.8 43.7 1.0 CB B:HIS131 5.0 50.5 1.0

Zinc binding site 5 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn280 b:49.5 occ:1.00 NE2 B:HIS232 2.0 46.7 1.0 O32 B:FA41002 2.0 71.2 1.0 NE2 B:HIS222 2.2 41.2 1.0 NE2 B:HIS226 2.3 47.0 1.0 O33 B:FA41002 2.5 79.7 1.0 N22 B:FA41002 2.7 69.9 1.0 C21 B:FA41002 2.9 72.4 1.0 CE1 B:HIS232 2.9 47.9 1.0 CD2 B:HIS232 3.0 49.2 1.0 CD2 B:HIS222 3.2 38.4 1.0 CD2 B:HIS226 3.2 47.5 1.0 CE1 B:HIS222 3.2 40.6 1.0 CE1 B:HIS226 3.2 47.8 1.0 ND1 B:HIS232 4.1 49.1 1.0 CG B:HIS232 4.1 50.0 1.0 OE2 B:GLU223 4.2 46.7 1.0 C18 B:FA41002 4.3 70.0 1.0 ND1 B:HIS222 4.3 39.8 1.0 CG B:HIS222 4.3 38.8 1.0 ND1 B:HIS226 4.4 48.7 1.0 CG B:HIS226 4.4 47.7 1.0 N17 B:FA41002 4.6 65.7 1.0

Zinc binding site 6 out of 6 in the Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Collagenase-3 (Mmp-13) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn281 b:53.6 occ:1.00 NE2 B:HIS172 2.0 56.3 1.0 NE2 B:HIS187 2.0 47.2 1.0 ND1 B:HIS200 2.0 47.5 1.0 OD2 B:ASP174 2.1 57.5 1.0 CE1 B:HIS187 2.7 47.5 1.0 CG B:ASP174 2.9 59.3 1.0 CE1 B:HIS200 2.9 48.4 1.0 CD2 B:HIS172 2.9 56.1 1.0 CE1 B:HIS172 3.0 56.0 1.0 OD1 B:ASP174 3.0 59.5 1.0 CG B:HIS200 3.1 47.7 1.0 CD2 B:HIS187 3.2 46.5 1.0 CB B:HIS200 3.6 45.0 1.0 O B:TYR176 3.8 60.5 1.0 ND1 B:HIS187 3.9 47.0 1.0 ND1 B:HIS172 4.0 55.6 1.0 NE2 B:HIS200 4.1 47.2 1.0 CG B:HIS172 4.1 55.8 1.0 CG B:HIS187 4.2 47.3 1.0 CD2 B:HIS200 4.2 47.3 1.0 CB B:ASP174 4.3 60.4 1.0 CB B:TYR176 4.7 61.6 1.0 C B:TYR176 4.7 60.7 1.0 CE1 B:PHE189 4.8 47.5 1.0 CE2 B:PHE178 4.9 53.9 1.0 CZ B:PHE189 4.9 49.2 1.0 CZ B:PHE178 5.0 52.9 1.0

T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka. Crystal Structures of the Catalytic Domain of Human Stromelysin-1 (Mmp-3) and Collagenase-3 (Mmp-13) with A Hydroxamic Acid Inhibitor Sm-25453 Biochem.Biophys.Res.Commun. V. 344 315 2006.
ISSN: ISSN 0006-291X
PubMed: 16603129
DOI: 10.1016/J.BBRC.2006.03.098